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- EMDB-60702: Capsid of Vibrio cholerae phage mature VP1 -

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Basic information

Entry
Database: EMDB / ID: EMD-60702
TitleCapsid of Vibrio cholerae phage mature VP1
Map data
Sample
  • Virus: Vibrio cholerae phage (bacteria)
    • Protein or peptide: major capsid of VP1
    • Protein or peptide: SHP of VP1
Keywordsphage / virus / vibrio cholera phage / VIRAL PROTEIN
Biological speciesVibrio cholerae (bacteria) / Vibrio cholerae phage (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 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
DepositionJul 5, 2024-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60702.png

Downloads & links

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Map

FileDownload / File: emd_60702.map.gz / Format: CCP4 / Size: 290.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 424 pix.
= 466.4 Å		1.1 Å/pix.
x 424 pix.
= 466.4 Å		1.1 Å/pix.
x 424 pix.
= 466.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5
Minimum - Maximum-6.598915 - 17.800837999999999
Average (Standard dev.)0.0032656202 (±0.8140461)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-212-212-212
Dimensions424424424
Spacing424424424
CellA=B=C: 466.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60702_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_60702_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Vibrio cholerae phage

EntireName: Vibrio cholerae phage (bacteria)
Components
  • Virus: Vibrio cholerae phage (bacteria)
    • Protein or peptide: major capsid of VP1
    • Protein or peptide: SHP of VP1

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Supramolecule #1: Vibrio cholerae phage

SupramoleculeName: Vibrio cholerae phage / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 666 / Sci species name: Vibrio cholerae phage / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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Macromolecule #1: major capsid of VP1

MacromoleculeName: major capsid of VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 43.886555 KDa
SequenceString: MATIAGLRGT GDWGNQERPT DFRETILWME PNGQAPLQAL MSKMSSQPTT DPEFSWWEEK LTHNRLEVKT EAAAGVTTLA VDTDQAWAC VKGDILMVES VGGLWANEIL KVVEDPTAGN ALKVARGFAG TTAAVIPAGT FIIAIGTSFA EGSLAPKSAT R NPVKLNNF ...String:
MATIAGLRGT GDWGNQERPT DFRETILWME PNGQAPLQAL MSKMSSQPTT DPEFSWWEEK LTHNRLEVKT EAAAGVTTLA VDTDQAWAC VKGDILMVES VGGLWANEIL KVVEDPTAGN ALKVARGFAG TTAAVIPAGT FIIAIGTSFA EGSLAPKSAT R NPVKLNNF CQIFKKSYEI TKTADATKAR TGSALANDKK RRMFDYYRDV EMAFIYGRKS ETVGENGKPE RTTGGLLNFI TT NRTQFGT GAGKTELTED SLIDFFANVF NYDGQGAGNQ RIAFVGNTAL TKINKLARNS PSTRINFDKQ VTQVYGMNFT RWV LPQGEI FFKTHPLFNV HPELSKAMMV LNPKGIKERV LRATKPENDI QQVGQDSIKG QWIGEFGLEV NHEETMAFAG GIA

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Macromolecule #2: SHP of VP1

MacromoleculeName: SHP of VP1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 11.801501 KDa
SequenceString:
MLVHYGKLSD MPTVVDVNTT MGTDVPEDLL EIYVGCYAAD GKTPAAGTGV LTFHGSWNGV HKRLIGTVDL AAAGEVIAYN PPLMFGGCK KLFVSYTGVG TQIVDVYVHR GE

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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

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 441860
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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