ArticleUltramicroscopy2019
Analysis of discrete local variability and structural covariance in macromolecular assemblies using Cryo-EM and focused classification.
Article in Ultramicroscopy, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Review
- Engineered Cas9 complexes establish an experimentally grounded benchmark for heterogeneous cryoEM reconstruction methods.bioRxiv : the preprint server for biology · 2026Article
- Conformational ensembles of the magnesium channel CorA reveal structural basis for channel gating.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- RNA sample optimization for cryo-EM analysis.Nature protocols · 2025Review
- Automated model-free analysis of cryo-EM volume ensembles with SIREn.Structure (London, England : 1993) · 2025Article
- Scaffold-enabled high-resolution cryo-EM structure determination of RNA.Nature communications · 2025Article
- Automated model-free analysis of cryo-EM volume ensembles with SIREn.bioRxiv : the preprint server for biology · 2024Article
- The structure of the human 80S ribosome at 1.9 Å resolution reveals the molecular role of chemical modifications and ions in RNA.Nature structural & molecular biology · 2024Article
- A generalizable scaffold-based approach for structure determination of RNAs by cryo-EM.Nucleic acids research · 2023Article
- An Unsupervised Classification Algorithm for Heterogeneous Cryo-EM Projection Images Based on Autoencoders.International journal of molecular sciences · 2023Article
- Article
- Cryo-EM for Small Molecules.Current protocols · 2022Review
- Emerging Themes in CryoEM─Single Particle Analysis Image Processing.Chemical reviews · 2022Review
- Cryo-EM structure of the HIV-1 Pol polyprotein provides insights into virion maturation.Science advances · 2022Article
- Continuum dynamics and statistical correction of compositional heterogeneity in multivalent IDP oligomers resolved by single-particle EM.Journal of molecular biology · 2022Article
- Article
- Protein Synthesis in the Developing Neocortex at Near-Atomic Resolution Reveals Ebp1-Mediated Neuronal Proteostasis at the 60S Tunnel Exit.Molecular cell · 2021Article
- Light-coupled cryo-plunger for time-resolved cryo-EM.Journal of structural biology · 2020Article
- Cryo-electron microscopy analysis of small membrane proteins.Current opinion in structural biology · 2020Review
- Development of imaging scaffolds for cryo-electron microscopy.Current opinion in structural biology · 2020Review
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6 authors.
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Abstract
Single-particle electron cryo-microscopy and computational image classification can be used to analyze structural variability in macromolecules and their assemblies. In some cases, a particle may contain different regions that each display a range of distinct conformations. We have developed strategies, implemented within the Frealign and cisTEM image processing packages, to focus-classify on specific regions of a particle and detect potential covariance. The strategies are based on masking the region of interest using either a 2-D mask applied to reference projections and particle images, or a 3-D mask applied to the 3-D volume. We show that focused classification approaches can be used to study structural covariance, a concept that is likely to gain more importance as datasets grow in size, allowing the distinction of more structural states and smaller differences between states. Finally, we apply the approaches to an experimental dataset containing the HIV-1 Transactivation Response (TAR) element RNA fused into the large bacterial ribosomal subunit to deconvolve structural mobility within localized regions of interest, and to a dataset containing assembly intermediates of the large subunit to measure structural covariance.
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