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- PDB-7qoi: Unique vertex of the phicrAss001 virion -

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Basic information

Entry
Database: PDB / ID: 7qoi
TitleUnique vertex of the phicrAss001 virion
Components
  • (Ring protein ...) x 2
  • Auxiliary capsid protein gp36
  • Cargo protein 1 gp45
  • 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 / virus tail / host cell membrane / virion component / viral capsid / symbiont entry into host cell / virion attachment to host cell / membrane
Similarity search - Function
Bacteriophage B103, Gp8, head fibre / Head fiber protein
Similarity search - Domain/homology
Portal protein / Ring protein 2 / Ring protein 1 / Portal vertex auxiliary protein / Head fiber trimeric protein / Cargo protein 1 / Auxiliary capsid protein / Major capsid protein
Similarity search - Component
Biological speciesBacteroides phage crAss001 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.62 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
AA: Major capsid protein gp32
AB: Major capsid protein gp32
AC: Major capsid protein gp32
AD: Major capsid protein gp32
AE: Major capsid protein gp32
AF: Major capsid protein gp32
Aa: Auxiliary capsid protein gp36
Ab: Auxiliary capsid protein gp36
Ad: Auxiliary capsid protein gp36
Ae: Auxiliary capsid protein gp36
Af: Auxiliary capsid protein gp36
Ag: Portal vertex capsid protein gp57
Ah: Portal vertex capsid protein gp57
Ai: Head fiber trimer protein gp21
Aj: Head fiber trimer protein gp21
Ak: Head fiber trimer protein gp21
BA: Major capsid protein gp32
BB: Major capsid protein gp32
BC: Major capsid protein gp32
BD: Major capsid protein gp32
BE: Major capsid protein gp32
BF: Major capsid protein gp32
Ba: Auxiliary capsid protein gp36
Bb: Auxiliary capsid protein gp36
Bd: Auxiliary capsid protein gp36
Be: Auxiliary capsid protein gp36
Bf: Auxiliary capsid protein gp36
Bg: Portal vertex capsid protein gp57
Bh: Portal vertex capsid protein gp57
Bi: Head fiber trimer protein gp21
Bj: Head fiber trimer protein gp21
Bk: Head fiber trimer protein gp21
CA: Major capsid protein gp32
CB: Major capsid protein gp32
CC: Major capsid protein gp32
CD: Major capsid protein gp32
CE: Major capsid protein gp32
CF: Major capsid protein gp32
Ca: Auxiliary capsid protein gp36
Cb: Auxiliary capsid protein gp36
Cd: Auxiliary capsid protein gp36
Ce: Auxiliary capsid protein gp36
Cf: Auxiliary capsid protein gp36
Cg: Portal vertex capsid protein gp57
Ch: Portal vertex capsid protein gp57
Ci: Head fiber trimer protein gp21
Cj: Head fiber trimer protein gp21
Ck: Head fiber trimer protein gp21
DA: Major capsid protein gp32
DB: Major capsid protein gp32
DC: Major capsid protein gp32
DD: Major capsid protein gp32
DE: Major capsid protein gp32
DF: Major capsid protein gp32
Da: Auxiliary capsid protein gp36
Db: Auxiliary capsid protein gp36
Dd: Auxiliary capsid protein gp36
De: Auxiliary capsid protein gp36
Df: Auxiliary capsid protein gp36
Dg: Portal vertex capsid protein gp57
Dh: Portal vertex capsid protein gp57
Di: Head fiber trimer protein gp21
Dj: Head fiber trimer protein gp21
Dk: Head fiber trimer protein gp21
EA: Major capsid protein gp32
EB: Major capsid protein gp32
EC: Major capsid protein gp32
ED: Major capsid protein gp32
EE: Major capsid protein gp32
EF: Major capsid protein gp32
Ea: Auxiliary capsid protein gp36
Eb: Auxiliary capsid protein gp36
Ed: Auxiliary capsid protein gp36
Ee: Auxiliary capsid protein gp36
Ef: Auxiliary capsid protein gp36
Eg: Portal vertex capsid protein gp57
Eh: Portal vertex capsid protein gp57
Ei: Head fiber trimer protein gp21
Ej: Head fiber trimer protein gp21
Ek: Head fiber trimer protein gp21
FA: Portal protein gp20
FB: Portal protein gp20
FC: Portal protein gp20
FD: Portal protein gp20
FE: Portal protein gp20
FF: Portal protein gp20
FG: Portal protein gp20
FH: Portal protein gp20
FI: Portal protein gp20
FJ: Portal protein gp20
FK: Portal protein gp20
FL: Portal protein gp20
FM: Ring protein 1 gp43
FN: Ring protein 1 gp43
FO: Ring protein 1 gp43
FP: Ring protein 1 gp43
FQ: Ring protein 1 gp43
FR: Ring protein 1 gp43
FS: Ring protein 1 gp43
FT: Ring protein 1 gp43
FU: Ring protein 1 gp43
FV: Ring protein 1 gp43
FW: Ring protein 1 gp43
FX: Ring protein 1 gp43
FY: Ring protein 2 gp40
FZ: Ring protein 2 gp40
GA: Ring protein 2 gp40
GB: Ring protein 2 gp40
GC: Ring protein 2 gp40
GD: Ring protein 2 gp40
GE: Ring protein 2 gp40
GF: Ring protein 2 gp40
GG: Ring protein 2 gp40
GH: Ring protein 2 gp40
GI: Ring protein 2 gp40
GJ: Ring protein 2 gp40
GK: Cargo protein 1 gp45
GL: Cargo protein 1 gp45
GM: Cargo protein 1 gp45
GN: Cargo protein 1 gp45
GO: Cargo protein 1 gp45
GP: Cargo protein 1 gp45
GQ: Cargo protein 1 gp45
GR: Cargo protein 1 gp45
GS: Cargo protein 1 gp45
GT: Cargo protein 1 gp45
GU: Cargo protein 1 gp45
GV: Cargo protein 1 gp45
IK: Cargo protein 1 gp45
IL: Cargo protein 1 gp45
IM: Cargo protein 1 gp45
IN: Cargo protein 1 gp45
IO: Cargo protein 1 gp45
IP: Cargo protein 1 gp45
IQ: Cargo protein 1 gp45
IR: Cargo protein 1 gp45
IS: Cargo protein 1 gp45
IT: Cargo protein 1 gp45
IU: Cargo protein 1 gp45
IV: Cargo protein 1 gp45
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,828,915167
Polymers6,828,259140
Non-polymers65627
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 6 types, 116 molecules AAABACADAEAFBABBBCBDBEBFCACBCCCDCECFDADBDCDDDEDFEAEBECEDEEEF...

#1: Protein ...
Major capsid protein gp32


Mass: 57098.598 Da / Num. of mol.: 30 / 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.: 25 / 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.: 10 / 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.: 15 / 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.: 12 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus) / References: UniProt: A0A385DT68
#8: Protein ...
Cargo protein 1 gp45 /


Mass: 90913.836 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus) / References: UniProt: A0A385DV85

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Ring protein ... , 2 types, 24 molecules FMFNFOFPFQFRFSFTFUFVFWFXFYFZGAGBGCGDGEGFGGGHGIGJ

#6: Protein
Ring protein 1 gp43


Mass: 27479.625 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus) / References: UniProt: A0A385DT91
#7: Protein
Ring protein 2 gp40


Mass: 26216.832 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus) / References: UniProt: A0A385DT87

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Non-polymers , 1 types, 27 molecules

#9: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 27 / 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-#8 / Source: NATURAL
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: UCSF ChimeraX / Version: 1.3/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / Type: package
EM software
IDNameVersionCategory
10RELION3.1final Euler assignment
12RELION3.13D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 122709 / Symmetry type: POINT
Atomic model buildingB value: 160 / Protocol: AB INITIO MODEL / Space: REAL

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