New methods for indexing multi-lattice diffraction data

Efficient in situ screening of and data collection from microcrystals in crystallization plates

A considerable bottleneck in serial crystallography at XFEL and synchrotron sources is the efficient production of large quantities of homogenous, well diffracting microcrystals. Efficient high-throughput screening of batch-grown microcrystals and the determination of ground-state structures from different conditions is thus of considerable value in the early stages of a project. Here, a highly sample-efficient methodology to measure serial crystallography data from microcrystals by raster scanning within standard in situ 96-well crystallization plates is described. Structures were determined from very small quantities of microcrystal suspension and the results were compared with those from other sample-delivery methods. The analysis of a two-dimensional batch crystallization screen using this method is also described as a useful guide for further optimization and the selection of appropriate conditions for scaling up microcrystallization.

Deep residual networks for crystallography trained on synthetic data

The use of artificial intelligence to process diffraction images is challenged by the need to assemble large and precisely designed training data sets. To address this, a codebase called Resonet was developed for synthesizing diffraction data and training residual neural networks on these data. Here, two per-pattern capabilities of Resonet are demonstrated: (i) interpretation of crystal resolution and (ii) identification of overlapping lattices. Resonet was tested across a compilation of diffraction images from synchrotron experiments and X-ray free-electron laser experiments. Crucially, these models readily execute on graphics processing units and can thus significantly outperform conventional algorithms. While Resonet is currently utilized to provide real-time feedback for macromolecular crystallography users at the Stanford Synchrotron Radiation Lightsource, its simple Python-based interface makes it easy to embed in other processing frameworks. This work highlights the utility of physics-based simulation for training deep neural networks and lays the groundwork for the development of additional models to enhance diffraction collection and analysis.

Megahertz pulse trains enable multi-hit serial femtosecond crystallography experiments at X-ray free electron lasers

The European X-ray Free Electron Laser (XFEL) and Linac Coherent Light Source (LCLS) II are extremely intense sources of X-rays capable of generating Serial Femtosecond Crystallography (SFX) data at megahertz (MHz) repetition rates. Previous work has shown that it is possible to use consecutive X-ray pulses to collect diffraction patterns from individual crystals. Here, we exploit the MHz pulse structure of the European XFEL to obtain two complete datasets from the same lysozyme crystal, first hit and the second hit, before it exits the beam. The two datasets, separated by <1 µs, yield up to 2.1 Å resolution structures. Comparisons between the two structures reveal no indications of radiation damage or significant changes within the active site, consistent with the calculated dose estimates. This demonstrates MHz SFX can be used as a tool for tracking sub-microsecond structural changes in individual single crystals, a technique we refer to as multi-hit SFX.

Free-electron lasers are capable of high repetition rates and it is assumed that protein crystals often do not survive the first X-ray pulse. Here the authors address these issues with a demonstration of multi-hit serial crystallography in which multiple FEL pulses interact with the sample without destroying it.

Hedgehog-Interacting Protein is a multimodal antagonist of Hedgehog signalling

Hedgehog (HH) morphogen signalling, crucial for cell growth and tissue patterning in animals, is initiated by the binding of dually lipidated HH ligands to cell surface receptors. Hedgehog-Interacting Protein (HHIP), the only reported secreted inhibitor of Sonic Hedgehog (SHH) signalling, binds directly to SHH with high nanomolar affinity, sequestering SHH. Here, we report the structure of the HHIP N-terminal domain (HHIP-N) in complex with a glycosaminoglycan (GAG). HHIP-N displays a unique bipartite fold with a GAG-binding domain alongside a Cysteine Rich Domain (CRD). We show that HHIP-N is required to convey full HHIP inhibitory function, likely by interacting with the cholesterol moiety covalently linked to HH ligands, thereby preventing this SHH-attached cholesterol from binding to the HH receptor Patched (PTCH1). We also present the structure of the HHIP C-terminal domain in complex with the GAG heparin. Heparin can bind to both HHIP-N and HHIP-C, thereby inducing clustering at the cell surface and generating a high-avidity platform for SHH sequestration and inhibition. Our data suggest a multimodal mechanism, in which HHIP can bind two specific sites on the SHH morphogen, alongside multiple GAG interactions, to inhibit SHH signalling.

DIALS as a toolkit

The DIALS software for the processing of X‐ray diffraction data is presented, with an emphasis on how the suite may be used as a toolkit for data processing. The description starts with an overview of the history and intent of the toolkit, usage as an automated system, command‐line use, and ultimately how new tools can be written using the API to perform bespoke analysis. Consideration is also made to the application of DIALS to techniques outside of macromolecular X‐ray crystallography.

A reference-based multi-lattice indexing method integrating prior information correction and iterative refinement in protein crystallography

A new multi-lattice indexing method based on the principle of whole-pattern matching given cell dimensions and space-group symmetry is presented for macromolecular crystallography. The proposed method, termed the multi-crystal data processing suite (MCDPS), features a local correction for prior information accompanied by iterative refinement of experimental parameters, both of which are numerically and experimentally demonstrated to be critical for accurately identifying multiple crystal lattices. Further analysis of data reduction and structure determination with conventional single-crystal programs reveals that the processed multi-lattice data sets are comparable in quality to typical single-crystal ones in terms of crystallographic metrics. Importantly, it is confirmed that careful exclusion of overlapping reflections prior to scaling is necessary to guarantee an accurate data reduction result. The potential for multi-lattice indexing in solving the general macroscopic twinning problem is also explored.

Constrained geometrical analysis of complete K-line patterns for calibrationless auto-indexing

Indexing of Kikuchi and Kossel lines is a crucial step in K-line pattern analysis. Previous approaches mostly rely on the knowledge of unit-cell parameters and experimental geometry. An auto-indexing procedure is introduced that is able to find the unknown lattice, its orientation and the indices of the lines. To achieve this, the unbiased extraction of the precise conical geometrical information from the patterns is combined with existing auto-indexing procedures developed in the field of crystallography. A subsequent lattice-constrained refinement of all lines to the experimental pattern yields reliable lattice and experimental parameters simultaneously. Beyond providing detailed mathematical formulae, the procedure is also demonstrated on an experimental Kossel line pattern.

Tetramerisation of the CRISPR ring nuclease Crn3/Csx3 facilitates cyclic oligoadenylate cleavage

Type III CRISPR systems detect foreign RNA and activate the cyclase domain of the Cas10 subunit, generating cyclic oligoadenylate (cOA) molecules that act as a second messenger to signal infection, activating nucleases that degrade the nucleic acid of both invader and host. This can lead to dormancy or cell death; to avoid this, cells need a way to remove cOA from the cell once a viral infection has been defeated. Enzymes specialised for this task are known as ring nucleases, but are limited in their distribution. Here, we demonstrate that the widespread CRISPR associated protein Csx3, previously described as an RNA deadenylase, is a ring nuclease that rapidly degrades cyclic tetra-adenylate (cA4). The enzyme has an unusual cooperative reaction mechanism involving an active site that spans the interface between two dimers, sandwiching the cA4 substrate. We propose the name Crn3 (CRISPR associated ring nuclease 3) for the Csx3 family.

Crystal Structure of Exotoxin A from Aeromonas Pathogenic Species

Aeromonas exotoxin A (AE) is a bacterial virulence factor recently discovered in a clinical case of necrotising fasciitis caused by the flesh-eating Aeromonas hydrophila. Here, database mining shows that AE is present in the genome of several emerging Aeromonas pathogenic species. The X-ray crystal structure of AE was solved at 2.3 Å and presents all the hallmarks common to diphthamide-specific mono-ADP-ribosylating toxins, suggesting AE is a fourth member of this family alongside the diphtheria toxin, Pseudomonas exotoxin A and cholix. Structural homology indicates AE may use a similar mechanism of cytotoxicity that targets eukaryotic elongation factor 2 and thus inhibition of protein synthesis. The structure of AE also highlights unique features including a metal binding site, and a negatively charged cleft that could play a role in interdomain interactions and may affect toxicity. This study raises new opportunities to engineer alternative toxin-based molecules with pharmaceutical potential.

An efficient method for indexing grazing-incidence X-ray diffraction data of epitaxially grown thin films

Crystal structure identification of thin organic films entails a number of technical and methodological challenges. In particular, if molecular crystals are epitaxially grown on single-crystalline substrates a complex scenario of multiple preferred orientations of the adsorbate, several symmetry-related in-plane alignments and the occurrence of unknown polymorphs is frequently observed. In theory, the parameters of the reduced unit cell and its orientation can simply be obtained from the matrix of three linearly independent reciprocal-space vectors. However, if the sample exhibits unit cells in various orientations and/or with different lattice parameters, it is necessary to assign all experimentally obtained reflections to their associated individual origin. In the present work, an effective algorithm is described to accomplish this task in order to determine the unit-cell parameters of complex systems comprising different orientations and polymorphs. This method is applied to a polycrystalline thin film of the conjugated organic material 6,13-pentacenequinone (PQ) epitaxially grown on an Ag(111) surface. All reciprocal vectors can be allocated to unit cells of the same lattice constants but grown in various orientations [sixfold rotational symmetry for the contact planes (102) and (102)]. The as-determined unit cell is identical to that reported in a previous study determined for a fibre-textured PQ film. Preliminary results further indicate that the algorithm is especially effective in analysing epitaxially grown crystallites not only for various orientations, but also if different polymorphs are present in the film.

Atomic structures determined from digitally defined nanocrystalline regions

Nanocrystallography has transformed our ability to interrogate the atomic structures of proteins, peptides, organic molecules and materials. By probing atomic level details in ordered sub-10 nm regions of nanocrystals, scanning nanobeam electron diffraction extends the reach of nanocrystallography and in principle obviates the need for diffraction from large portions of one or more crystals. Scanning nanobeam electron diffraction is now applied to determine atomic structures from digitally defined regions of beam-sensitive peptide nanocrystals. Using a direct electron detector, thousands of sparse diffraction patterns over multiple orientations of a given crystal are recorded. Each pattern is assigned to a specific location on a single nanocrystal with axial, lateral and angular coordinates. This approach yields a collection of patterns that represent a tilt series across an angular wedge of reciprocal space: a scanning nanobeam diffraction tomogram. Using this diffraction tomogram, intensities can be digitally extracted from any desired region of a scan in real or diffraction space, exclusive of all other scanned points. Intensities from multiple regions of a crystal or from multiple crystals can be merged to increase data completeness and mitigate missing wedges. It is demonstrated that merged intensities from digitally defined regions of two crystals of a segment from the OsPYL/RCAR5 protein produce fragment-based ab initio solutions that can be refined to atomic resolution, analogous to structures determined by selected-area electron diffraction. In allowing atomic structures to now be determined from digitally outlined regions of a nanocrystal, scanning nanobeam diffraction tomography breaks new ground in nanocrystallography.

A New Paroxetine-Based GRK2 Inhibitor Reduces Internalization of the μ-Opioid Receptor

G protein-coupled receptor (GPCR) kinases (GRKs) play a key role in terminating signals initiated by agonist-bound GPCRs. However, chronic stimulation of GPCRs, such as that which occurs during heart failure, leads to the overexpression of GRKs and maladaptive downregulation of GPCRs on the cell surface. We previously reported the discovery of potent and selective families of GRK inhibitors based on either the paroxetine or GSK180736A scaffold. A new inhibitor, CCG258747, which is based on paroxetine, demonstrates increased potency against the GRK2 subfamily and favorable pharmacokinetic parameters in mice. CCG258747 and the closely related compound CCG258208 also showed high selectivity for the GRK2 subfamily in a kinome panel of 104 kinases. We developed a cell-based assay to screen the ability of CCG258747 and 10 other inhibitors with different GRK subfamily selectivities and with either the paroxetine or GSK180736A scaffold to block internalization of the μ-opioid receptor (MOR). CCG258747 showed the best efficacy in blocking MOR internalization among the compounds tested. Furthermore, we show that compounds based on paroxetine had much better cell permeability than those based on GSK180736A, which explains why GSK180736A-based inhibitors, although being potent in vitro, do not always show efficacy in cell-based assays. This study validates the paroxetine scaffold as the most effective for GRK inhibition in living cells, confirming that GRK2 predominantly drives internalization of MOR in the cell lines we tested and underscores the utility of high-resolution cell-based assays for assessment of compound efficacy. SIGNIFICANCE STATEMENT: G protein-coupled receptor kinases (GRKs) are attractive targets for developing therapeutics for heart failure. We have synthesized a new GRK2 subfamily-selective inhibitor, CCG258747, which has nanomolar potency against GRK2 and excellent selectivity over other kinases. A live-cell receptor internalization assay was used to test the ability of GRK2 inhibitors to impart efficacy on a GRK-dependent process in cells. Our data indicate that CCG258747 blocked the internalization of the μ-opioid receptor most efficaciously because it has the ability to cross cell membranes.

Characterization of a membrane binding loop leads to engineering botulinum neurotoxin B with improved therapeutic efficacy

Botulinum neurotoxins (BoNTs) are a family of bacterial toxins with seven major serotypes (BoNT/A–G). The ability of these toxins to target and bind to motor nerve terminals is a key factor determining their potency and efficacy. Among these toxins, BoNT/B is one of the two types approved for medical and cosmetic uses. Besides binding to well-established receptors, an extended loop in the C-terminal receptor-binding domain (H_C) of BoNT/B (H_C/B) has been proposed to also contribute to toxin binding to neurons by interacting with lipid membranes (termed lipid-binding loop [LBL]). Analogous loops exist in the H_Cs of BoNT/C, D, G, and a chimeric toxin DC. However, it has been challenging to detect and characterize binding of LBLs to lipid membranes. Here, using the nanodisc system and biolayer interferometry assays, we find that H_C/DC, C, and G, but not H_C/B and H_C/D, are capable of binding to receptor-free lipids directly, with H_C/DC having the highest level of binding. Mutagenesis studies demonstrate the critical role of consecutive aromatic residues at the tip of the LBL for binding of H_C/DC to lipid membranes. Taking advantage of this insight, we then create a “gain-of-function” mutant H_C/B by replacing two nonaromatic residues at the tip of its LBL with tryptophan. Cocrystallization studies confirm that these two tryptophan residues do not alter the structure of H_C/B or the interactions with its receptors. Such a mutated H_C/B gains the ability to bind receptor-free lipid membranes and shows enhanced binding to cultured neurons. Finally, full-length BoNT/B containing two tryptophan mutations in its LBL, together with two additional mutations (E1191M/S1199Y) that increase binding to human receptors, is produced and evaluated in mice in vivo using Digit Abduction Score assays. This mutant toxin shows enhanced efficacy in paralyzing local muscles at the injection site and lower systemic diffusion, thus extending both safety range and duration of paralysis compared with the control BoNT/B. These findings establish a mechanistic understanding of LBL–lipid interactions and create a modified BoNT/B with improved therapeutic efficacy.

Botulinum neurotoxins are a family of bacterial toxins, some of which are approved for medical and cosmetic uses. This study shows that introducing aromatic residues to a lipid binding loop improved therapeutic efficacy of botulinum neurotoxin B by enhancing its ability to bind to lipid membranes at motor nerve terminals.

A practical overview of molecular replacement: Clostridioides difficile PilA1, a difficult case study

Many biologists are now routinely seeking to determine the three-dimensional structures of their proteins of choice, illustrating the importance of this knowledge, but also of the simplification and streamlining of structure-determination processes. Despite the fact that most software packages offer simple pipelines, for the non-expert navigating the outputs and understanding the key aspects can be daunting. Here, the structure determination of the type IV pili (TFP) protein PilA1 from Clostridioides difficile is used to illustrate the different steps involved, the key decision criteria and important considerations when using the most common pipelines and software. Molecular-replacement pipelines within CCP4i2 are presented to illustrate the more commonly used processes. Previous knowledge of the biology and structure of TFP pilins, particularly the presence of a long, N-terminal α-helix required for pilus formation, allowed informed decisions to be made during the structure-determination strategy. The PilA1 structure was finally successfully determined using ARCIMBOLDO and the ab initio MR strategy used is described.

Structural basis for the interaction of the chaperone Cbp3 with newly synthesized cytochrome b during mitochondrial respiratory chain assembly

Assembly of the mitochondrial respiratory chain requires the coordinated synthesis of mitochondrial and nuclear encoded subunits, redox co-factor acquisition, and correct joining of the subunits to form functional complexes. The conserved Cbp3-Cbp6 chaperone complex binds newly synthesized cytochrome b and supports the ordered acquisition of the heme co-factors. Moreover, it functions as a translational activator by interacting with the mitoribosome. Cbp3 consists of two distinct domains: an N-terminal domain present in mitochondrial Cbp3 homologs and a highly conserved C-terminal domain comprising a ubiquinol-cytochrome c chaperone region. Here, we solved the crystal structure of this C-terminal domain from a bacterial homolog at 1.4 Å resolution, revealing a unique all-helical fold. This structure allowed mapping of the interaction sites of yeast Cbp3 with Cbp6 and cytochrome b via site-specific photo-cross-linking. We propose that mitochondrial Cbp3 homologs carry an N-terminal extension that positions the conserved C-terminal domain at the ribosomal tunnel exit for an efficient interaction with its substrate, the newly synthesized cytochrome b protein.

XGANDALF - extended gradient descent algorithm for lattice finding

Serial crystallography records still diffraction patterns from single, randomly oriented crystals, then merges data from hundreds or thousands of them to form a complete data set. To process the data, the diffraction patterns must first be indexed, equivalent to determining the orientation of each crystal. A novel automatic indexing algorithm is presented, which in tests usually gives significantly higher indexing rates than alternative programs currently available for this task. The algorithm does not require prior knowledge of the lattice parameters but can make use of that information if provided, and also allows indexing of diffraction patterns generated by several crystals in the beam. Cases with a small number of Bragg spots per pattern appear to particularly benefit from the new approach. The algorithm has been implemented and optimized for fast execution, making it suitable for real-time feedback during serial crystallography experiments. It is implemented in an open-source C++ library and distributed under the LGPLv3 licence. An interface to it has been added to the CrystFEL software suite.

Structural Basis of Lysosomal Phospholipase A2 Inhibition by Zn2

Lysosomal phospholipase A₂ (LPLA₂/PLA2G15) is a key enzyme involved in lipid homeostasis and is characterized by both phospholipase A2 and transacylase activity and by an acidic pH optimum. Divalent cations such as Ca²⁺ and Mg²⁺ have previously been shown to have little effect on the activity of LPLA₂, but the discovery of a novel crystal form of LPLA₂ with Zn²⁺ bound in the active site suggested a role for this divalent cation in regulating enzyme activity. In this complex, the cation directly coordinates the serine and histidine of the α/β-hydrolase triad and stabilizes a closed conformation. This closed conformation is characterized by an inward shift of the lid loop, which extends over the active site and effectively blocks access to one of its lipid acyl chain binding tracks. Therefore, we hypothesized that Zn²⁺ would inhibit LPLA₂ activity at a neutral but not acidic pH because histidine would be positively charged at lower pH. Indeed, Zn²⁺ was found to inhibit the esterase activity of LPLA₂ in a noncompetitive manner exclusively at a neutral pH (between 6.5 and 8.0). Because lysosomes are reservoirs of Zn²⁺ in cells, the pH optimum of LPLA₂ might allow it to catalyze acyl transfer unimpeded within the organelle. We conjecture that Zn²⁺ inhibition of LPLA₂ at higher pH maintains a lower activity of the esterase in environments where its activity is not typically required.

Rapid sample delivery for megahertz serial crystallography at X-ray FELs

Liquid microjets are a common means of delivering protein crystals to the focus of X-ray free-electron lasers (FELs) for serial femtosecond crystallography measurements. The high X-ray intensity in the focus initiates an explosion of the microjet and sample. With the advent of X-ray FELs with megahertz rates, the typical velocities of these jets must be increased significantly in order to replenish the damaged material in time for the subsequent measurement with the next X-ray pulse. This work reports the results of a megahertz serial diffraction experiment at the FLASH FEL facility using 4.3 nm radiation. The operation of gas-dynamic nozzles that produce liquid microjets with velocities greater than 80 m s-1 was demonstrated. Furthermore, this article provides optical images of X-ray-induced explosions together with Bragg diffraction from protein microcrystals exposed to trains of X-ray pulses repeating at rates of up to 4.5 MHz. The results indicate the feasibility for megahertz serial crystallography measurements with hard X-rays and give guidance for the design of such experiments.

Indexing of grazing-incidence X-ray diffraction patterns: the case of fibre-textured thin films

Crystal structure solutions from thin films are often performed by grazing-incidence X-ray diffraction (GIXD) experiments. In particular, on isotropic substrates the thin film crystallites grow in a fibre texture showing a well defined crystallographic plane oriented parallel to the substrate surface with random in-plane order of the microcrystallites forming the film. In the present work, analytical mathematical expressions are derived for indexing experimental diffraction patterns, a highly challenging task which hitherto mainly relied on trial-and-error approaches. The six lattice constants a, b, c, α, β and γ of the crystallographic unit cell are thereby determined, as well as the rotation parameters due to the unknown preferred orientation of the crystals with respect to the substrate surface. The mathematical analysis exploits a combination of GIXD data and information acquired by the specular X-ray diffraction. The presence of a sole specular diffraction peak series reveals fibre-textured growth with a crystallographic plane parallel to the substrate, which allows establishment of the Miller indices u, v and w as the rotation parameters. Mathematical expressions are derived which reduce the system of unknown parameters from the three- to the two-dimensional space. Thus, in the first part of the indexing routine, the integers u and v as well as the Laue indices h and k of the experimentally observed diffraction peaks are assigned by systematically varying the integer variables, and by calculating the three lattice parameters a, b and γ. Because of the symmetry of the derived equations, determining the missing parameters then becomes feasible: (i) w of the surface parallel plane, (ii) the Laue indices l of the diffraction peak and (iii) analogously the lattice constants c, α and ß. In a subsequent step, the reduced unit-cell geometry can be identified. Finally, the methodology is demonstrated by application to an example, indexing the diffraction pattern of a thin film of the organic semiconductor pentacenequinone grown on the (0001) surface of highly oriented pyrolytic graphite. The preferred orientation of the crystallites, the lattice constants of the triclinic unit cell and finally, by molecular modelling, the full crystal structure solution of the as-yet-unknown polymorph of pentacenequinone are determined.

Electron diffraction data processing with DIALS

Electron diffraction is a relatively novel alternative to X-ray crystallography for the structure determination of macromolecules from three-dimensional nanometre-sized crystals. The continuous-rotation method of data collection has been adapted for the electron microscope. However, there are important differences in geometry that must be considered for successful data integration. The wavelength of electrons in a TEM is typically around 40 times shorter than that of X-rays, implying a nearly flat Ewald sphere, and consequently low diffraction angles and a high effective sample-to-detector distance. Nevertheless, the DIALS software package can, with specific adaptations, successfully process continuous-rotation electron diffraction data. Pathologies encountered specifically in electron diffraction make data integration more challenging. Errors can arise from instrumentation, such as beam drift or distorted diffraction patterns from lens imperfections. The diffraction geometry brings additional challenges such as strong correlation between lattice parameters and detector distance. These issues are compounded if calibration is incomplete, leading to uncertainty in experimental geometry, such as the effective detector distance and the rotation rate or direction. Dynamic scattering, absorption, radiation damage and incomplete wedges of data are additional factors that complicate data processing. Here, recent features of DIALS as adapted to electron diffraction processing are shown, including diagnostics for problematic diffraction geometry refinement, refinement of a smoothly varying beam model and corrections for distorted diffraction images. These novel features, combined with the existing tools in DIALS, make data integration and refinement feasible for electron crystallography, even in difficult cases.

Determination of Patterson group symmetry from sparse multi-crystal data sets in the presence of an indexing ambiguity

Combining X-ray diffraction data from multiple samples requires determination of the symmetry and resolution of any indexing ambiguity. For the partial data sets typical of in situ room-temperature experiments, determination of the correct symmetry is often not straightforward. The potential for indexing ambiguity in polar space groups is also an issue, although methods to resolve this are available if the true symmetry is known. Here, a method is presented to simultaneously resolve the determination of the Patterson symmetry and the indexing ambiguity for partial data sets.

Structure and function of the type III pullulan hydrolase from Thermococcus kodakarensis

Pullulan-hydrolysing enzymes, more commonly known as debranching enzymes for starch and other polysaccharides, are of great interest and have been widely used in the starch-saccharification industry. Type III pullulan hydrolase from Thermococcus kodakarensis (TK-PUL) possesses both pullulanase and α-amylase activities. Until now, only two enzymes in this class, which are capable of hydrolysing both α-1,4- and α-1,6-glycosidic bonds in pullulan to produce a mixture of maltose, panose and maltotriose, have been described. TK-PUL shows highest activity in the temperature range 95-100°C and has a pH optimum in the range 3.5-4.2. Its unique ability to hydrolyse maltotriose into maltose and glucose has not been reported for other homologous enzymes. The crystal structure of TK-PUL has been determined at a resolution of 2.8 Å and represents the first analysis of a type III pullulan hydrolyse. The structure reveals that the last part of the N-terminal domain and the C-terminal domain are significantly different from homologous structures. In addition, the loop regions at the active-site end of the central catalytic domain are quite different. The enzyme has a well defined calcium-binding site and possesses a rare vicinal disulfide bridge. The thermostability of TK-PUL and its homologues may be attributable to several factors, including the increased content of salt bridges, helical segments, Pro, Arg and Tyr residues and the decreased content of serine.

High resolution crystal structures of the receptor-binding domain of Clostridium botulinum neurotoxin serotypes A and FA

The binding specificity of botulinum neurotoxins (BoNTs) is primarily a consequence of their ability to bind to multiple receptors at the same time. BoNTs consist of three distinct domains, a metalloprotease light chain (LC), a translocation domain (H_N) and a receptor-binding domain (H_C). Here we report the crystal structure of H_C/FA, complementing an existing structure through the modelling of a previously unresolved loop which is important for receptor-binding. Our H_C/FA structure also contains a previously unidentified disulphide bond, which we have also observed in one of two crystal forms of H_C/A1. This may have implications for receptor-binding and future recombinant toxin production.

DIALS: implementation and evaluation of a new integration package

The DIALS project is a collaboration between Diamond Light Source, Lawrence Berkeley National Laboratory and CCP4 to develop a new software suite for the analysis of crystallographic X-ray diffraction data, initially encompassing spot finding, indexing, refinement and integration. The design, core algorithms and structure of the software are introduced, alongside results from the analysis of data from biological and chemical crystallography experiments.

An acoustic on-chip goniometer for room temperature macromolecular crystallography

This paper describes the design, development and successful use of an on-chip goniometer for room-temperature macromolecular crystallography via acoustically induced rotations. We present for the first time a low cost, rate-tunable, acoustic actuator for gradual in-fluid sample reorientation about varying axes and its utilisation for protein structure determination on a synchrotron beamline. The device enables the efficient collection of diffraction data via a rotation method from a sample within a surface confined droplet. This method facilitates efficient macromolecular structural data acquisition in fluid environments for dynamical studies.

Lifetimes and spatio-temporal response of protein crystals in intense X-ray microbeams

Serial synchrotron-based crystallography using intense microfocused X-ray beams, fast-framing detectors and protein microcrystals held at 300 K promises to expand the range of accessible structural targets and to increase overall structure-pipeline throughputs. To explore the nature and consequences of X-ray radiation damage under microbeam illumination, the time-, dose- and temperature-dependent evolution of crystal diffraction have been measured with maximum dose rates of 50 MGy s-1. At all temperatures and dose rates, the integrated diffraction intensity for a fixed crystal orientation shows non-exponential decays with dose. Non-exponential decays are a consequence of non-uniform illumination and the resulting spatial evolution of diffracted intensity within the illuminated crystal volume. To quantify radiation-damage lifetimes and the damage state of diffracting crystal regions, a revised diffraction-weighted dose (DWD) is defined and it is shown that for Gaussian beams the DWD becomes nearly independent of actual dose at large doses. An apparent delayed onset of radiation damage seen in some intensity-dose curves is in fact a consequence of damage. Intensity fluctuations at high dose rates may arise from the impulsive release of gaseous damage products. Accounting for these effects, data collection at the highest dose rates increases crystal radiation lifetimes near 300 K (but not at 100 K) by a factor of ∼1.5-2 compared with those observed at conventional dose rates. Improved quantification and modeling of the complex spatio-temporal evolution of protein microcrystal diffraction in intense microbeams will enable more efficient data collection, and will be essential in improving the accuracy of structure factors and structural models.

Structural Determinants Influencing the Potency and Selectivity of Indazole-Paroxetine Hybrid G Protein-Coupled Receptor Kinase 2 Inhibitors

G protein-coupled receptor kinases (GRKs) phosphorylate activated receptors to promote arrestin binding, decoupling from heterotrimeric G proteins, and internalization. GRK2 and GRK5 are overexpressed in the failing heart and thus have become therapeutic targets. Previously, we discovered two classes of GRK2-selective inhibitors, one stemming from GSK180736A, a Rho-associated coiled-coil containing kinase 1 (ROCK1) inhibitor, the other from paroxetine, a selective serotonin-reuptake inhibitor. These two classes of compounds bind to the GRK2 active site in a similar configuration but contain different hinge-binding "warheads": indazole and benzodioxole, respectively. We surmised from our prior studies that an indazole would be the stronger hinge binder and would impart increased potency when substituted for benzodioxole in paroxetine derivatives. To test this hypothesis, we synthesized a series of hybrid compounds that allowed us to compare the effects of inhibitors that differ only in the identity of the warhead. The indazole-paroxetine analogs were indeed more potent than their respective benzodioxole derivatives but lost selectivity. To investigate how these two warheads dictate selectivity, we determined the crystal structures of three of the indazole hybrid compounds (CCG224061, CCG257284, and CCG258748) in complex with GRK2-Gβγ Comparison of these structures with those of analogous benzodioxole-containing complexes confirmed that the indazole-paroxetine hybrids form stronger interactions with the hinge of the kinase but also stabilize a distinct conformation of the kinase domain of GRK2 compared with previous complexes with paroxetine analogs. This conformation is analogous to one that can be assumed by GRK5, at least partially explaining the loss in selectivity.

X-ray data processing

The method of molecular structure determination by X-ray crystallography is a little over a century old. The history is described briefly, along with developments in X-ray sources and detectors. The fundamental processes involved in measuring diffraction patterns on area detectors, i.e. autoindexing, refining crystal and detector parameters, integrating the reflections themselves and putting the resultant measurements on to a common scale are discussed, with particular reference to the most commonly used software in the field.

The structure of the tetanus toxin reveals pH-mediated domain dynamics

The tetanus neurotoxin (TeNT) is a highly potent toxin produced by Clostridium tetani that inhibits neurotransmission of inhibitory interneurons, causing spastic paralysis in the tetanus disease. TeNT differs from the other clostridial neurotoxins by its unique ability to target the central nervous system by retrograde axonal transport. The crystal structure of the tetanus toxin reveals a "closed" domain arrangement stabilised by two disulphide bridges, and the molecular details of the toxin's interaction with its polysaccharide receptor. An integrative analysis combining X-ray crystallography, solution scattering and single particle electron cryo-microscopy reveals pH-mediated domain rearrangements that may give TeNT the ability to adapt to the multiple environments encountered during intoxication, and facilitate binding to distinct receptors.

FELIX: an algorithm for indexing multiple crystallites in X-ray free-electron laser snapshot diffraction images

A novel algorithm for indexing multiple crystals in snapshot X-ray diffraction images, especially suited for serial crystallography data, is presented. The algorithm, FELIX, utilizes a generalized parametrization of the Rodrigues-Frank space, in which all crystal systems can be represented without singularities. The new algorithm is shown to be capable of indexing more than ten crystals per image in simulations of cubic, tetragonal and monoclinic crystal diffraction patterns. It is also used to index an experimental serial crystallography dataset from lysozyme microcrystals. The increased number of indexed crystals is shown to result in a better signal-to-noise ratio, and fewer images are needed to achieve the same data quality as when indexing one crystal per image. The relative orientations between the multiple crystals indexed in an image show a slight tendency of the lysozme microcrystals to adhere on ([Formula: see text]10) facets.

Structural Basis of Egg Coat-Sperm Recognition at Fertilization

Recognition between sperm and the egg surface marks the beginning of life in all sexually reproducing organisms. This fundamental biological event depends on the species-specific interaction between rapidly evolving counterpart molecules on the gametes. We report biochemical, crystallographic, and mutational studies of domain repeats 1–3 of invertebrate egg coat protein VERL and their interaction with cognate sperm protein lysin. VERL repeats fold like the functionally essential N-terminal repeat of mammalian sperm receptor ZP2, whose structure is also described here. Whereas sequence-divergent repeat 1 does not bind lysin, repeat 3 binds it non-species specifically via a high-affinity, largely hydrophobic interface. Due to its intermediate binding affinity, repeat 2 selectively interacts with lysin from the same species. Exposure of a highly positively charged surface of VERL-bound lysin suggests that complex formation both disrupts the organization of egg coat filaments and triggers their electrostatic repulsion, thereby opening a hole for sperm penetration and fusion.

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Sperm-binding repeats of mollusk VERL and mouse ZP2 egg coat proteins fold similarly

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Structures of VERL/lysin complexes reveal the atomic basis of egg coat-sperm recognition

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A medium-affinity VERL repeat selectively binds lysin from the same species

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VERL/lysin recognition suggests a mechanism for sperm penetration through the egg coat

Frutapin, a lectin from Artocarpus incisa (breadfruit): cloning, expression and molecular insights

Artocarpus incisa (breadfruit) seeds contain three different lectins (Frutalin, Frutapin (FTP) and Frutackin) with distinct carbohydrate specificities. The most abundant lectin is Frutalin, an α-D-galactose-specific carbohydrate-binding glycoprotein with antitumour properties and potential for tumour biomarker discovery as already reported. FTP is the second most abundant, but proved difficult to purify with very low yields and contamination with Frutalin frustrating its characterization. Here, we report for the first time high-level production and isolation of biologically active recombinant FTP in Escherichia coli BL21, optimizing conditions with the best set yielding >40 mg/l culture of soluble active FTP. The minimal concentration for agglutination of red blood cells was 62.5 µg/ml of FTP, a process effectively inhibited by mannose. Apo-FTP, FTP–mannose and FTP–glucose crystals were obtained, and they diffracted X-rays to a resolution of 1.58 (P2₁2₁2₁), 1.70 (P3₁21) and 1.60 (P3₁21) Å respectively. The best solution showed four monomers per asymmetric unit. Molecular dynamics (MD) simulation suggested that FTP displays higher affinity for mannose than glucose. Cell studies revealed that FTP was non-cytotoxic to cultured mouse fibroblast 3T3 cells below 0.5 mg/ml and was also capable of stimulating cell migration at 50 µg/ml. In conclusion, our optimized expression system allowed high amounts of correctly folded soluble FTP to be isolated. This recombinant bioactive lectin will now be tested in future studies for therapeutic potential; for example in wound healing and tissue regeneration.

A nucleotide-controlled conformational switch modulates the activity of eukaryotic IMP dehydrogenases

Inosine-5′-monophosphate dehydrogenase (IMPDH) is an essential enzyme for nucleotide metabolism and cell proliferation. Despite IMPDH is the target of drugs with antiviral, immunosuppressive and antitumor activities, its physiological mechanisms of regulation remain largely unknown. Using the enzyme from the industrial fungus Ashbya gossypii, we demonstrate that the binding of adenine and guanine nucleotides to the canonical nucleotide binding sites of the regulatory Bateman domain induces different enzyme conformations with significantly distinct catalytic activities. Thereby, the comparison of their high-resolution structures defines the mechanistic and structural details of a nucleotide-controlled conformational switch that allosterically modulates the catalytic activity of eukaryotic IMPDHs. Remarkably, retinopathy-associated mutations lie within the mechanical hinges of the conformational change, highlighting its physiological relevance. Our results expand the mechanistic repertoire of Bateman domains and pave the road to new approaches targeting IMPDHs.

Structure of the family B DNA polymerase from the hyperthermophilic archaeon Pyrobaculum calidifontis

The family B DNA polymerase from Pyrobaculum calidifontis (Pc-polymerase) consists of 783 amino acids and is magnesium-ion dependent. It has an optimal pH of 8.5, an optimal temperature of 75°C and a half-life of 4.5 h at 95°C, giving it greater thermostability than the widely used Taq DNA polymerase. The enzyme is also capable of PCR-amplifying larger DNA fragments of up to 7.5 kb in length. It was shown to have functional, error-correcting 3'-5' exonuclease activity, as do the related high-fidelity DNA polymerases from Pyrococcus furiosus, Thermococcus kodakarensis KOD1 and Thermococcus gorgonarius, which have extensive commercial applications. Pc-polymerase has a quite low sequence identity of approximately 37% to these enzymes, which, in contrast, have very high sequence identity to each other, suggesting that the P. calidifontis enzyme is distinct. Here, the structure determination of Pc-polymerase is reported, which has been refined to an R factor of 24.47% and an R_free of 28.81% at 2.80 Å resolution. The domains of the enzyme are arranged in a circular fashion to form a disc with a narrow central channel. One face of the disc has a number of connected crevices in it, which allow the protein to bind duplex and single-stranded DNA. The central channel is thought to allow incoming nucleoside triphosphates to access the active site. The enzyme has a number of unique structural features which distinguish it from other archaeal DNA polymerases and may account for its high processivity. A model of the complex with the primer-template duplex of DNA indicates that the largest conformational change that occurs upon DNA binding is the movement of the thumb domain, which rotates by 7.6° and moves by 10.0 Å. The surface potential of the enzyme is dominated by acidic groups in the central region of the molecule, where catalytic magnesium ions bind at the polymerase and exonuclease active sites. The outer regions are richer in basic amino acids that presumably interact with the sugar-phosphate backbone of DNA. The large number of salt bridges may contribute to the high thermal stability of this enzyme.

Structural and mechanistic insights into an archaeal DNA-guided Argonaute protein

Argonaute (Ago) proteins in eukaryotes are known as key players in post-transcriptional gene silencing¹, while recent studies on prokaryotic Agos hint at their role in the protection against invading DNA^2,3. Here, we present crystal structures of the apo enzyme and a binary Ago-guide complex of the archaeal Methanocaldococcus jannaschii (Mj) Ago. Binding of a guide DNA leads to large structural rearrangements. This includes the structural transformation of a hinge region containing a switch helix, which has been shown for human Ago2 to be critical for the dynamic target search process^4-6. To identify key residues crucial for MjAgo function, we analysed the effect of several MjAgo mutants. We observe that the nature of the 3' and 5' nucleotides in particular, as well as the switch helix, appear to impact MjAgo cleavage activity. In summary, we provide insights into the molecular mechanisms that drive DNA-guided DNA silencing by an archaeal Ago.

Lysine relay mechanism coordinates intermediate transfer in vitamin B6 biosynthesis

Substrate channeling has emerged as a common mechanism for enzymatic intermediate transfer. A conspicuous gap in knowledge concerns the use of covalent lysine imines in the transfer of carbonyl-group-containing intermediates, despite their wideuse in enzymatic catalysis. Here we show how imine chemistry operates in the transfer of covalent intermediates in pyridoxal 5'-phosphate biosynthesis by the Arabidopsis thaliana enzyme Pdx1. An initial ribose 5-phosphate lysine imine is converted to the chromophoric I320 intermediate, simultaneously bound to two lysine residues and partially vacating the active site, which creates space for glyceraldehyde 3-phosphate to bind. Crystal structures show how substrate binding, catalysis and shuttling are coupled to conformational changes around strand β6 of the Pdx1 (βα)8-barrel. The dual-specificity active site and imine relay mechanism for migration of carbonyl intermediates provide elegant solutions to the challenge of coordinating a complex sequence of reactions that follow a path of over 20 Å between substrate- and product-binding sites.

Ind_X: program for indexing single-crystal diffraction patterns

Indexing is an essential step in analysis of diffraction patterns. Diffraction of monochromatic radiation by a single crystal provides approximate positions of some nodes of the reciprocal lattice of the crystal, and the indexing problem lies in determining a lattice matching these positions. Ind_X is a program for indexing diffraction data given in the form of several approximate reciprocal lattice nodes. The applied method relies on testing potential volumes of the primitive cell of the reciprocal lattice. A subset of reciprocal lattice vectors supporting a given test volume is used to obtain tentative lattice bases. These are bases of low-index superlattices of lattices based on triplets of supporting vectors. The Ind_X solution of the indexing problem consists of a list of best bases. The method turns out to be quite robust to data inaccuracies and spurious reflections. The program is relatively versatile, easily operated and freely accessible.

Structure Determination Using X-Ray Free-Electron Laser Pulses

The intense X-ray pulses from free-electron lasers, of only femtoseconds duration, outrun most of the processes that lead to structural degradation in X-ray exposures of macromolecules. Using these sources it is therefore possible to increase the dose to macromolecular crystals by several orders of magnitude higher than usually tolerable in conventional measurements, allowing crystal size to be decreased dramatically in diffraction measurements and without the need to cool the sample. Such pulses lead to the eventual vaporization of the sample, which has required a measurement approach, called serial crystallography, of consolidating snapshot diffraction patterns of many individual crystals. This in turn has further separated the connection between dose and obtainable diffraction information, with the only requirement from a single pattern being that to give enough information to place it, in three-dimensional reciprocal space, in relation to other patterns. Millions of extremely weak patterns can be collected and combined in this way, requiring methods to rapidly replenish the sample into the beam while generating the lowest possible background . The method is suited to time-resolved measurements over timescales below 1 ps to several seconds, and opens new opportunities for phasing. Some straightforward considerations of achievable signal levels are discussed and compared with a wide variety of recent experiments carried out at XFEL, synchrotron, and even laboratory sources, to discuss the capabilities of these new approaches and give some perspectives on their further development.

Receptor Activation of HIV-1 Env Leads to Asymmetric Exposure of the gp41 Trimer

Structural rearrangements of HIV-1 glycoprotein Env promote viral entry through membrane fusion. Env is a symmetric homotrimer with each protomer composed of surface subunit gp120 and transmembrane subunit gp41. Cellular CD4- and chemokine receptor-binding to gp120 coordinate conformational changes in gp41, first to an extended prehairpin intermediate (PHI) and, ultimately, into a fusogenic trimer-of-hairpins (TOH). HIV-1 fusion inhibitors target gp41 in the PHI and block TOH formation. To characterize structural transformations into and through the PHI, we employed asymmetric Env trimers containing both high and low affinity binding sites for individual fusion inhibitors. Asymmetry was achieved using engineered Env heterotrimers composed of protomers deficient in either CD4- or chemokine receptor-binding. Linking receptor engagement to inhibitor affinity allowed us to assess conformational changes of individual Env protomers in the context of a functioning trimer. We found that the transition into the PHI could occur symmetrically or asymmetrically depending on the stoichiometry of CD4 binding. Sequential engagement of multiple CD4s promoted progressive exposure of individual fusion inhibitor binding sites in a CD4-dependent fashion. By contrast, engagement of only a single CD4 molecule led to a delayed, but symmetric, exposure of the gp41 trimer. This complex coupling between Env-CD4 interaction and gp41 exposure explained the multiphasic fusion-inhibitor titration observed for a mutant Env homotrimer with a naturally asymmetric gp41. Our results suggest that the spatial and temporal exposure of gp41 can proceed in a nonconcerted, asymmetric manner depending on the number of CD4s that engage the Env trimer. The findings have important implications for the mechanism of viral membrane fusion and the development of vaccine candidates designed to elicit neutralizing antibodies targeting gp41 in the PHI.

For HIV, cellular invasion requires merging viral and cellular membranes, an event achieved through the activity of the viral fusion protein Env. Env consists of three gp120 and three gp41 subunits symmetrically arranged on the viral surface. The gp120 subunits bind cellular receptors, which, in turn, coordinate gp41 conformational changes that promote membrane fusion. Understanding these structural rearrangements illuminates the mechanism of viral membrane fusion, and also spurs development of targeted inhibitors of viral entry and vaccine candidates that elicit antiviral immune responses. In this study, we employed a novel strategy to investigate individual subunits in the context of functioning Env complexes. The strategy links distinct gp120-receptor interactions to conformational changes that expose specific gp41 subunits. We found that, despite the initial symmetric arrangement of its subunits, Env conformational changes most often proceed quite asymmetrically, leading to exposure of only one-third of the gp41 trimer for much of the fusion event. This finding might explain why attempts to elicit potent anti-HIV antibodies to a fully exposed gp41 trimer have been largely unsuccessful. The study gives us a glimpse of the early structural transitions leading to Env-mediated membrane fusion and provides a framework for interrogating the fusion proteins of other membrane-encapsulated viruses.

Crystal structure of a peptidyl-dipeptidase K-26-DCP from Actinomycete in complex with its natural inhibitor

Several soil‐derived Actinobacteria produce secondary metabolites that are proven specific and potent inhibitors of the human angiotensin‐I‐converting enzyme (ACE), a key target for the modulation of hypertension through its role in the renin–angiotensin–aldosterone system. K‐26‐DCP is a zinc dipeptidyl carboxypeptidase (DCP) produced by Astrosporangium hypotensionis, and an ancestral homologue of ACE. Here we report the high‐resolution crystal structures of K‐26‐DCP and of its complex with the natural microbial tripeptide product K‐26. The experimental results provide the structural basis for better understanding the specificity of K‐26 for human ACE over bacterial DCPs.

Database

Structural data are available in the PDB under the accession numbers 5L43 and 5L44.

TakeTwo: an indexing algorithm suited to still images with known crystal parameters

The indexing methods currently used for serial femtosecond crystallography were originally developed for experiments in which crystals are rotated in the X-ray beam, providing significant three-dimensional information. On the other hand, shots from both X-ray free-electron lasers and serial synchrotron crystallography experiments are still images, in which the few three-dimensional data available arise only from the curvature of the Ewald sphere. Traditional synchrotron crystallography methods are thus less well suited to still image data processing. Here, a new indexing method is presented with the aim of maximizing information use from a still image given the known unit-cell dimensions and space group. Efficacy for cubic, hexagonal and orthorhombic space groups is shown, and for those showing some evidence of diffraction the indexing rate ranged from 90% (hexagonal space group) to 151% (cubic space group). Here, the indexing rate refers to the number of lattices indexed per image.

On the release of cppxfel for processing X-ray free-electron laser images

As serial femtosecond crystallography expands towards a variety of delivery methods, including chip-based methods, and smaller collected data sets, the requirement to optimize the data analysis to produce maximum structure quality is becoming increasingly pressing. Here cppxfel, a software package primarily written in C++, which showcases several data analysis techniques, is released. This software package presently indexes images using DIALS (diffraction integration for advanced light sources) and performs an initial orientation matrix refinement, followed by post-refinement of individual images against a reference data set. Cppxfel is released with the hope that the unique and useful elements of this package can be repurposed for existing software packages. However, as released, it produces high-quality crystal structures and is therefore likely to be also useful to experienced users of X-ray free-electron laser (XFEL) software who wish to maximize the information extracted from a limited number of XFEL images.

Diffraction-geometry refinement in the DIALS framework

A comprehensive description of the methods used within the DIALS framework for diffraction-geometry refinement using predicted reflection centroids is given. Examples of the advanced features of the software are provided.

Rapid data collection and modern computing resources provide the opportunity to revisit the task of optimizing the model of diffraction geometry prior to integration. A comprehensive description is given of new software that builds upon established methods by performing a single global refinement procedure, utilizing a smoothly varying model of the crystal lattice where appropriate. This global refinement technique extends to multiple data sets, providing useful constraints to handle the problem of correlated parameters, particularly for small wedges of data. Examples of advanced uses of the software are given and the design is explained in detail, with particular emphasis on the flexibility and extensibility it entails.

The Structure of a Novel Thermophilic Esterase from the Planctomycetes Species, Thermogutta terrifontis Reveals an Open Active Site Due to a Minimal 'Cap' Domain

A carboxyl esterase (TtEst2) has been identified in a novel thermophilic bacterium, Thermogutta terrifontis from the phylum Planctomycetes and has been cloned and over-expressed in Escherichia coli. The enzyme has been characterized biochemically and shown to have activity toward small p-nitrophenyl (pNP) carboxylic esters with optimal activity for pNP-acetate. The enzyme shows moderate thermostability retaining 75% activity after incubation for 30 min at 70°C. The crystal structures have been determined for the native TtEst2 and its complexes with the carboxylic acid products propionate, butyrate, and valerate. TtEst2 differs from most enzymes of the α/β-hydrolase family 3 as it lacks the majority of the ‘cap’ domain and its active site cavity is exposed to the solvent. The bound ligands have allowed the identification of the carboxyl pocket in the enzyme active site. Comparison of TtEst2 with structurally related enzymes has given insight into how differences in their substrate preference can be rationalized based upon the properties of their active site pockets.

Structural analysis of Clostridium botulinum neurotoxin type D as a platform for the development of targeted secretion inhibitors

The botulinum neurotoxin type D is one of seven highly potent toxins produced by Clostridium botulinum which inhibit neurotransmission at cholinergic nerve terminals. A functional fragment derived from the toxin, LHn, consisting of the catalytic and translocation domains, has been heralded as a platform for the development of targeted secretion inhibitors. These secretion inhibitors are aimed at retargeting the toxin towards a specific cell type to inhibit vesicular secretion. Here we report crystal structures of LHn from serotype D at 2.3 Å, and that of SXN101959 at 3.1 Å resolution. SXN101959, a derivative that combines LHn from serotype D with a fragment of the growth hormone releasing hormone, has previously revealed promising results in inhibiting growth hormone release in pituitary somatotrophs. These structures offer for the first time insights into the translocation domain interaction with the catalytic domain in serotype D. Furthermore, structural information from small-angle X-ray scattering of LHn/D is compared among serotypes A, B, and D. Taken together, these results demonstrate the robustness of the ‘LHn fold’ across serotypes and its use in engineering additional polypeptide components with added functionality. Our study demonstrates the suitability of botulinum neurotoxin, and serotype D in particular, as a basis for engineering novel secretion inhibitors.

MicroED data collection and processing

MicroED, a method at the intersection of X-ray crystallography and electron cryo-microscopy, has rapidly progressed by exploiting advances in both fields and has already been successfully employed to determine the atomic structures of several proteins from sub-micron-sized, three-dimensional crystals. A major limiting factor in X-ray crystallography is the requirement for large and well ordered crystals. By permitting electron diffraction patterns to be collected from much smaller crystals, or even single well ordered domains of large crystals composed of several small mosaic blocks, MicroED has the potential to overcome the limiting size requirement and enable structural studies on difficult-to-crystallize samples. This communication details the steps for sample preparation, data collection and reduction necessary to obtain refined, high-resolution, three-dimensional models by MicroED, and presents some of its unique challenges.

A revised partiality model and post-refinement algorithm for X-ray free-electron laser data

Research towards using X-ray free-electron laser (XFEL) data to solve structures using experimental phasing methods such as sulfur single-wavelength anomalous dispersion (SAD) has been hampered by shortcomings in the diffraction models for X-ray diffraction from FELs. Owing to errors in the orientation matrix and overly simple partiality models, researchers have required large numbers of images to converge to reliable estimates for the structure-factor amplitudes, which may not be feasible for all biological systems. Here, data for cytoplasmic polyhedrosis virus type 17 (CPV17) collected at 1.3 Å wavelength at the Linac Coherent Light Source (LCLS) are revisited. A previously published definition of a partiality model for reflections illuminated by self-amplified spontaneous emission (SASE) pulses is built upon, which defines a fraction between 0 and 1 based on the intersection of a reflection with a spread of Ewald spheres modelled by a super-Gaussian wavelength distribution in the X-ray beam. A method of post-refinement to refine the parameters of this model is suggested. This has generated a merged data set with an overall discrepancy (by calculating the R(split) value) of 3.15% to 1.46 Å resolution from a 7225-image data set. The atomic numbers of C, N and O atoms in the structure are distinguishable in the electron-density map. There are 13 S atoms within the 237 residues of CPV17, excluding the initial disordered methionine. These only possess 0.42 anomalous scattering electrons each at 1.3 Å wavelength, but the 12 that have single predominant positions are easily detectable in the anomalous difference Fourier map. It is hoped that these improvements will lead towards XFEL experimental phase determination and structure determination by sulfur SAD and will generally increase the utility of the method for difficult cases.

Structure of CPV17 polyhedrin determined by the improved analysis of serial femtosecond crystallographic data

The X-ray free-electron laser (XFEL) allows the analysis of small weakly diffracting protein crystals, but has required very many crystals to obtain good data. Here we use an XFEL to determine the room temperature atomic structure for the smallest cytoplasmic polyhedrosis virus polyhedra yet characterized, which we failed to solve at a synchrotron. These protein microcrystals, roughly a micron across, accrue within infected cells. We use a new physical model for XFEL diffraction, which better estimates the experimental signal, delivering a high-resolution XFEL structure (1.75 Å), using fewer crystals than previously required for this resolution. The crystal lattice and protein core are conserved compared with a polyhedrin with less than 10% sequence identity. We explain how the conserved biological phenotype, the crystal lattice, is maintained in the face of extreme environmental challenge and massive evolutionary divergence. Our improved methods should open up more challenging biological samples to XFEL analysis.

Serial femtosecond crystallography and the use of X-ray free-electron lasers (XFEL) promise to revolutionize structural biology. Here, the authors describe refinements that reduce the redundancy required to obtain quality XFEL data and report a 1.75-Å structure—not obtainable by synchrotron radiation—using less than 6,000 crystals.

Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns

Still diffraction patterns from peptide nanocrystals with small unit cells are challenging to index using conventional methods owing to the limited number of spots and the lack of crystal orientation information for individual images. New indexing algorithms have been developed as part of the Computational Crystallography Toolbox (cctbx) to overcome these challenges. Accurate unit-cell information derived from an aggregate data set from thousands of diffraction patterns can be used to determine a crystal orientation matrix for individual images with as few as five reflections. These algorithms are potentially applicable not only to amyloid peptides but also to any set of diffraction patterns with sparse properties, such as low-resolution virus structures or high-throughput screening of still images captured by raster-scanning at synchrotron sources. As a proof of concept for this technique, successful integration of X-ray free-electron laser (XFEL) data to 2.5 Å resolution for the amyloid segment GNNQQNY from the Sup35 yeast prion is presented.