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- PDB-5myu: VipA-N2/VipB contracted sheath of type VI secretion system -

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Basic information

Entry
Database: PDB / ID: 5myu
TitleVipA-N2/VipB contracted sheath of type VI secretion system
Components
  • Type VI secretion system protein ImpC
  • Uncharacterized protein
KeywordsPROTEIN TRANSPORT / Bacterial type VI secretion system / protein export
Function / homology
Function and homology information


Type VI secretion system TssC-like / TssC1, N-terminal / TssC1, C-terminal / EvpB/VC_A0108, tail sheath N-terminal domain / EvpB/VC_A0108, tail sheath gpW/gp25-like domain / Type VI secretion system sheath protein TssB1 / Type VI secretion system, VipA, VC_A0107 or Hcp2
Similarity search - Domain/homology
Type VI secretion system contractile sheath small subunit / Type VI secretion protein / Type VI secretion system contractile sheath large subunit / Type VI secretion system contractile sheath small subunit
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4 Å
AuthorsWang, J. / Brackmann, B. / Castano-Diez, D. / Kudryashev, M. / Goldie, D. / Maier, T. / Stahlberg, H. / Basler, M.
Funding support Switzerland, 3items
OrganizationGrant numberCountry
SNSF31003A_159525 Switzerland
SNSF NCCR TransCure Switzerland
University of Basel Switzerland
CitationJournal: Nat Microbiol / Year: 2017
Title: Cryo-EM structure of the extended type VI secretion system sheath-tube complex.
Authors: Jing Wang / Maximilian Brackmann / Daniel Castaño-Díez / Mikhail Kudryashev / Kenneth N Goldie / Timm Maier / Henning Stahlberg / Marek Basler /
Abstract: The bacterial type VI secretion system (T6SS) uses contraction of a long sheath to quickly thrust a tube with associated effectors across membranes of eukaryotic and bacterial cells . Only limited ...The bacterial type VI secretion system (T6SS) uses contraction of a long sheath to quickly thrust a tube with associated effectors across membranes of eukaryotic and bacterial cells . Only limited structural information is available about the inherently unstable precontraction state of the T6SS. Here, we obtain a 3.7 Å resolution structure of a non-contractile sheath-tube complex using cryo-electron microscopy and show that it resembles the extended T6SS inside Vibrio cholerae cells. We build a pseudo-atomic model of the complete sheath-tube assembly, which provides a mechanistic understanding of coupling sheath contraction with pushing and rotating the inner tube for efficient target membrane penetration. Our data further show that sheath contraction exposes a buried recognition domain to specifically trigger the disassembly and recycling of the T6SS sheath by the cognate ATP-dependent unfoldase ClpV.
History
DepositionJan 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 8, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 24, 2018Group: Advisory / Data collection / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
a: Uncharacterized protein
A: Type VI secretion system protein ImpC
b: Uncharacterized protein
B: Type VI secretion system protein ImpC
c: Uncharacterized protein
C: Type VI secretion system protein ImpC
d: Uncharacterized protein
D: Type VI secretion system protein ImpC
e: Uncharacterized protein
E: Type VI secretion system protein ImpC
f: Uncharacterized protein
F: Type VI secretion system protein ImpC


Theoretical massNumber of molelcules
Total (without water)377,31112
Polymers377,31112
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area52000 Å2
ΔGint-348 kcal/mol
Surface area174120 Å2
MethodPISA
Number of models3

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Components

#1: Protein
Uncharacterized protein


Mass: 13916.752 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Production host: Vibrio cholerae (bacteria) / References: UniProt: A0A023PRF3, UniProt: Q9KN58*PLUS
#2: Protein
Type VI secretion system protein ImpC / Uncharacterized protein ImpC


Mass: 48968.332 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: ERS013138_01484, ERS013140_01660, ERS013165_01090, ERS013186_01572, ERS013198_01471, ERS013199_00294, ERS013200_00406, ERS013201_01395, ERS013202_00755, ERS013206_01101, ERS013207_02465
Production host: Vibrio cholerae (bacteria) / References: UniProt: A0A023PTI7, UniProt: Q9KN57*PLUS

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Type IV secretion system sheath-tube / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL
Source (natural)Organism: Vibrio cholerae (bacteria)
Buffer solutionpH: 7.5
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
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 29.4 ° / Axial rise/subunit: 21.7 Å / Axial symmetry: C6
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7000 / Num. of class averages: 1 / Symmetry type: HELICAL
Atomic model buildingProtocol: RIGID BODY FIT

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