[English] 日本語
Yorodumi
- PDB-7qol: Tail assembly of the phicrAss001 virion with C6 symmetry imposed -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qol
TitleTail assembly of the phicrAss001 virion with C6 symmetry imposed
Components
  • (Ring protein ...) x 4
  • (Tail hub protein ...) x 2
  • Cargo protein 1 gp45
  • Muzzle bound helix
  • Muzzle protein gp44
  • Portal protein gp20
  • Tail fiber protein gp22
KeywordsVIRUS / crAssphage / bacteriophage / DNA virus / portal / connector / tail / ring / muzzle
Function / homology
Function and homology information


virus tail / biological process involved in interaction with host / host cell membrane / viral life cycle / virion component / viral capsid / symbiont entry into host cell / membrane
Similarity search - Function
Right handed beta helix domain / Right handed beta helix region / Parallel beta-helix repeat / Parallel beta-helix repeats / Pectin lyase fold / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
Portal protein / Ring protein 2 / Ring protein 1 / Tail hub protein A / Ring protein 3 / Cargo protein 1 / Ring protein 4/5 / Muzzle protein / Tail hub protein B / Polygalacturonase/tailspike protein
Similarity search - Component
Biological speciesBacteroides phage crAss001 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.33 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Portal protein gp20
B: Ring protein 1 gp43
C: Ring protein 2 gp40
D: Ring protein 3 gp35
E: Ring protein 4/5 gp34
F: Ring protein 4/5 gp34
G: Tail hub protein A gp38
H: Tail hub protein A gp38
I: Tail hub protein B gp39
J: Tail fiber protein gp22
K: Tail fiber protein gp22
L: Tail fiber protein gp22
M: Cargo protein 1 gp45
N: Cargo protein 1 gp45
O: Portal protein gp20
Q: Ring protein 1 gp43
S: Ring protein 2 gp40
T: Ring protein 3 gp35
U: Ring protein 4/5 gp34
V: Ring protein 4/5 gp34
W: Tail hub protein A gp38
Z: Tail hub protein A gp38
a: Tail hub protein B gp39
b: Tail fiber protein gp22
c: Tail fiber protein gp22
d: Tail fiber protein gp22
e: Cargo protein 1 gp45
f: Cargo protein 1 gp45
P: Muzzle protein gp44
R: Muzzle bound helix
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,654,37232
Polymers1,654,32330
Non-polymers492
Water362
1
A: Portal protein gp20
B: Ring protein 1 gp43
C: Ring protein 2 gp40
D: Ring protein 3 gp35
E: Ring protein 4/5 gp34
F: Ring protein 4/5 gp34
G: Tail hub protein A gp38
H: Tail hub protein A gp38
I: Tail hub protein B gp39
J: Tail fiber protein gp22
K: Tail fiber protein gp22
L: Tail fiber protein gp22
M: Cargo protein 1 gp45
N: Cargo protein 1 gp45
O: Portal protein gp20
Q: Ring protein 1 gp43
S: Ring protein 2 gp40
T: Ring protein 3 gp35
U: Ring protein 4/5 gp34
V: Ring protein 4/5 gp34
W: Tail hub protein A gp38
Z: Tail hub protein A gp38
a: Tail hub protein B gp39
b: Tail fiber protein gp22
c: Tail fiber protein gp22
d: Tail fiber protein gp22
e: Cargo protein 1 gp45
f: Cargo protein 1 gp45
P: Muzzle protein gp44
R: Muzzle bound helix
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)9,926,232192
Polymers9,925,940180
Non-polymers29212
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
Buried area99100 Å2
ΔGint-473 kcal/mol
Surface area268490 Å2

-
Components

-
Protein , 4 types, 13 molecules AOJKLbcdMNefP

#1: 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
#8: Protein
Tail fiber protein gp22 / Tail fiber protein gp22


Mass: 92401.672 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus) / References: UniProt: A0A385DVT1
#9: Protein
Cargo protein 1 gp45 / / Cargo protein C1 gp45


Mass: 90913.836 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus) / References: UniProt: A0A385DV85
#10: Protein Muzzle protein gp44 / Muzzle protein


Mass: 156459.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus) / References: UniProt: A0A385DVD6

-
Ring protein ... , 4 types, 10 molecules BQCSDTEFUV

#2: Protein Ring protein 1 gp43 / Ring protein 1 gp43


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


Mass: 26216.832 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus) / References: UniProt: A0A385DT87
#4: Protein Ring protein 3 gp35


Mass: 26076.506 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus) / References: UniProt: A0A385DV73
#5: Protein
Ring protein 4/5 gp34


Mass: 26680.965 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus) / References: UniProt: A0A385DVC3

-
Tail hub protein ... , 2 types, 6 molecules GHWZIa

#6: Protein
Tail hub protein A gp38 / Tail hub protein A gp38


Mass: 24813.201 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus) / References: UniProt: A0A385DTH1
#7: Protein Tail hub protein B gp39


Mass: 13411.116 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus) / References: UniProt: A0A385DVM6

-
Protein/peptide , 1 types, 1 molecules R

#11: Protein/peptide Muzzle bound helix


Mass: 1209.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus)

-
Non-polymers , 2 types, 4 molecules

#12: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#13: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Bacteroides phage crAss001 / Type: VIRUS / Entity ID: #1-#9 / 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

-
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)

-
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: C6 (6 fold cyclic)
3D reconstructionResolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46280 / Symmetry type: POINT
Atomic model buildingB value: 129 / Protocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00452637
ELECTRON MICROSCOPYf_angle_d0.69171270
ELECTRON MICROSCOPYf_dihedral_angle_d14.42119707
ELECTRON MICROSCOPYf_chiral_restr0.0477858
ELECTRON MICROSCOPYf_plane_restr0.0059243

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more