ArticleJournal of structural biology2014
Combined approaches to flexible fitting and assessment in virus capsids undergoing conformational change.
Article in Journal of structural biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 24 citations in OpenAlex.
- TEMPy2: a Python library with improved 3D electron microscopy density-fitting and validation workflows.Acta crystallographica. Section D, Structural biology · 2021Article
- Automated Modeling and Validation of Protein Complexes in Cryo-EM Maps.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Tools for the cryo-EM gold rush: going from the cryo-EM map to the atomistic model.Bioscience reports · 2017Review
- Article
- Improved metrics for comparing structures of macromolecular assemblies determined by 3D electron-microscopy.Journal of structural biology · 2017Article
- Flexible Fitting of Atomic Models into Cryo-EM Density Maps Guided by Helix Correspondences.Biophysical journal · 2017Article
- Structural Study of Heterogeneous Biological Samples by Cryoelectron Microscopy and Image Processing.BioMed research international · 2017Review
- Multiple capsid-stabilizing interactions revealed in a high-resolution structure of an emerging picornavirus causing neonatal sepsis.Nature communications · 2016Article
- Computational Methodologies for Real-Space Structural Refinement of Large Macromolecular Complexes.Annual review of biophysics · 2016Review
- Refinement of atomic models in high resolution EM reconstructions using Flex-EM and local assessment.Methods (San Diego, Calif.) · 2016Article
- Two distinct trimeric conformations of natively membrane-anchored full-length herpes simplex virus 1 glycoprotein B.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Resolution and Probabilistic Models of Components in CryoEM Maps of Mature P22 Bacteriophage.Biophysical journal · 2016Article
- Crystal Structure of the Measles Virus Nucleoprotein Core in Complex with an N-Terminal Region of Phosphoprotein.Journal of virology · 2015Article
- Structural Basis of Human Parechovirus Neutralization by Human Monoclonal Antibodies.Journal of virology · 2015Article
- Article
- Conformational changes during pore formation by the perforin-related protein pleurotolysin.PLoS biology · 2015Article
- Article
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
Abstract
Fitting of atomic components into electron cryo-microscopy (cryoEM) density maps is routinely used to understand the structure and function of macromolecular machines. Many fitting methods have been developed, but a standard protocol for successful fitting and assessment of fitted models has yet to be agreed upon among the experts in the field. Here, we created and tested a protocol that highlights important issues related to homology modelling, density map segmentation, rigid and flexible fitting, as well as the assessment of fits. As part of it, we use two different flexible fitting methods (Flex-EM and iMODfit) and demonstrate how combining the analysis of multiple fits and model assessment could result in an improved model. The protocol is applied to the case of the mature and empty capsids of Coxsackievirus A7 (CAV7) by flexibly fitting homology models into the corresponding cryoEM density maps at 8.2 and 6.1Å resolution. As a result, and due to the improved homology models (derived from recently solved crystal structures of a close homolog - EV71 capsid - in mature and empty forms), the final models present an improvement over previously published models. In close agreement with the capsid expansion observed in the EV71 structures, the new CAV7 models reveal that the expansion is accompanied by ∼5° counterclockwise rotation of the asymmetric unit, predominantly contributed by the capsid protein VP1. The protocol could be applied not only to viral capsids but also to many other complexes characterised by a combination of atomic structure modelling and cryoEM density fitting.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.