Validation, analysis and annotation of cryo-EM structures

The process of turning 2D micrographs into 3D atomic models of the imaged macromolecules has been under rapid development and scrutiny in the field of cryo-EM. Here, some important methods for validation at several stages in this process are described. Firstly, how Fourier shell correlation of two independent maps and phase randomization beyond a certain frequency address the assessment of map resolution is reviewed. Techniques for local resolution estimation and map sharpening are also touched upon. The topic of validating models which are either built de novo or based on a known atomic structure fitted into a cryo-EM map is then approached. Map-model comparison using Q-scores and Fourier shell correlation plots is used to assure the agreement of the model with the observed map density. The importance of annotating the model with B factors to account for the resolvability of individual atoms in the map is illustrated. Finally, the timely topic of detecting and validating water molecules and metal ions in maps that have surpassed ∼2 Å resolution is described.

Evaluating Local and Directional Resolution of Cryo-EM Density Maps

A systematic and quantitative evaluation of cryo-EM maps is necessary to judge their quality and to capture all possible sources of error. A single value for global resolution is insufficient to accurately describe the quality of a reconstructed density. We describe the estimation and evaluation of two additional resolution measures, local and directional resolution, using methods based on the Fourier shell correlation (FSC). We apply the protocol to samples that encompass different types of pathologies a user is expected to encounter and provide analyses on how to interpret the output files and resulting maps. Implementation of these tools will facilitate density interpretation and can guide the user in adapting their experiments to improve the quality of cryo-EM maps, and by extension atomic models.

Protocols for Processing and Interpreting cryoEM Data Using Bsoft: A Case Study of the Retinal Adhesion Protein, Retinoschisin

The goal of cryoEM is to determine the structures of biomolecules from electron micrographs. In many cases the processing is straightforward and can be handled with routine protocols. In other cases, the properties and behavior of the specimen require adaptions to properly interpret the data. Here I describe the protocols for examining the higher order assemblies of the retinal adhesion protein, retinoschisin (RS1), using the Bsoft package. The protocols for micrograph preprocessing, 2D classification and 3D alignment and reconstruction follow the usual patterns for the majority of cryoEM specimens. The interpretation of the results is specific to the branched network of RS1 filaments. The 2D class averages are used to determine the relative positions of the RS1 molecules, thus defining the interacting interfaces in the network. The major interface of the linear filament is then further examined by reconstructing the "unit cell" and fitting the molecular models.

Non-uniformity of projection distributions attenuates resolution in Cryo-EM

Virtually all single-particle cryo-EM experiments currently suffer from specimen adherence to the air-water interface, leading to a non-uniform distribution in the set of projection views. Whereas it is well accepted that uniform projection distributions can lead to high-resolution reconstructions, non-uniform (anisotropic) distributions can negatively affect map quality, elongate structural features, and in some cases, prohibit interpretation altogether. Although some consequences of non-uniform sampling have been described qualitatively, we know little about how sampling quantitatively affects resolution in cryo-EM. Here, we show how inhomogeneity in any projection distribution scheme attenuates the global Fourier Shell Correlation (FSC) in relation to the number of particles and a single geometrical parameter, which we term the sampling compensation factor (SCF). The reciprocal of the SCF is defined as the average over Fourier shells of the reciprocal of the per-particle sampling and normalized to unity for uniform distributions. The SCF therefore ranges from one to zero, with values close to the latter implying large regions of poorly sampled or completely missing data in Fourier space. Using two synthetic test cases, influenza hemagglutinin and human apoferritin, we demonstrate how any amount of sampling inhomogeneity always attenuates the FSC compared to a uniform distribution. We advocate quantitative evaluation of the SCF criterion to approximate the effect of non-uniform sampling on resolution within experimental single-particle cryo-EM reconstructions.

Single-particle reconstruction statistics: a diagnostic tool in solving biomolecular structures by cryo-EM

In single-particle analysis (SPA), the aim is to obtain a 3D reconstruction of a biological molecule from 2D electron micrographs to the highest level of detail or resolution as possible. Current practice is to collect large volumes of data, hoping to reach high-resolution maps through sheer numbers. However, adding more particles from a specific data set eventually leads to diminishing improvements in resolution. Understanding what these resolution limits are and how to deal with them are important in optimization and automation of SPA. This study revisits the theory of 3D reconstruction and demonstrates how the associated statistics can provide a diagnostic tool to improve SPA. Small numbers of images already give sufficient information on micrograph quality and the amount of data required to reach high resolution. Such feedback allows the microscopist to improve sample-preparation and imaging parameters before committing to extensive data collection. Once a larger data set is available, a B factor can be determined describing the suppression of the signal owing to one or more causes, such as specimen movement, radiation damage, alignment inaccuracy and structural variation. Insight into the causes of signal suppression can then guide the user to consider appropriate actions to obtain better reconstructions.

The first single particle analysis Map Challenge: A summary of the assessments

The recent successes of cryo-electron microscopy fostered great expectation of solving many new and previously recalcitrant biomolecular structures. However, it also brings with it the danger of compromising the validity of the outcomes if not done properly. The Map Challenge is a first step in assessing the state of the art and to shape future developments in data processing. The organizers presented seven cases for single particle reconstruction, and 27 members of the community responded with 66 submissions. Seven groups analyzed these submissions, resulting in several assessment reports, summarized here. We devised a range of analyses to evaluate the submitted maps, including visual impressions, Fourier shell correlation, pairwise similarity and interpretation through modeling. Unfortunately, we did not find strong trends. We ascribe this to the complexity of the challenge, dealing with multiple cases, software packages and processing approaches. This puts the user in the spotlight, where his/her choices becomes the determinant of map quality. The future focus should therefore be on promulgating best practices and encapsulating these in the software. Such practices include adherence to validation principles, most notably the processing of independent sets, proper resolution-limited alignment, appropriate masking and map sharpening. We consider the Map Challenge to be a highly valuable exercise that should be repeated frequently or on an ongoing basis.

Map Challenge assessment: Fair comparison of single particle cryoEM reconstructions

Cryo-electron microscopy (cryoEM) is capable of achieving near-atomic resolution of biomolecular structures due to recent advances in hardware. Despite the long history of image processing software development for cryoEM, uncertainty about best practices and validation remains. The Map Challenge was therefore designed to test the current state of single particle reconstruction. As the first such challenge, the participants were given the freedom to analyze the cases in whichever way they wanted. Therefore, the maps submitted feature different sizes, sampling and orientations, making assessment non-trivial. To be fair, I developed a method to pose all maps in each case in the same configuration with minimal interpolation. I assessed the quality of these maps by visual inspection and Fourier shell correlation (FSC). Comparing the even-odd FSC with an FSC calculated against a reference structure analysis, I concluded that the quality of the maps related more to the user than to other factors, such as the software package used. Poor quality maps suffer either from lack of data or poor choices made by the user. Some maps appear significantly better than a reference or consensus of other maps, indicating overfitting. Best practices to avoid problems include an understanding of the effects of reference map modifications on particle image alignment, and generating appropriate masks. Ultimately, none of the issues revealed in the Map Challenge is insurmountable, as underscored by the excellent quality of reconstructions achieved by a significant number of participants.

Conical Fourier shell correlation applied to electron tomograms

The resolution of electron tomograms is anisotropic due to geometrical constraints during data collection, such as the limited tilt range and single axis tilt series acquisition. Acquisition of dual axis tilt series can decrease these effects. However, in cryo-electron tomography, to limit the electron radiation damage that occurs during imaging, the total dose should not increase and must be fractionated over the two tilt series. Here we set out to determine whether it is beneficial fractionate electron dose for recording dual axis cryo electron tilt series or whether it is better to perform single axis acquisition. To assess the quality of tomographic reconstructions in different directions here we introduce conical Fourier shell correlation (cFSCe/o). Employing cFSCe/o, we compared the resolution isotropy of single-axis and dual-axis (cryo-)electron tomograms using even/odd split data sets. We show that the resolution of dual-axis simulated and cryo-electron tomograms in the plane orthogonal to the electron beam becomes more isotropic compared to single-axis tomograms and high resolution peaks along the tilt axis disappear. cFSCe/o also allowed us to compare different methods for the alignment of dual-axis tomograms. We show that different tomographic reconstruction programs produce different anisotropic resolution in dual axis tomograms. We anticipate that cFSCe/o can also be useful for comparisons of acquisition and reconstruction parameters, and different hardware implementations.

Precise improvement of ISAF reconstruction algorithm based on the computational radius of density function

The output of icosahedral symmetry-adapted functions (ISAF) reconstruction algorithm is a virus capsid, where the density function of every outside point is theoretically zero. However, original ISAF algorithm takes reconstructed map as a solid sphere and density function of every point in the whole sphere is calculated. The density functions outside virus capsid may not be always zero, which may sometimes produce noise. In this study, Fourier shell correlation (FSC) is used for proving that density function calculation of original ISAF algorithm can reduce reconstruction precision. Subsequently, the range of virus capsid is determined with radial density function curve and the original ISAF algorithm is improved by calculating density function inside virus capsid. The experimental results on Cryo-electron microscopy (Cryo-EM) data of cytoplasmic polyhedrosis virus (CPV) indicate that the improved ISAF algorithm can generate more details of virus capsid and achieve a higher resolution.

CryoEM and molecular dynamics of the circadian KaiB-KaiC complex indicates that KaiB monomers interact with KaiC and block ATP binding clefts

The circadian control of cellular processes in cyanobacteria is regulated by a posttranslational oscillator formed by three Kai proteins. During the oscillator cycle, KaiA serves to promote autophosphorylation of KaiC while KaiB counteracts this effect. Here, we present a crystallographic structure of the wild-type Synechococcus elongatus KaiB and a cryo-electron microscopy (cryoEM) structure of a KaiBC complex. The crystal structure shows the expected dimer core structure and significant conformational variations of the KaiB C-terminal region, which is functionally important in maintaining rhythmicity. The KaiBC sample was formed with a C-terminally truncated form of KaiC, KaiC-Δ489, which is persistently phosphorylated. The KaiB-KaiC-Δ489 structure reveals that the KaiC hexamer can bind six monomers of KaiB, which form a continuous ring of density in the KaiBC complex. We performed cryoEM-guided molecular dynamics flexible fitting simulations with crystal structures of KaiB and KaiC to probe the KaiBC protein-protein interface. This analysis indicated a favorable binding mode for the KaiB monomer on the CII end of KaiC, involving two adjacent KaiC subunits and spanning an ATP binding cleft. A KaiC mutation, R468C, which has been shown to affect the affinity of KaiB for KaiC and lengthen the period in a bioluminescence rhythm assay, is found within the middle of the predicted KaiBC interface. The proposed KaiB binding mode blocks access to the ATP binding cleft in the CII ring of KaiC, which provides insight into how KaiB might influence the phosphorylation status of KaiC.

Electron microscopy analysis of a disaccharide analog complex reveals receptor interactions of adeno-associated virus

Mechanistic studies of macromolecular complexes often feature X-ray structures of complexes with bound ligands. The attachment of adeno-associated virus (AAV) to cell surface glycosaminoglycans (GAGs) is an example that has not proven amenable to crystallography, because the binding of GAG analogs disrupts lattice contacts. The interactions of AAV with GAGs are of interest in mediating the cell specificity of AAV-based gene therapy vectors. Previous electron microscopy led to differing conclusions on the exact binding site and the existence of large ligand-induced conformational changes in the virus. Conformational changes are expected during cell entry, but it has remained unclear whether the electron microscopy provided evidence of their induction by GAG-binding. Taking advantage of automated data collection, careful processing and new methods of structure refinement, the structure of AAV-DJ complexed with sucrose octasulfate is determined by electron microscopy difference map analysis to 4.8Å resolution. At this higher resolution, individual sulfate groups are discernible, providing a stereochemical validation of map interpretation, and highlighting interactions with two surface arginines that have been implicated in genetic studies. Conformational changes induced by the SOS are modest and limited to the loop most directly interacting with the ligand. While the resolution attainable will depend on sample order and other factors, there are an increasing number of macromolecular complexes that can be studied by cryo-electron microscopy at resolutions beyond 5Å, for which the approaches used here could be used to characterize the binding of inhibitors and other small molecule effectors when crystallography is not tractable.