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- PDB-5mxn: Atomic model of the VipA/VipB/Hcp, the type six secretion system ... -

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Basic information

Entry
Database: PDB / ID: 5mxn
TitleAtomic model of the VipA/VipB/Hcp, the type six secretion system non-contractile sheath-tube of Vibrio cholerae from cryo-EM
Components
  • (Type VI secretion protein) x 2
  • Haemolysin co-regulated protein
KeywordsTRANSPORT PROTEIN / Type IV secretion system / protein export
Function / homology
Function and homology information


: / Hcp1-like / 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 / Type VI secretion system effector Hcp ...: / Hcp1-like / 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 / Type VI secretion system effector Hcp / Hcp1-like superfamily / Type VI secretion system effector, Hcp / Pnp Oxidase; Chain A / Roll / Mainly Beta
Similarity search - Domain/homology
Type VI secretion protein / Type VI secretion system contractile sheath small subunit / Haemolysin co-regulated 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: 3.7 Å
AuthorsWang, J. / Brackmann, M. / Castano-Diez, D. / Kudryashev, M. / Goldie, K. / Maier, T. / Stahlberg, H. / Basler, M.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
SNSF31003A_159525 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 23, 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 1.3May 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
1: Haemolysin co-regulated protein
A: Type VI secretion protein
a: Type VI secretion protein
2: Haemolysin co-regulated protein
B: Type VI secretion protein
b: Type VI secretion protein
3: Haemolysin co-regulated protein
C: Type VI secretion protein
c: Type VI secretion protein
4: Haemolysin co-regulated protein
D: Type VI secretion protein
d: Type VI secretion protein
5: Haemolysin co-regulated protein
E: Type VI secretion protein
e: Type VI secretion protein
6: Haemolysin co-regulated protein
F: Type VI secretion protein
f: Type VI secretion protein


Theoretical massNumber of molelcules
Total (without water)539,42618
Polymers539,42618
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area84580 Å2
ΔGint-575 kcal/mol
Surface area229790 Å2
MethodPISA
Number of models3

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Components

#1: Protein
Haemolysin co-regulated protein / Hcp / Type VI secretion system effector / Hcp1 family protein


Mass: 18878.055 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: hcp, hcpA, BFX32_16515, DA89_871, DN30_6, EN12_06865, EN12_14165
Production host: Vibrio cholerae (bacteria) / References: UniProt: P72350
#2: Protein
Type VI secretion protein / VipB / Type VI secretion system protein ImpC


Mass: 53514.449 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: BFX10_13915, BFX32_16935, DA89_2095, DN30_1329, EN12_14575, ERS013193_00899
Production host: Vibrio cholerae (bacteria) / References: UniProt: A0A085SGI6, UniProt: Q9KN57*PLUS
#3: Protein
Type VI secretion protein / VipA / Type VI secretion system protein ImpB / Type VI secretion system-associated protein / ...VipA / Type VI secretion system protein ImpB / Type VI secretion system-associated protein / Uncharacterized protein ImpB


Mass: 17511.895 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: BFX10_13910, BFX32_16930, DA89_2094, DN30_1328, EN12_14570
Production host: Vibrio cholerae (bacteria) / References: UniProt: A0A085SRC0, UniProt: Q9KN58*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 six secretion system tube in complex with non-contractile sheath
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 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
7Rosetta3.7model fitting
12RELION23D reconstruction
13PHENIX1.11.1-2575model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 23.5 ° / Axial rise/subunit: 37.8 Å / Axial symmetry: C6
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10000 / Num. of class averages: 1 / Symmetry type: HELICAL

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