7QOI

Unique vertex of the phicrAss001 virion


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.62 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major capsid protein gp32504Bacteroides phage crAss001Mutation(s): 0 
UniProt
Find proteins for A0A385DVU6 (Bacteroides phage crAss001)
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Go to UniProtKB:  A0A385DVU6
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UniProt GroupA0A385DVU6
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Auxiliary capsid protein gp36333Bacteroides phage crAss001Mutation(s): 0 
UniProt
Find proteins for A0A385DVS7 (Bacteroides phage crAss001)
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UniProt GroupA0A385DVS7
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Portal vertex capsid protein gp57104Bacteroides phage crAss001Mutation(s): 0 
UniProt
Find proteins for A0A385DTA3 (Bacteroides phage crAss001)
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UniProt GroupA0A385DTA3
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Head fiber trimer protein gp2197Bacteroides phage crAss001Mutation(s): 0 
UniProt
Find proteins for A0A385DTC5 (Bacteroides phage crAss001)
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UniProt GroupA0A385DTC5
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Portal protein gp20806Bacteroides phage crAss001Mutation(s): 0 
UniProt
Find proteins for A0A385DT68 (Bacteroides phage crAss001)
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UniProt GroupA0A385DT68
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Ring protein 1 gp43236Bacteroides phage crAss001Mutation(s): 0 
UniProt
Find proteins for A0A385DT91 (Bacteroides phage crAss001)
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UniProt GroupA0A385DT91
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Ring protein 2 gp40225Bacteroides phage crAss001Mutation(s): 0 
UniProt
Find proteins for A0A385DT87 (Bacteroides phage crAss001)
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UniProt GroupA0A385DT87
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cargo protein 1 gp45842Bacteroides phage crAss001Mutation(s): 0 
UniProt
Find proteins for A0A385DV85 (Bacteroides phage crAss001)
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UniProt GroupA0A385DV85
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
AF [auth FB]
BF [auth FC]
CF [auth FD]
DF [auth FE]
EF [auth FF]
AF [auth FB],
BF [auth FC],
CF [auth FD],
DF [auth FE],
EF [auth FF],
FF [auth FG],
GF [auth FH],
HF [auth FI],
IF [auth FJ],
JF [auth FK],
KE [auth AB],
KF [auth FL],
LE [auth AC],
ME [auth AD],
NE [auth AE],
OE [auth BB],
PE [auth BD],
QE [auth CB],
RE [auth CD],
SE [auth CE],
TE [auth CF],
UE [auth DB],
VE [auth DE],
WE [auth DF],
XE [auth EB],
YE [auth ED],
ZE [auth FA]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.62 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX

Structure Validation

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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