7QOK

Tail muzzle assembly of the phicrAss001 virion with C6 symmetry imposed


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.38 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural atlas of a human gut crassvirus.

Bayfield, O.W.Shkoporov, A.N.Yutin, N.Khokhlova, E.V.Smith, J.L.R.Hawkins, D.E.D.P.Koonin, E.V.Hill, C.Antson, A.A.

(2023) Nature 617: 409-416

  • DOI: https://doi.org/10.1038/s41586-023-06019-2
  • Primary Citation of Related Structures:  
    7QOF, 7QOG, 7QOH, 7QOI, 7QOJ, 7QOK, 7QOL

  • PubMed Abstract: 

    CrAssphage and related viruses of the order Crassvirales (hereafter referred to as crassviruses) were originally discovered by cross-assembly of metagenomic sequences. They are the most abundant viruses in the human gut, are found in the majority of individual gut viromes, and account for up to 95% of the viral sequences in some individuals 1-4 . Crassviruses are likely to have major roles in shaping the composition and functionality of the human microbiome, but the structures and roles of most of the virally encoded proteins are unknown, with only generic predictions resulting from bioinformatic analyses 4,5 . Here we present a cryo-electron microscopy reconstruction of Bacteroides intestinalis virus ΦcrAss001 6 , providing the structural basis for the functional assignment of most of its virion proteins. The muzzle protein forms an assembly about 1 MDa in size at the end of the tail and exhibits a previously unknown fold that we designate the 'crass fold', that is likely to serve as a gatekeeper that controls the ejection of cargos. In addition to packing the approximately 103 kb of virus DNA, the ΦcrAss001 virion has extensive storage space for virally encoded cargo proteins in the capsid and, unusually, within the tail. One of the cargo proteins is present in both the capsid and the tail, suggesting a general mechanism for protein ejection, which involves partial unfolding of proteins during their extrusion through the tail. These findings provide a structural basis for understanding the mechanisms of assembly and infection of these highly abundant crassviruses.


  • Organizational Affiliation

    York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK. oliver.bayfield@york.ac.uk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Muzzle protein gp441,371Bacteroides phage crAss001Mutation(s): 0 
UniProt
Find proteins for A0A385DVD6 (Bacteroides phage crAss001)
Explore A0A385DVD6 
Go to UniProtKB:  A0A385DVD6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A385DVD6
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Muzzle bound helix14Bacteroides phage crAss001Mutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ring protein 4/5 gp34
C, D
238Bacteroides phage crAss001Mutation(s): 0 
UniProt
Find proteins for A0A385DVC3 (Bacteroides phage crAss001)
Explore A0A385DVC3 
Go to UniProtKB:  A0A385DVC3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A385DVC3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.38 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-29
    Type: Initial release
  • Version 1.1: 2023-05-03
    Changes: Database references
  • Version 1.2: 2023-05-17
    Changes: Database references
  • Version 1.3: 2023-05-24
    Changes: Database references
  • Version 1.4: 2024-07-17
    Changes: Data collection