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Martynowycz MW, Clabbers MTB, Hattne J, Gonen T. Ab initio phasing macromolecular structures using electron-counted MicroED data. Nat Methods 2022; 19:724-729. [PMID: 35637302 PMCID: PMC9184278 DOI: 10.1038/s41592-022-01485-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 04/07/2022] [Indexed: 12/31/2022]
Abstract
Structures of two globular proteins were determined ab initio using microcrystal electron diffraction (MicroED) data that were collected on a direct electron detector in counting mode. Microcrystals were identified using a scanning electron microscope (SEM) and thinned with a focused ion beam (FIB) to produce crystalline lamellae of ideal thickness. Continuous-rotation data were collected using an ultra-low exposure rate to enable electron counting in diffraction. For the first sample, triclinic lysozyme extending to a resolution of 0.87 Å, an ideal helical fragment of only three alanine residues provided initial phases. These phases were improved using density modification, allowing the entire atomic structure to be built automatically. A similar approach was successful on a second macromolecular sample, proteinase K, which is much larger and diffracted to a resolution of 1.5 Å. These results demonstrate that macromolecules can be determined to sub-ångström resolution by MicroED and that ab initio phasing can be successfully applied to counting data.
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Affiliation(s)
- Michael W. Martynowycz
- grid.19006.3e0000 0000 9632 6718Howard Hughes Medical Institute, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Department of Biological Chemistry, University of California, Los Angeles, CA USA
| | - Max T. B. Clabbers
- grid.19006.3e0000 0000 9632 6718Department of Biological Chemistry, University of California, Los Angeles, CA USA
| | - Johan Hattne
- grid.19006.3e0000 0000 9632 6718Howard Hughes Medical Institute, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Department of Biological Chemistry, University of California, Los Angeles, CA USA
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California, Los Angeles, CA, USA. .,Department of Biological Chemistry, University of California, Los Angeles, CA, USA. .,Department of Physiology, University of California, Los Angeles, CA, USA.
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Rius J, Torrelles X. A new density-modification procedure extending the application of the recent |ρ|-based phasing algorithm to larger crystal structures. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2021; 77:339-347. [PMID: 34196295 PMCID: PMC8248888 DOI: 10.1107/s2053273321004915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/10/2021] [Indexed: 11/10/2022]
Abstract
The incorporation of the new peakness-enhancing fast Fourier transform compatible ipp procedure (ipp = inner-pixel preservation) into the recently published SM algorithm based on |ρ| [Rius (2020). Acta Cryst A76, 489-493] improves its phasing efficiency for larger crystal structures with atomic resolution data. Its effectiveness is clearly demonstrated via a collection of test crystal structures (taken from the Protein Data Bank) either starting from random phase values or by using the randomly shifted modulus function (a Patterson-type synthesis) as initial ρ estimate. It has been found that in the presence of medium scatterers (e.g. S or Cl atoms) crystal structures with 1500 × c atoms in the unit cell (c = number of centerings) can be routinely solved. In the presence of strong scatterers like Fe, Cu or Zn atoms this number increases to around 5000 × c atoms. The implementation of this strengthened SM algorithm is simple, since it only includes a few easy-to-adjust parameters.
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Affiliation(s)
- Jordi Rius
- Institut de Ciència de Materials de Barcelona, CSIC, Campus de la UAB, Bellaterra, Catalonia 08193, Spain
| | - Xavier Torrelles
- Institut de Ciència de Materials de Barcelona, CSIC, Campus de la UAB, Bellaterra, Catalonia 08193, Spain
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Borges RJ, Meindl K, Triviño J, Sammito M, Medina A, Millán C, Alcorlo M, Hermoso JA, Fontes MRDM, Usón I. SEQUENCE SLIDER: expanding polyalanine fragments for phasing with multiple side-chain hypotheses. Acta Crystallogr D Struct Biol 2020; 76:221-237. [PMID: 32133987 PMCID: PMC7057211 DOI: 10.1107/s2059798320000339] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 01/13/2020] [Indexed: 02/07/2023] Open
Abstract
Fragment-based molecular-replacement methods can solve a macromolecular structure quasi-ab initio. ARCIMBOLDO, using a common secondary-structure or tertiary-structure template or a library of folds, locates these with Phaser and reveals the rest of the structure by density modification and autotracing in SHELXE. The latter stage is challenging when dealing with diffraction data at lower resolution, low solvent content, high β-sheet composition or situations in which the initial fragments represent a low fraction of the total scattering or where their accuracy is low. SEQUENCE SLIDER aims to overcome these complications by extending the initial polyalanine fragment with side chains in a multisolution framework. Its use is illustrated on test cases and previously unknown structures. The selection and order of fragments to be extended follows the decrease in log-likelihood gain (LLG) calculated with Phaser upon the omission of each single fragment. When the starting substructure is derived from a remote homolog, sequence assignment to fragments is restricted by the original alignment. Otherwise, the secondary-structure prediction is matched to that found in fragments and traces. Sequence hypotheses are trialled in a brute-force approach through side-chain building and refinement. Scoring the refined models through their LLG in Phaser may allow discrimination of the correct sequence or filter the best partial structures for further density modification and autotracing. The default limits for the number of models to pursue are hardware dependent. In its most economic implementation, suitable for a single laptop, the main-chain trace is extended as polyserine rather than trialling models with different sequence assignments, which requires a grid or multicore machine. SEQUENCE SLIDER has been instrumental in solving two novel structures: that of MltC from 2.7 Å resolution data and that of a pneumococcal lipoprotein with 638 residues and 35% solvent content.
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Affiliation(s)
- Rafael Junqueira Borges
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Baldiri Reixach 15, 08028 Barcelona, Spain
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu-SP 18618-689, Brazil
| | - Kathrin Meindl
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Baldiri Reixach 15, 08028 Barcelona, Spain
| | - Josep Triviño
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Baldiri Reixach 15, 08028 Barcelona, Spain
| | - Massimo Sammito
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, England
| | - Ana Medina
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Baldiri Reixach 15, 08028 Barcelona, Spain
| | - Claudia Millán
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Baldiri Reixach 15, 08028 Barcelona, Spain
| | - Martin Alcorlo
- Department of Crystallography and Structural Biology, Instituto de Química-Física ‘Rocasolano’, Consejo Superior de Investigaciones Científicas (CSIC), 28006 Madrid, Spain
| | - Juan A. Hermoso
- Department of Crystallography and Structural Biology, Instituto de Química-Física ‘Rocasolano’, Consejo Superior de Investigaciones Científicas (CSIC), 28006 Madrid, Spain
| | - Marcos Roberto de Mattos Fontes
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu-SP 18618-689, Brazil
| | - Isabel Usón
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Baldiri Reixach 15, 08028 Barcelona, Spain
- ICREA at IBMB–CSIC, Baldiri Reixach 13-15, 08028 Barcelona, Spain
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Alex JM, McArdle P, Crowley PB. Supramolecular stacking in a high Z′ calix[8]arene–porphyrin assembly. CrystEngComm 2020. [DOI: 10.1039/c9ce01646e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A co-crystal structure of sulfonato-calix[8]arene (sclx8) and trimethylanilinium-porphyrin (tmap) at 1.0 Å resolution is reported.
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Affiliation(s)
- Jimi M. Alex
- School of Chemistry
- National University of Ireland Galway
- Galway
- Ireland
| | - Patrick McArdle
- School of Chemistry
- National University of Ireland Galway
- Galway
- Ireland
| | - Peter B. Crowley
- School of Chemistry
- National University of Ireland Galway
- Galway
- Ireland
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Ab initio solution of macromolecular crystal structures without direct methods. Proc Natl Acad Sci U S A 2017; 114:3637-3641. [PMID: 28325875 DOI: 10.1073/pnas.1701640114] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The majority of macromolecular crystal structures are determined using the method of molecular replacement, in which known related structures are rotated and translated to provide an initial atomic model for the new structure. A theoretical understanding of the signal-to-noise ratio in likelihood-based molecular replacement searches has been developed to account for the influence of model quality and completeness, as well as the resolution of the diffraction data. Here we show that, contrary to current belief, molecular replacement need not be restricted to the use of models comprising a substantial fraction of the unknown structure. Instead, likelihood-based methods allow a continuum of applications depending predictably on the quality of the model and the resolution of the data. Unexpectedly, our understanding of the signal-to-noise ratio in molecular replacement leads to the finding that, with data to sufficiently high resolution, fragments as small as single atoms of elements usually found in proteins can yield ab initio solutions of macromolecular structures, including some that elude traditional direct methods.
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Mooers BHM. Direct-methods structure determination of a trypanosome RNA-editing substrate fragment with translational pseudosymmetry. Acta Crystallogr D Struct Biol 2016; 72:477-87. [PMID: 27050127 PMCID: PMC4822560 DOI: 10.1107/s2059798316001224] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Accepted: 01/19/2016] [Indexed: 11/10/2022] Open
Abstract
Using direct methods starting from random phases, the crystal structure of a 32-base-pair RNA (675 non-H RNA atoms in the asymmetric unit) was determined using only the native diffraction data (resolution limit 1.05 Å) and the computer program SIR2014. The almost three helical turns of the RNA in the asymmetric unit introduced partial or imperfect translational pseudosymmetry (TPS) that modulated the intensities when averaged by the l Miller indices but still escaped automated detection. Almost six times as many random phase sets had to be tested on average to reach a correct structure compared with a similar-sized RNA hairpin (27 nucleotides, 580 non-H RNA atoms) without TPS. More sensitive methods are needed for the automated detection of partial TPS.
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Affiliation(s)
- Blaine H. M. Mooers
- Department of Biochemistry and Molecular Biology, and Stephenson Cancer Center, University of Oklahoma Health Sciences Center, 975 NE 10th Street, BRC 466, Oklahoma City, OK 73104, USA
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Structural insights into the effects of 2'-5' linkages on the RNA duplex. Proc Natl Acad Sci U S A 2014; 111:3050-5. [PMID: 24516151 DOI: 10.1073/pnas.1317799111] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The mixture of 2'-5' and 3'-5' linkages generated during the nonenzymatic replication of RNA has long been regarded as a central problem for the origin of the RNA world. However, we recently observed that both a ribozyme and an RNA aptamer retain considerable functionality in the presence of prebiotically plausible levels of linkage heterogeneity. To better understand the RNA structure and function in the presence of backbone linkage heterogeneity, we obtained high-resolution X-ray crystal structures of a native 10-mer RNA duplex (1.32 Å) and two variants: one containing one 2'-5' linkage per strand (1.55 Å) and one containing three such linkages per strand (1.20 Å). We found that RNA duplexes adjust their local structures to accommodate the perturbation caused by 2'-5' linkages, with the flanking nucleotides buffering the disruptive effects of the isomeric linkage and resulting in a minimally altered global structure. Although most 2'-linked sugars were in the expected 2'-endo conformation, some were partially or fully in the 3'-endo conformation, suggesting that the energy difference between these conformations was relatively small. Our structural and molecular dynamic studies also provide insight into the diminished thermal and chemical stability of the duplex state associated with the presence of 2'-5' linkages. Our results contribute to the view that a low level of 2'-5' substitution would not have been fatal in an early RNA world and may in contrast have been helpful for both the emergence of nonenzymatic RNA replication and the early evolution of functional RNAs.
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Caliandro R, Dibenedetto D, Cascarano GL, Mazzone A, Nico G. Automatic α-helix identification in Patterson maps. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2011; 68:1-12. [PMID: 22194328 DOI: 10.1107/s0907444911046282] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 11/02/2011] [Indexed: 11/10/2022]
Abstract
α-Helices are peculiar atomic arrangements characterizing protein structures. Their occurrence can be used within crystallographic methods as minimal a priori information to drive the phasing process towards solution. Recently, brute-force methods have been developed which search for all possible positions of α-helices in the crystal cell by molecular replacement and explore all of them systematically. Knowing the α-helix orientations in advance would be a great advantage for this kind of approach. For this purpose, a fully automatic procedure to find α-helix orientations within the Patterson map has been developed. The method is based on Fourier techniques specifically addressed to the identification of helical shapes and operating on Patterson maps described in spherical coordinates. It supplies a list of candidate orientations, which are then refined by using a figure of merit based on a rotation function calculated for a template polyalanine helix oriented along the current direction. The orientation search algorithm has been optimized to work at 3 Å resolution, while the candidates are refined against all measured reflections. The procedure has been applied to a large number of protein test structures, showing an overall efficiency of 77% in finding α-helix orientations, which decreases to 48% on limiting the number of candidate solutions (to 13 on average). The information obtained may be used in many aspects in the framework of molecular-replacement phasing, as well as to constrain the generation of models in computational modelling programs. The procedure will be accessible through the next release of IL MILIONE and could be decisive in the solution of new unknown structures.
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Insights into the oxidative degradation of cellulose by a copper metalloenzyme that exploits biomass components. Proc Natl Acad Sci U S A 2011; 108:15079-84. [PMID: 21876164 DOI: 10.1073/pnas.1105776108] [Citation(s) in RCA: 657] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The enzymatic degradation of recalcitrant plant biomass is one of the key industrial challenges of the 21st century. Accordingly, there is a continuing drive to discover new routes to promote polysaccharide degradation. Perhaps the most promising approach involves the application of "cellulase-enhancing factors," such as those from the glycoside hydrolase (CAZy) GH61 family. Here we show that GH61 enzymes are a unique family of copper-dependent oxidases. We demonstrate that copper is needed for GH61 maximal activity and that the formation of cellodextrin and oxidized cellodextrin products by GH61 is enhanced in the presence of small molecule redox-active cofactors such as ascorbate and gallate. By using electron paramagnetic resonance spectroscopy and single-crystal X-ray diffraction, the active site of GH61 is revealed to contain a type II copper and, uniquely, a methylated histidine in the copper's coordination sphere, thus providing an innovative paradigm in bioinorganic enzymatic catalysis.
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Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AGW, McCoy A, McNicholas SJ, Murshudov GN, Pannu NS, Potterton EA, Powell HR, Read RJ, Vagin A, Wilson KS. Overview of the CCP4 suite and current developments. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:235-42. [PMID: 21460441 PMCID: PMC3069738 DOI: 10.1107/s0907444910045749] [Citation(s) in RCA: 9974] [Impact Index Per Article: 767.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Accepted: 11/07/2010] [Indexed: 11/10/2022]
Abstract
The CCP4 (Collaborative Computational Project, Number 4) software suite is a collection of programs and associated data and software libraries which can be used for macromolecular structure determination by X-ray crystallography. The suite is designed to be flexible, allowing users a number of methods of achieving their aims. The programs are from a wide variety of sources but are connected by a common infrastructure provided by standard file formats, data objects and graphical interfaces. Structure solution by macromolecular crystallography is becoming increasingly automated and the CCP4 suite includes several automation pipelines. After giving a brief description of the evolution of CCP4 over the last 30 years, an overview of the current suite is given. While detailed descriptions are given in the accompanying articles, here it is shown how the individual programs contribute to a complete software package.
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Affiliation(s)
- Martyn D Winn
- STFC Daresbury Laboratory, Daresbury, Warrington, England.
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