CERES: a cryo-EM re-refinement system for continuous improvement of deposited models.

Dorothee Liebschner,Paul D Adams,Nigel W Moriarty,Billy K Poon,Vincent B Chen,Pavel V Afonine

doi:10.1107/s2059798320015879

Abstract

The field of electron cryomicroscopy (cryo-EM) has advanced quickly in recent years as the result of numerous technological and methodological developments. This has led to an increase in the number of atomic structures determined using this method. Recently, several tools for the analysis of cryo-EM data and models have been developed within the Phenix software package, such as phenix.real_space_refine for the refinement of atomic models against real-space maps. Also, new validation metrics have been developed for low-resolution cryo-EM models. To understand the quality of deposited cryo-EM structures and how they might be improved, models deposited in the Protein Data Bank that have map resolutions of better than 5 Å were automatically re-refined using current versions of Phenix tools. The results are available on a publicly accessible web page (https://cci.lbl.gov/ceres). The implementation of a Cryo-EM Re-refinement System (CERES) for the improvement of models deposited in the wwPDB, and the results of the re-refinements, are described. Based on these results, contents are proposed for a `cryo-EM Table 1', which summarizes experimental details and validation metrics in a similar way to `Table 1' in crystallography. The consistent use of robust metrics for the evaluation of cryo-EM models and data should accompany every structure deposition and be reported in scientific publications.

Highlights

Cryo-EM is an experimental technique that in the past has commonly been used to investigate large protein complexes, filaments and viruses
While the method was often limited to low resolution (5–9 A ), technological advances, such as the development of direct electron detectors (Faruqi et al, 2003; Milazzo et al, 2005; Deptuch et al, 2007; Li et al, 2013) and improvements in image processing (Campbell et al, 2012; Scheres, 2012; Bai et al, 2015), have led to an exponential increase in the number of cryo-EM models deposited in the Protein Data Bank (PDB; Berman et al, 2000; wwPDB Consortium, 2019)
As of the time of preparation of this manuscript, $2750 map–model pairs successfully passed at least one step of the re-refinement procedure3 and the results are displayed on the Cryo-EM Re-refinement System (CERES) website https://cci.lbl.gov/ceres

Summary

Introduction

Cryo-EM is an experimental technique that in the past has commonly been used to investigate large protein complexes, filaments and viruses. Cryo-EM is the third principal method for macromolecular structure determination (Fig. 1), representing 3.1% of deposited models in the PDB. While this is currently behind X-ray crystallography (88.8%) and nuclear magnetic resonance (NMR; 7.9%), some researchers project that deposition numbers will reach those of crystallography in only five years (Hand, 2020). Lowresolution cryo-EM density maps can be used to dock models from X-ray crystallography or NMR, but density maps of 5 Aresolution or better can be used to solve structures de novo

Methods

Results

Conclusion