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- PDB-7qoh: Unique vertex of the phicrAss001 virion with C5 symmetry imposed -

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Basic information

Entry
Database: PDB / ID: 7qoh
TitleUnique vertex of the phicrAss001 virion with C5 symmetry imposed
Components
  • Auxiliary capsid protein gp36
  • Head fiber trimer protein gp21
  • Major capsid protein gp32
  • Portal protein gp20
  • Portal vertex capsid protein gp57
KeywordsVIRUS / crAssphage / bacteriophage / DNA virus / portal / vertex / capsid / connector
Function / homology
Function and homology information


viral capsid, decoration / virion component / viral capsid / symbiont entry into host cell / virion attachment to host cell
Similarity search - Function
Bacteriophage B103, Gp8, head fibre / Head fiber protein
Similarity search - Domain/homology
Portal protein / Portal vertex auxiliary protein / Head fiber trimeric protein / Auxiliary capsid protein / Major capsid protein
Similarity search - Component
Biological speciesBacteroides phage crAss001 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsBayfield, 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.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
Citation
Journal: Nature / Year: 2023
Title: Structural atlas of a human gut crassvirus.
Authors: Oliver W Bayfield / Andrey N Shkoporov / Natalya Yutin / Ekaterina V Khokhlova / Jake L R Smith / Dorothy E D P Hawkins / Eugene V Koonin / Colin Hill / Alfred A Antson /
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 ...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. 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. Here we present a cryo-electron microscopy reconstruction of Bacteroides intestinalis virus ΦcrAss001, 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.
#1: Journal: Res Sq / Year: 2023
Title: Structural atlas of the most abundant human gut virus
Authors: Antson, A. / Bayfield, O. / Shkoporov, A. / Yutin, N. / Khokhlova, E. / Smith, J. / Hawkins, D. / Koonin, E. / Hill, C.
History
DepositionDec 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2May 17, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3May 24, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major capsid protein gp32
B: Major capsid protein gp32
C: Major capsid protein gp32
D: Major capsid protein gp32
E: Major capsid protein gp32
F: Major capsid protein gp32
a: Auxiliary capsid protein gp36
b: Auxiliary capsid protein gp36
d: Auxiliary capsid protein gp36
e: Auxiliary capsid protein gp36
f: Auxiliary capsid protein gp36
g: Portal vertex capsid protein gp57
h: Portal vertex capsid protein gp57
i: Head fiber trimer protein gp21
j: Head fiber trimer protein gp21
k: Head fiber trimer protein gp21
l: Portal protein gp20
m: Portal protein gp20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)763,29124
Polymers763,14518
Non-polymers1466
Water0
1
A: Major capsid protein gp32
B: Major capsid protein gp32
C: Major capsid protein gp32
D: Major capsid protein gp32
E: Major capsid protein gp32
F: Major capsid protein gp32
a: Auxiliary capsid protein gp36
b: Auxiliary capsid protein gp36
d: Auxiliary capsid protein gp36
e: Auxiliary capsid protein gp36
f: Auxiliary capsid protein gp36
g: Portal vertex capsid protein gp57
h: Portal vertex capsid protein gp57
i: Head fiber trimer protein gp21
j: Head fiber trimer protein gp21
k: Head fiber trimer protein gp21
l: Portal protein gp20
m: Portal protein gp20
hetero molecules
x 5


Theoretical massNumber of molelcules
Total (without water)3,816,454120
Polymers3,815,72590
Non-polymers72930
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4

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Components

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Protein , 5 types, 18 molecules ABCDEFabdefghijklm

#1: Protein
Major capsid protein gp32


Mass: 57098.598 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus) / References: UniProt: A0A385DVU6
#2: Protein
Auxiliary capsid protein gp36


Mass: 36154.094 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus) / References: UniProt: A0A385DVS7
#3: Protein Portal vertex capsid protein gp57


Mass: 11327.080 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus) / References: UniProt: A0A385DTA3
#4: Protein Head fiber trimer protein gp21


Mass: 10294.763 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus) / References: UniProt: A0A385DTC5
#5: Protein Portal protein gp20


Mass: 93122.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus) / References: UniProt: A0A385DT68

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Non-polymers , 1 types, 6 molecules

#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Bacteroides phage crAss001 / Type: VIRUS / Entity ID: #1-#5 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Bacteroides phage crAss001 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1500 nm / Nominal defocus min: 300 nm
Image recordingElectron dose: 51 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategory
10RELION3.1final Euler assignment
12RELION3.13D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 122709 / Symmetry type: POINT
Atomic model buildingB value: 157 / Protocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00537887
ELECTRON MICROSCOPYf_angle_d0.7951384
ELECTRON MICROSCOPYf_dihedral_angle_d13.84213818
ELECTRON MICROSCOPYf_chiral_restr0.0545675
ELECTRON MICROSCOPYf_plane_restr0.0076639

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