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- EMDB-14100: Asymmetric reconstruction of the phicrAss001 virion -

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Basic information

Entry
Database: EMDB / ID: EMD-14100
TitleAsymmetric reconstruction of the phicrAss001 virion
Map data
Sample
  • Virus: Bacteroides phage crAss001 (virus)
Function / homology
Function and homology information


viral capsid, decoration / virus tail / biological process involved in interaction with host / host cell membrane / viral life cycle / 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 / 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 / Portal vertex auxiliary protein / Head fiber trimeric protein / Tail hub protein A / Ring protein 3 / Cargo protein 1 / Ring protein 4/5 / Muzzle protein ...Portal protein / Ring protein 2 / Ring protein 1 / Portal vertex auxiliary protein / Head fiber trimeric protein / Tail hub protein A / Ring protein 3 / Cargo protein 1 / Ring protein 4/5 / Muzzle protein / Head fiber dimeric protein / Tail hub protein B / Auxiliary capsid protein / Polygalacturonase/tailspike protein / Major capsid protein
Similarity search - Component
Biological speciesBacteroides phage crAss001 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsBayfield OW / Shkoporov AN / Yutin N / Khokhlova EV / Smith JLR / Hawkins DEDP / Koonin EV / Hill C / Antson AA
Funding support United Kingdom, 1 items
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 30, 2021-
Header (metadata) releaseMar 29, 2023-
Map releaseMar 29, 2023-
UpdateMay 24, 2023-
Current statusMay 24, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14100.png

Downloads & links

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Map

FileDownload / File: emd_14100.map.gz / Format: CCP4 / Size: 1.6 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2 Å/pix.
x 750 pix.
= 1499.099 Å		2 Å/pix.
x 750 pix.
= 1499.099 Å		2 Å/pix.
x 750 pix.
= 1499.099 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.9988 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.21052565 - 0.26827955
Average (Standard dev.)0.00044751813 (±0.010205168)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions750750750
Spacing750750750
CellA=B=C: 1499.0992 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_14100_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #2

Fileemd_14100_additional_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Bacteroides phage crAss001

EntireName: Bacteroides phage crAss001 (virus)
Components
  • Virus: Bacteroides phage crAss001 (virus)

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Supramolecule #1: Bacteroides phage crAss001

SupramoleculeName: Bacteroides phage crAss001 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#13 / NCBI-ID: 2301731 / Sci species name: Bacteroides phage crAss001 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 51.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 27445
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER / Overall B value: 102
Output model

PDB-8ckb:
Asymmetric reconstruction of the crAss001 virion

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