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- PDB-7qof: Icosahedral capsid of the phicrAss001 virion -

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Basic information

Entry
Database: PDB / ID: 7qof
TitleIcosahedral capsid of the phicrAss001 virion
Components
  • Auxiliary capsid protein gp36
  • Head fiber dimer protein gp29
  • Head fiber trimer protein gp21
  • Major capsid protein gp32
KeywordsVIRUS / crAssphage / bacteriophage / DNA virus
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
Head fiber trimeric protein / Head fiber dimeric protein / Auxiliary capsid protein / Major capsid protein
Similarity search - Component
Biological speciesBacteroides phage crAss001 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.01 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
Revision 1.4Jul 17, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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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
G: Major capsid protein gp32
H: Major capsid protein gp32
I: Major capsid protein gp32
a: Auxiliary capsid protein gp36
b: Auxiliary capsid protein gp36
c: Auxiliary capsid protein gp36
d: Auxiliary capsid protein gp36
e: Auxiliary capsid protein gp36
f: Auxiliary capsid protein gp36
g: Auxiliary capsid protein gp36
h: Auxiliary capsid protein gp36
i: Auxiliary capsid protein gp36
j: Head fiber trimer protein gp21
k: Head fiber trimer protein gp21
l: Head fiber dimer protein gp29
hetero molecules


Theoretical massNumber of molelcules
Total (without water)875,81522
Polymers875,79121
Non-polymers241
Water00
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
G: Major capsid protein gp32
H: Major capsid protein gp32
I: Major capsid protein gp32
a: Auxiliary capsid protein gp36
b: Auxiliary capsid protein gp36
c: Auxiliary capsid protein gp36
d: Auxiliary capsid protein gp36
e: Auxiliary capsid protein gp36
f: Auxiliary capsid protein gp36
g: Auxiliary capsid protein gp36
h: Auxiliary capsid protein gp36
i: Auxiliary capsid protein gp36
j: Head fiber trimer protein gp21
k: Head fiber trimer protein gp21
l: Head fiber dimer protein gp29
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)52,548,9131320
Polymers52,547,4551260
Non-polymers1,45860
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein
Major capsid protein gp32


Mass: 57098.598 Da / Num. of mol.: 9 / 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.: 9 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus) / References: UniProt: A0A385DVS7
#3: Protein Head fiber trimer protein gp21


Mass: 13110.960 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus) / References: UniProt: A0A385DVL5
#4: Protein Head fiber dimer protein gp29


Mass: 10294.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus) / References: UniProt: A0A385DTC5
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
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-#4 / 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 FIELD / 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: 1.16_3549: / Classification: refinement
EM software
IDNameVersionCategory
10RELION3.1final Euler assignment
12RELION3.13D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55063 / Symmetry type: POINT
Atomic model buildingB value: 152 / Protocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00561274
ELECTRON MICROSCOPYf_angle_d0.61383149
ELECTRON MICROSCOPYf_dihedral_angle_d15.20536474
ELECTRON MICROSCOPYf_chiral_restr0.0489292
ELECTRON MICROSCOPYf_plane_restr0.00410725

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