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- PDB-9in6: Capsid of Vibrio cholerae phage mature VP1 -

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Basic information

Entry
Database: PDB / ID: 9in6
TitleCapsid of Vibrio cholerae phage mature VP1
Components
  • SHP of VP1
  • major capsid of VP1
KeywordsVIRAL PROTEIN / phage / virus / vibrio cholera phage
Biological speciesVibrio cholerae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsLiu, H.R. / Pang, H.
Funding support China, 3items
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: to be published
Title: Three-dimensional structures of Vibrio cholerae typing podophage VP1 in two states
Authors: Liu, H.R. / Pang, H.
History
DepositionJul 5, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
M: major capsid of VP1
N: major capsid of VP1
O: major capsid of VP1
P: major capsid of VP1
Q: major capsid of VP1
R: major capsid of VP1
T: major capsid of VP1
c: SHP of VP1


Theoretical massNumber of molelcules
Total (without water)319,0078
Polymers319,0078
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
major capsid of VP1


Mass: 43886.555 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Vibrio cholerae (bacteria)
#2: Protein SHP of VP1


Mass: 11801.501 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio cholerae (bacteria)

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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: Vibrio cholerae phage / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Vibrio cholerae phage (bacteria)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Buffer solutionpH: 7.4
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 FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1600 nm
Image recordingElectron dose: 32 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 441860 / Symmetry type: POINT

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