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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 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 protein / Type VI secretion protein / Putative type VI secretion protein
Function and homology information
Biological speciesEscherichia coli O44:H18
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsPark, Y.J. / Lacourse, K.D. / Cambillau, C. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / DiMaio, F. / Mougous, J.D. / Veesler, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
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 /
Abstract: Type VI secretion systems (T6SSs) translocate effectors into target cells and are made of a contractile sheath and a tube docked onto a multi-protein transmembrane complex via a baseplate. Although ...Type VI secretion systems (T6SSs) translocate effectors into target cells and are made of a contractile sheath and a tube docked onto a multi-protein transmembrane complex via a baseplate. Although some information is available about the mechanisms of tail contraction leading to effector delivery, the detailed architecture and function of the baseplate remain unknown. Here, we report the 3.7 Å resolution cryo-electron microscopy reconstruction of an enteroaggregative Escherichia coli baseplate subcomplex assembled from TssK, TssF and TssG. The structure reveals two TssK trimers interact with a locally pseudo-3-fold symmetrical complex comprising two copies of TssF and one copy of TssG. TssF and TssG are structurally related to each other and to components of the phage T4 baseplate and of the type IV secretion system, strengthening the evolutionary relationships among these macromolecular machines. These results, together with bacterial two-hybrid assays, provide a structural framework to understand the T6SS baseplate architecture.
History
DepositionNov 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 20, 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
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
Polymers389,97911
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area54680 Å2
ΔGint-347 kcal/mol
Surface area129340 Å2

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Components

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


Mass: 66557.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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 Putative type VI secretion protein / Type VI secretion system / TssG


Mass: 33787.875 Da / Num. of mol.: 1 / Fragment: UNP residues 31-333
Source method: isolated from a genetically manipulated source
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 method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O44:H18 (strain 042 / EAEC) (bacteria)
Strain: strain 042 / EAEC / Production host: Escherichia coli (E. coli)
#4: Protein
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 method: isolated from a genetically manipulated source
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 / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: TssK-TssF-TssG T6SS baseplate subcomplex / Type: COMPLEX / Entity ID: all / 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 divisions/in. / 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
MicroscopyModel: 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
11RELION3final Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36496 / Symmetry type: POINT

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