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- EMDB-60230: capsid of Vivrio cholerae typing phage VP1 -

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Basic information

Entry
Database: EMDB / ID: EMD-60230
Titlecapsid of Vivrio cholerae typing phage VP1
Map data
Sample
  • Virus: Vibrio cholerae phage VP1 (bacteria)
KeywordsComplex / Protein transport / VIRAL PROTEIN
Biological speciesVibrio cholerae phage VP1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.64 Å
AuthorsLiu HR / Pang H
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)32071209 China
National Natural Science Foundation of China (NSFC)32200994 China
CitationJournal: Structure / Year: 2024
Title: Three-dimensional structures of Vibrio cholerae typing podophage VP1 in two states.
Authors: Hao Pang / Fenxia Fan / Jing Zheng / Hao Xiao / Zhixue Tan / Jingdong Song / Biao Kan / Hongrong Liu /
Abstract: Lytic podophages (VP1-VP5) play crucial roles in subtyping Vibrio cholerae O1 biotype El Tor. However, until now no structures of these phages have been available, which hindered our understanding of ...Lytic podophages (VP1-VP5) play crucial roles in subtyping Vibrio cholerae O1 biotype El Tor. However, until now no structures of these phages have been available, which hindered our understanding of the molecular mechanisms of infection and DNA release. Here, we determined the cryoelectron microscopy (cryo-EM) structures of mature and DNA-ejected VP1 structures at near-atomic and subnanometer resolutions, respectively. The VP1 head is composed of 415 copies of the major capsid protein gp7 and 11 turret-shaped spikes. The VP1 tail consists of an adapter, a nozzle, a slender ring, and a tail needle, and is flanked by three extended fibers I and six trimeric fibers II. Conformational changes of fiber II in DNA-ejected VP1 may cause the release of the tail needle and core proteins, forming an elongated tail channel. Our structures provide insights into the molecular mechanisms of infection and DNA release for podophages with a tail needle.
History
DepositionMay 20, 2024-
Header (metadata) releaseAug 7, 2024-
Map releaseAug 7, 2024-
UpdateDec 18, 2024-
Current statusDec 18, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60230.png

Downloads & links

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Map

FileDownload / File: emd_60230.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 280 pix.
= 308. Å		1.1 Å/pix.
x 280 pix.
= 308. Å		1.1 Å/pix.
x 280 pix.
= 308. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.8
Minimum - Maximum-5.5986347 - 15.144143
Average (Standard dev.)-0.0028747818 (±0.63013256)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-255-255-255
Dimensions280280280
Spacing280280280
CellA=B=C: 308.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60230_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60230_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Vibrio cholerae phage VP1

EntireName: Vibrio cholerae phage VP1 (bacteria)
Components
  • Virus: Vibrio cholerae phage VP1 (bacteria)

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Supramolecule #1: Vibrio cholerae phage VP1

SupramoleculeName: Vibrio cholerae phage VP1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 666 / Sci species name: Vibrio cholerae phage VP1 / 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 150540
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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