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- PDB-6gj1: The baseplate complex from the type VI secretion system -

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Basic information

Entry
Database: PDB / ID: 6gj1
TitleThe baseplate complex from the type VI secretion system
Components
  • Putative type VI secretion proteinType VI secretion system
  • TssE
  • TssG
KeywordsSTRUCTURAL PROTEIN / Secretion / baseplate / complex
Function / homologyGpW/Gp25/IraD / Type VI secretion system, TssF-like / Type VI secretion, TssG-like / Type VI secretion system-related protein / Gene 25-like lysozyme / Type VI secretion system, TssF / Type VI secretion, TssG / Uncharacterized protein / Uncharacterized protein / Putative type VI secretion protein
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.7 Å resolution
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 Fronzes / Eric Durand
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 15, 2018 / Release: Oct 17, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 17, 2018Structure modelrepositoryInitial release
1.1Oct 24, 2018Structure modelData collection / Database referencescitation / citation_author_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

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Structure visualization

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Assembly

Deposited unit
A: Putative type VI secretion protein
B: Putative type VI secretion protein
C: TssG
D: TssE


Theoretical massNumber of molelcules
Total (without water)190,6514
Polyers190,6514
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein/peptide Putative type VI secretion protein / Type VI secretion system


Mass: 66557.125 Da / Num. of mol.: 2 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: EC042_4542 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D3GUX3
#2: Protein/peptide TssG /


Mass: 41216.344 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: EC55989_3321 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7LFT6
#3: Protein/peptide TssE


Mass: 16320.783 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: EC55989_3319 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7LFT4

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Type VI secretion system baseplate complexType VI secretion system
Type: COMPLEX / Entity ID: 1,2,3 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (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
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
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
4GctfCTF correction
10cryoSPARCinitial Euler assignment
11RELIONfinal Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 32504 / Symmetry type: POINT

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