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- PDB-8zkk: Portal-tail of Vibrio cholerae typing phage mature VP1 -

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Basic information

Entry
Database: PDB / ID: 8zkk
TitlePortal-tail of Vibrio cholerae typing phage mature VP1
Components
  • adaptor gp12
  • gp13
  • nozzle gp16
  • portal gp5
  • ring protein gp10
KeywordsVIRAL PROTEIN / phage / virus / vibrio cholera phage
Biological speciesVibrio cholerae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 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: 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 16, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details
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.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.2Dec 18, 2024Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
O: nozzle gp16
A: portal gp5
B: adaptor gp12
U: portal gp5
D: adaptor gp12
m: ring protein gp10
p: gp13
u: gp13
z: gp13


Theoretical massNumber of molelcules
Total (without water)309,1159
Polymers309,1159
Non-polymers00
Water00
1
O: nozzle gp16
A: portal gp5
B: adaptor gp12
U: portal gp5
D: adaptor gp12
m: ring protein gp10
p: gp13
u: gp13
z: gp13
x 6


Theoretical massNumber of molelcules
Total (without water)1,854,69254
Polymers1,854,69254
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5

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Components

#1: Protein nozzle gp16


Mass: 59015.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio cholerae (bacteria)
#2: Protein portal gp5


Mass: 73263.602 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vibrio cholerae (bacteria)
#3: Protein adaptor gp12


Mass: 23592.850 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vibrio cholerae (bacteria)
#4: Protein ring protein gp10


Mass: 26311.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio cholerae (bacteria)
#5: Protein gp13


Mass: 10025.203 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Vibrio cholerae (bacteria)
Has protein modificationN

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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 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47456 / Symmetry type: POINT

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