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- PDB-6n38: Structure of the type VI secretion system TssK-TssF-TssG baseplat... -

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Basic information

Entry
Database: PDB / ID: 6n38
TitleStructure of the type VI secretion system TssK-TssF-TssG baseplate subcomplex revealed by cryo-electron microscopy - full map sharpened
Components
  • (Putative type VI secretion proteinType VI secretion system) x 3
  • Unassigned protein
KeywordsPROTEIN TRANSPORT / Type VI secretion system / enteroaggregative E. coli / protein secretion / baseplate / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homologyType VI secretion protein, VC_A0114 / Type VI secretion system, TssF-like / Type VI secretion, TssG-like / Bacterial Type VI secretion, VC_A0110, EvfL, ImpJ, VasE / Type VI secretion system, TssF / Type VI secretion, TssG / Putative type VI secretion protein / Putative type VI secretion protein / Putative type VI secretion protein
Function and homology information
Specimen sourceEscherichia coli O44:H18
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.7 Å resolution
AuthorsPark, Y.J. / Lacourse, K.D. / Cambillau, C. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / DiMaio, F. / Mougous, J.D. / Veesler, D.
CitationJournal: Nat Commun / Year: 2018
Title: Structure of the type VI secretion system TssK-TssF-TssG baseplate subcomplex revealed by cryo-electron microscopy.
Authors: Young-Jun Park / Kaitlyn D Lacourse / Christian Cambillau / Frank DiMaio / Joseph D Mougous / David Veesler
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 14, 2018 / Release: Dec 26, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 26, 2018Structure modelrepositoryInitial release
1.1Jan 2, 2019Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

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Assembly

Deposited unit
I: Putative type VI secretion protein
G: Putative type VI secretion protein
H: Putative type VI secretion protein
K: Unassigned protein
L: Unassigned protein
A: Putative type VI secretion protein
D: Putative type VI secretion protein
B: Putative type VI secretion protein
E: Putative type VI secretion protein
C: Putative type VI secretion protein
F: Putative type VI secretion protein


Theoretical massNumber of molelcules
Total (without water)389,97911
Polyers389,97911
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)54680
ΔGint (kcal/M)-347
Surface area (Å2)129340

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Components

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


Mass: 66557.125 Da / Num. of mol.: 2
Source: (gene. exp.) Escherichia coli O44:H18 (strain 042 / EAEC) (bacteria)
Strain: 042 / EAEC / Gene: EC042_4542 / Production host: Escherichia coli (E. coli) / References: UniProt: D3GUX3
#2: Protein/peptide Putative type VI secretion protein / Type VI secretion system / TssG


Mass: 33787.875 Da / Num. of mol.: 1 / Fragment: UNP residues 31-333
Source: (gene. exp.) Escherichia coli O44:H18 (strain 042 / EAEC) (bacteria)
Strain: 042 / EAEC / Gene: EC042_4543 / Production host: Escherichia coli (E. coli) / References: UniProt: D3GUX4
#3: Protein/peptide Unassigned protein


Mass: 1805.216 Da / Num. of mol.: 2
Source: (gene. exp.) Escherichia coli O44:H18 (strain 042 / EAEC) (bacteria)
Strain: strain 042 / EAEC / Production host: Escherichia coli (E. coli)
#4: Protein/peptide
Putative type VI secretion protein / Type VI secretion system / TssK


Mass: 36577.680 Da / Num. of mol.: 6 / Fragment: neck and shoulder domains (UNP residues 1-316)
Source: (gene. exp.) Escherichia coli O44:H18 (strain 042 / EAEC) (bacteria)
Strain: 042 / EAEC / Gene: EC042_4526 / Production host: Escherichia coli (E. coli) / References: UniProt: D3GU39

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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: TssK-TssF-TssG T6SS baseplate subcomplex / Type: COMPLEX / Entity ID: 1,2,3,4 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli O44:H18 (strain 042 / EAEC) (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.8
SpecimenConc.: 0.12 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: C-flat-1.2/1.3
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: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2Leginon3.2image acquisition
4GctfCTF correction
11RELION3.0final Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 36496 / Symmetry type: POINT

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