ArticleBiophysical journal2016
Resolution and Probabilistic Models of Components in CryoEM Maps of Mature P22 Bacteriophage.
Article in Biophysical journal, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Elucidating structural variability in p53 conformers using combinatorial refinement strategies and molecular dynamics.Cancer biology & therapy · 2024Article
- Cryo-EM structure and B-factor refinement with ensemble representation.Nature communications · 2024Article
- RETRACTED: Delineating Conformational Variability in Small Protein Structures Using Combinatorial Refinement StrategiesMicromachines · 2023Article
- Cryo-EM structure determination of small therapeutic protein targets at 3 Å-resolution using a rigid imaging scaffold.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Neck and capsid architecture of the robust Agrobacterium phage Milano.Communications biology · 2023Article
- Residue-level error detection in cryoelectron microscopy models.Structure (London, England : 1993) · 2023Article
- Polγ coordinates DNA synthesis and proofreading to ensure mitochondrial genome integrity.Nature structural & molecular biology · 2023Article
- Host Range Expansion ofJournal of virology · 2022Article
- Structurally derived universal mechanism for the catalytic cycle of the tail-anchored targeting factor Get3.Nature structural & molecular biology · 2022Article
- Cryo-EM analysis of Ebola virus nucleocapsid-like assembly.STAR protocols · 2022Article
- Simulation and Machine Learning Methods for Ion-Channel Structure Determination, Mechanistic Studies and Drug Design.Frontiers in pharmacology · 2022Review
- Validation, analysis and annotation of cryo-EM structures.Acta crystallographica. Section D, Structural biology · 2021Article
- Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge.Nature methods · 2021Article
- The N-terminus of varicella-zoster virus glycoprotein B has a functional role in fusion.PLoS pathogens · 2021Article
- Article
- Structure and mechanism of DNA delivery of a gene transfer agent.Nature communications · 2020Article
- Measurement of atom resolvability in cryo-EM maps with Q-scores.Nature methods · 2020Article
- Validation tests for cryo-EM maps using an independent particle set.Journal of structural biology: X · 2020Article
- Segmentation and Comparative Modeling in an 8.6-Å Cryo-EM Map of the Singapore Grouper Iridovirus.Structure (London, England : 1993) · 2019Article
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5 authors.
Funding
Abstract
CryoEM continues to produce density maps of larger and more complex assemblies with multiple protein components of mixed symmetries. Resolution is not always uniform throughout a cryoEM map, and it can be useful to estimate the resolution in specific molecular components of a large assembly. In this study, we present procedures to 1) estimate the resolution in subcomponents by gold-standard Fourier shell correlation (FSC); 2) validate modeling procedures, particularly at medium resolutions, which can include loop modeling and flexible fitting; and 3) build probabilistic models that combine high-accuracy priors (such as crystallographic structures) with medium-resolution cryoEM densities. As an example, we apply these methods to new cryoEM maps of the mature bacteriophage P22, reconstructed without imposing icosahedral symmetry. Resolution estimates based on gold-standard FSC show the highest resolution in the coat region (7.6 Å), whereas other components are at slightly lower resolutions: portal (9.2 Å), hub (8.5 Å), tailspike (10.9 Å), and needle (10.5 Å). These differences are indicative of inherent structural heterogeneity and/or reconstruction accuracy in different subcomponents of the map. Probabilistic models for these subcomponents provide new insights, to our knowledge, and structural information when taking into account uncertainty given the limitations of the observed density.
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