Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Cryo-EM structure and B-factor refinement with ensemble representation

View ORCID ProfileTristan Cragnolini, View ORCID ProfileJoseph Beton, View ORCID ProfileMaya Topf
doi: https://doi.org/10.1101/2022.06.08.495259
Tristan Cragnolini
1Institute of Structural and Molecular Biology, Birkbeck and University College London, London, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Tristan Cragnolini
  • For correspondence: t.cragnolini@mail.cryst.bbk.ac.uk maya.topf@cssb-hamburg.de
Joseph Beton
2Centre for Structural Systems Biology (CSSB), Leibniz-Institut für Experimentelle Virologie (LIV) and Universitätsklinikum Hamburg Eppendorf, (UKE), Hamburg, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Joseph Beton
Maya Topf
1Institute of Structural and Molecular Biology, Birkbeck and University College London, London, UK
2Centre for Structural Systems Biology (CSSB), Leibniz-Institut für Experimentelle Virologie (LIV) and Universitätsklinikum Hamburg Eppendorf, (UKE), Hamburg, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Maya Topf
  • For correspondence: t.cragnolini@mail.cryst.bbk.ac.uk maya.topf@cssb-hamburg.de
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

Abstract

Cryo-EM experiments produce images of macromolecular assemblies that are combined to produce three-dimensional density maps. It is common to fit atomic models of the contained molecules to interpret those maps, followed by a density-guided refinement. Here, we propose TEMPy-REFF, a novel method for atomic structure refinement in cryo-EM density maps. By representing the atomic positions as components of a mixture model, their variances as B-factors, and a model ensemble description, we significantly improve the fit to the map compared to what is currently achievable with state-of-the-art methods. We validate our method on a large benchmark of 366 cryo-EM maps from EMDB at 1.8-7.1Å resolution and their corresponding PDB assembly models. We also show that our approach can provide newly-modelled regions in EMDB deposited maps by combining it with AlphaFold-Multimer. Finally, our method provides a natural interpretation of maps into components, allowing us to accurately create composite maps.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
Back to top
PreviousNext
Posted June 09, 2022.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Cryo-EM structure and B-factor refinement with ensemble representation
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Cryo-EM structure and B-factor refinement with ensemble representation
Tristan Cragnolini, Joseph Beton, Maya Topf
bioRxiv 2022.06.08.495259; doi: https://doi.org/10.1101/2022.06.08.495259
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
Cryo-EM structure and B-factor refinement with ensemble representation
Tristan Cragnolini, Joseph Beton, Maya Topf
bioRxiv 2022.06.08.495259; doi: https://doi.org/10.1101/2022.06.08.495259

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Biophysics
Subject Areas
All Articles
  • Animal Behavior and Cognition (4383)
  • Biochemistry (9599)
  • Bioengineering (7092)
  • Bioinformatics (24864)
  • Biophysics (12615)
  • Cancer Biology (9957)
  • Cell Biology (14354)
  • Clinical Trials (138)
  • Developmental Biology (7949)
  • Ecology (12107)
  • Epidemiology (2067)
  • Evolutionary Biology (15989)
  • Genetics (10925)
  • Genomics (14743)
  • Immunology (9869)
  • Microbiology (23676)
  • Molecular Biology (9485)
  • Neuroscience (50871)
  • Paleontology (369)
  • Pathology (1539)
  • Pharmacology and Toxicology (2683)
  • Physiology (4015)
  • Plant Biology (8657)
  • Scientific Communication and Education (1509)
  • Synthetic Biology (2397)
  • Systems Biology (6436)
  • Zoology (1346)