8C38 | pdb_00008c38

Contracted cowpea chlorotic mottle virus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.64 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8C38

This is version 1.0 of the entry. See complete history

Literature

Fast viral dynamics revealed by microsecond time-resolved cryo-EM.

Harder, O.F.Barrass, S.V.Drabbels, M.Lorenz, U.J.

(2023) Nat Commun 14: 5649-5649

  • DOI: https://doi.org/10.1038/s41467-023-41444-x
  • Primary Citation Related Structures: 
    8C38, 8CPY

  • PubMed Abstract: 

    Observing proteins as they perform their tasks has largely remained elusive, which has left our understanding of protein function fundamentally incomplete. To enable such observations, we have recently proposed a technique that improves the time resolution of cryo-electron microscopy (cryo-EM) to microseconds. Here, we demonstrate that microsecond time-resolved cryo-EM enables observations of fast protein dynamics. We use our approach to elucidate the mechanics of the capsid of cowpea chlorotic mottle virus (CCMV), whose large-amplitude motions play a crucial role in the viral life cycle. We observe that a pH jump causes the extended configuration of the capsid to contract on the microsecond timescale. While this is a concerted process, the motions of the capsid proteins involve different timescales, leading to a curved reaction path. It is difficult to conceive how such a detailed picture of the dynamics could have been obtained with any other method, which highlights the potential of our technique. Crucially, our experiments pave the way for microsecond time-resolved cryo-EM to be applied to a broad range of protein dynamics that previously could not have been observed. This promises to fundamentally advance our understanding of protein function.


  • Organizational Affiliation
    • Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratory of Molecular Nanodynamics, CH-1015, Lausanne, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 61.1 kDa 
  • Atom Count: 3,593 
  • Modeled Residue Count: 479 
  • Deposited Residue Count: 570 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Capsid proteinA [auth C],
B [auth D],
C [auth I]
190Cowpea chlorotic mottle virusMutation(s): 0 
UniProt
Find proteins for P03601 (Cowpea chlorotic mottle virus)
Explore P03601 
Go to UniProtKB:  P03601
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03601
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.64 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.0.1
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerlandPP00P2_163681
European Research Council (ERC)European Union759145

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-18
    Type: Initial release