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- PDB-6giy: The baseplate complex from the type VI secretion system -

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Basic information

Entry
Database: PDB / ID: 6giy
TitleThe baseplate complex from the type VI secretion system
Components
  • TssF
  • TssG
  • TssK
KeywordsSTRUCTURAL PROTEIN / Secretion / baseplate / complex
Function / homologyType VI secretion system TssF / Type VI secretion system, TssF / Type VI secretion, TssG-like / Type VI secretion, TssG / Type VI secretion system TssK / Bacterial Type VI secretion, VC_A0110, EvfL, ImpJ, VasE / Type VI secretion system baseplate subunit TssG / Type VI secretion system baseplate subunit TssF / Type VI secretion system baseplate subunit TssK
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsRapisarda, C. / Fronzes, R.
CitationJournal: Nat Microbiol / Year: 2018
Title: Biogenesis and structure of a type VI secretion baseplate.
Authors: Yassine Cherrak / Chiara Rapisarda / Riccardo Pellarin / Guillaume Bouvier / Benjamin Bardiaux / Fabrice Allain / Christian Malosse / Martial Rey / Julia Chamot-Rooke / Eric Cascales / Rémi ...Authors: Yassine Cherrak / Chiara Rapisarda / Riccardo Pellarin / Guillaume Bouvier / Benjamin Bardiaux / Fabrice Allain / Christian Malosse / Martial Rey / Julia Chamot-Rooke / Eric Cascales / Rémi Fronzes / Eric Durand /
Abstract: To support their growth in a competitive environment and cause pathogenesis, bacteria have evolved a broad repertoire of macromolecular machineries to deliver specific effectors and toxins. Among ...To support their growth in a competitive environment and cause pathogenesis, bacteria have evolved a broad repertoire of macromolecular machineries to deliver specific effectors and toxins. Among these multiprotein complexes, the type VI secretion system (T6SS) is a contractile nanomachine that targets both prokaryotic and eukaryotic cells. The T6SS comprises two functional subcomplexes: a bacteriophage-related tail structure anchored to the cell envelope by a membrane complex. As in other contractile injection systems, the tail is composed of an inner tube wrapped by a sheath and built on the baseplate. In the T6SS, the baseplate is not only the tail assembly platform, but also docks the tail to the membrane complex and hence serves as an evolutionary adaptor. Here we define the biogenesis pathway and report the cryo-electron microscopy (cryo-EM) structure of the wedge protein complex of the T6SS from enteroaggregative Escherichia coli (EAEC). Using an integrative approach, we unveil the molecular architecture of the whole T6SS baseplate and its interaction with the tail sheath, offering detailed insights into its biogenesis and function. We discuss architectural and mechanistic similarities but also reveal key differences with the T4 phage and Mu phage baseplates.
History
DepositionMay 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / 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.identifier_ORCID
Revision 1.2Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: TssF
B: TssF
C: TssG
D: TssK
E: TssK
F: TssK
G: TssK
H: TssK
I: TssK


Theoretical massNumber of molelcules
Total (without water)473,7199
Polymers473,7199
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area57540 Å2
ΔGint-295 kcal/mol
Surface area181310 Å2
MethodPISA

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Components

#1: Protein TssF


Mass: 66557.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: EC55989_3322 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7LFT7
#2: Protein TssG /


Mass: 41216.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: EC55989_3321 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7LFT6
#3: Protein
TssK


Mass: 49898.121 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: EC55989_3338 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7LG64

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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: Complex of TssK, TssF and TssG, components of the type VI secretion system baseplate
Type: CELL / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 0.2 mg/ml / Embedding 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 FIELDBright-field microscopy / Nominal magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 700 nm / Calibrated defocus min: 400 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 1.5 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
2EPUimage acquisition
4GctfCTF correction
7UCSF Chimeramodel fitting
8Cootmodel fitting
10cryoSPARCinitial Euler assignment
11RELIONfinal Euler assignment
13RELION3D reconstruction
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32504 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL

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