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- PDB-7spi: Models for C13 reconstruction of Outer Membrane Core Complex (OMC... -

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Basic information

Entry
Database: PDB / ID: 7spi
TitleModels for C13 reconstruction of Outer Membrane Core Complex (OMCC) of Type IV Secretion System (T4SS) encoded by a plasmid overproducing TraV, TraK and TraB of pED208
Components
  • TraB
  • TraK
  • TraV
KeywordsSTRUCTURAL PROTEIN / Symmetry alteration / Symmetry mismatch / Drug resistance / Type IV secretion system (T4SS)
Function / homology
Function and homology information


Pilus assembly TraK / Type-F conjugative transfer system secretin TraK / TraK protein / Type IV conjugative transfer system protein TraV / Type IV conjugative transfer system lipoprotein (TraV) / Bacterial conjugation TrbI-like protein / Type IV secretion system, VirB10 / TraB / TrbI / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Biological speciesSalmonella typhi (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsLiu, X. / Khara, P. / Baker, M.L. / Christie, P.J. / Hu, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2022
Title: Structure of a type IV secretion system core complex encoded by multi-drug resistance F plasmids.
Authors: Xiangan Liu / Pratick Khara / Matthew L Baker / Peter J Christie / Bo Hu /
Abstract: Bacterial type IV secretion systems (T4SSs) are largely responsible for the proliferation of multi-drug resistance. We solved the structure of the outer-membrane core complex (OMCC) of a T4SS encoded ...Bacterial type IV secretion systems (T4SSs) are largely responsible for the proliferation of multi-drug resistance. We solved the structure of the outer-membrane core complex (OMCC) of a T4SS encoded by a conjugative F plasmid at <3.0 Å resolution by cryoelectron microscopy. The OMCC consists of a 13-fold symmetrical outer ring complex (ORC) built from 26 copies of TraK and TraV C-terminal domains, and a 17-fold symmetrical central cone (CC) composed of 17 copies of TraB β-barrels. Domains of TraV and TraB also bind the CC and ORC substructures, establishing that these proteins undergo an intraprotein symmetry alteration to accommodate the C13:C17 symmetry mismatch. We present evidence that other pED208-encoded factors stabilize the C13:C17 architecture and define the importance of TraK, TraV and TraB domains to T4SS function. This work identifies OMCC structural motifs of proposed importance for structural transitions associated with F plasmid dissemination and F pilus biogenesis.
History
DepositionNov 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A1: TraV
A2: TraV
A3: TraV
A4: TraV
A5: TraV
A6: TraV
A7: TraV
A8: TraV
A9: TraV
A10: TraV
A11: TraV
A12: TraV
A13: TraV
B1: TraV
B2: TraV
B3: TraV
B4: TraV
B5: TraV
B6: TraV
B7: TraV
B8: TraV
B9: TraV
B10: TraV
B11: TraV
B12: TraV
B13: TraV
C1: TraK
C2: TraK
C3: TraK
C4: TraK
C5: TraK
C6: TraK
C7: TraK
C8: TraK
C9: TraK
C10: TraK
C11: TraK
C12: TraK
C13: TraK
D1: TraK
D2: TraK
D3: TraK
D4: TraK
D5: TraK
D6: TraK
D7: TraK
D8: TraK
D9: TraK
D10: TraK
D11: TraK
D12: TraK
D13: TraK
E1: TraB
E2: TraB
E3: TraB
E4: TraB
E5: TraB
E6: TraB
E7: TraB
E8: TraB
E9: TraB
E10: TraB
E11: TraB
E12: TraB
E13: TraB
F1: TraB
F2: TraB
F3: TraB
F4: TraB
F5: TraB
F6: TraB
F7: TraB
F8: TraB
F9: TraB
F10: TraB
F11: TraB
F12: TraB
F13: TraB


Theoretical massNumber of molelcules
Total (without water)2,478,76478
Polymers2,478,76478
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
TraV


Mass: 20928.650 Da / Num. of mol.: 26
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhi (bacteria) / Gene: traV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8KNL2
#2: Protein ...
TraK


Mass: 26648.465 Da / Num. of mol.: 26
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhi (bacteria) / Gene: traK / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8KNL8
#3: Protein ...
TraB


Mass: 47759.957 Da / Num. of mol.: 26
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhi (bacteria) / Gene: traB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8KNL7

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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: Outer membrane core complex of T4SS encoded by a plasmid overproducing TraV, TraK and TraB of pED208
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
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: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
2SerialEMimage acquisition
4cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C13 (13 fold cyclic)
3D reconstructionResolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 148000 / Symmetry type: POINT

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