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- PDB-7spc: Models for C17 reconstruction of Outer Membrane Core Complex (OMC... -

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Basic information

Entry
Database: PDB / ID: 7spc
TitleModels for C17 reconstruction of Outer Membrane Core Complex (OMCC) of Type IV Secretion System (T4SS) encoded by F-plasmid (pED208).
Components
  • TraB
  • TraV
KeywordsSTRUCTURAL PROTEIN / Symmetry alteration / Symmetry mismatch / Drug resistance / Type IV secretion system (T4SS)
Function / homologyType 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. / TraV / TraB
Function and homology information
Biological speciesSalmonella typhi (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.95 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 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AB1: TraV
AB2: TraV
AB3: TraV
AB4: TraV
AB5: TraV
AB6: TraV
AB7: TraV
AB8: TraV
AB9: TraV
AB10: TraV
AB11: TraV
AB12: TraV
AB13: TraV
AB14: TraV
AB15: TraV
AB16: TraV
AB17: TraV
EF1: TraB
EF2: TraB
EF3: TraB
EF4: TraB
EF5: TraB
EF6: TraB
EF7: TraB
EF8: TraB
EF9: TraB
EF10: TraB
EF11: TraB
EF12: TraB
EF13: TraB
EF14: TraB
EF15: TraB
EF16: TraB
EF17: TraB


Theoretical massNumber of molelcules
Total (without water)1,167,70634
Polymers1,167,70634
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.: 17 / Source method: isolated from a natural source / Source: (natural) Salmonella typhi (bacteria) / Plasmid details: pED208 / References: UniProt: Q8KNL2
#2: Protein
TraB


Mass: 47759.957 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Source: (natural) Salmonella typhi (bacteria) / References: UniProt: Q8KNL7
Has protein modificationY

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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 F-plasmid (pED208)
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
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: C17 (17 fold cyclic)
3D reconstructionResolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 70700 / Symmetry type: POINT

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