ArticleProceedings of the National Academy of Sciences of the United States of America2017
Accurate model annotation of a near-atomic resolution cryo-EM map.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers.
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72 citing papers in PubMed, 124 citations in OpenAlex.
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- Exploiting the full potential of cryo-EM maps.BBA advances · 2024Article
- Raman Multi-Omic Snapshot and Statistical Validation of Structural Differences between Herpes Simplex Type I and Epstein-Barr Viruses.International journal of molecular sciences · 2023Article
- A structural dendrogram of the actinobacteriophage major capsid proteins provides important structural insights into the evolution of capsid stability.Structure (London, England : 1993) · 2023Article
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- Assembly and Capsid Expansion Mechanism of Bacteriophage P22 Revealed by High-Resolution Cryo-EM Structures.Viruses · 2023Article
- Cryo-EM structures of human mCell research · 2022Article
- Structural basis of prokaryotic ubiquitin-like protein engagement and translocation by the mycobacterial Mpa-proteasome complex.Nature communications · 2022Article
- Cryo-electron tomography related radiation-damage parameters for individual-molecule 3D structure determination.Frontiers in chemistry · 2022Review
- Simulation and Machine Learning Methods for Ion-Channel Structure Determination, Mechanistic Studies and Drug Design.Frontiers in pharmacology · 2022Review
- Capsid Structure ofJournal of virology · 2021Article
- High Resolution Structure of the Mature Capsid ofInternational journal of molecular sciences · 2021Article
- Validation, analysis and annotation of cryo-EM structures.Acta crystallographica. Section D, Structural biology · 2021Article
- Dynamic closed states of a ligand-gated ion channel captured by cryo-EM and simulations.Life science alliance · 2021Article
12 more citing papers are in PubMed but not listed here.
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11 authors at 4 institutions in 1 country.
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Abstract
Electron cryomicroscopy (cryo-EM) has been used to determine the atomic coordinates (models) from density maps of biological assemblies. These models can be assessed by their overall fit to the experimental data and stereochemical information. However, these models do not annotate the actual density values of the atoms nor their positional uncertainty. Here, we introduce a computational procedure to derive an atomic model from a cryo-EM map with annotated metadata. The accuracy of such a model is validated by a faithful replication of the experimental cryo-EM map computed using the coordinates and associated metadata. The functional interpretation of any structural features in the model and its utilization for future studies can be made in the context of its measure of uncertainty. We applied this protocol to the 3.3-Å map of the mature P22 bacteriophage capsid, a large and complex macromolecular assembly. With this protocol, we identify and annotate previously undescribed molecular interactions between capsid subunits that are crucial to maintain stability in the absence of cementing proteins or cross-linking, as occur in other bacteriophages.
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