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- PDB-7okn: Structure of the outer-membrane core complex (inner ring) from a ... -

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Basic information

Entry
Database: PDB / ID: 7okn
TitleStructure of the outer-membrane core complex (inner ring) from a conjugative type IV secretion system
Components
  • TraB
  • Type IV conjugative transfer system lipoprotein TraV
KeywordsMEMBRANE PROTEIN / Type IV secretion system / F plasmid / outer-membrane core complex / conjugation
Function / homologyType IV conjugative transfer system protein TraV / Type IV conjugative transfer system lipoprotein (TraV) / Prokaryotic membrane lipoprotein lipid attachment site profile. / Type IV conjugative transfer system lipoprotein TraV
Function and homology information
Biological speciesSalmonella enterica (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsAmin, H. / Ilangovan, A. / Costa, T.R.D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust215164/Z/18/Z United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: Architecture of the outer-membrane core complex from a conjugative type IV secretion system.
Authors: Himani Amin / Aravindan Ilangovan / Tiago R D Costa /
Abstract: Conjugation is one of the most important processes that bacteria utilize to spread antibiotic resistance genes among bacterial populations. Interbacterial DNA transfer requires a large double ...Conjugation is one of the most important processes that bacteria utilize to spread antibiotic resistance genes among bacterial populations. Interbacterial DNA transfer requires a large double membrane-spanning nanomachine called the type 4 secretion system (T4SS) made up of the inner-membrane complex (IMC), the outer-membrane core complex (OMCC) and the conjugative pilus. The iconic F plasmid-encoded T4SS has been central in understanding conjugation for several decades, however atomic details of its structure are not known. Here, we report the structure of a complete conjugative OMCC encoded by the pED208 plasmid from E. coli, solved by cryo-electron microscopy at 3.3 Å resolution. This 2.1 MDa complex has a unique arrangement with two radial concentric rings, each having a different symmetry eventually contributing to remarkable differences in protein stoichiometry and flexibility in comparison to other OMCCs. Our structure suggests that F-OMCC is a highly dynamic complex, with implications for pilus extension and retraction during conjugation.
History
DepositionMay 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Assembly

Deposited unit
A: TraB
B: Type IV conjugative transfer system lipoprotein TraV
C: TraB
D: Type IV conjugative transfer system lipoprotein TraV
E: TraB
F: Type IV conjugative transfer system lipoprotein TraV
G: TraB
H: Type IV conjugative transfer system lipoprotein TraV
I: TraB
J: Type IV conjugative transfer system lipoprotein TraV
K: TraB
L: Type IV conjugative transfer system lipoprotein TraV
M: TraB
N: Type IV conjugative transfer system lipoprotein TraV
O: TraB
P: Type IV conjugative transfer system lipoprotein TraV
Q: TraB
R: Type IV conjugative transfer system lipoprotein TraV
S: TraB
T: Type IV conjugative transfer system lipoprotein TraV
U: TraB
V: Type IV conjugative transfer system lipoprotein TraV
W: TraB
X: Type IV conjugative transfer system lipoprotein TraV
Y: TraB
Z: Type IV conjugative transfer system lipoprotein TraV
a: TraB
b: Type IV conjugative transfer system lipoprotein TraV
c: TraB
d: Type IV conjugative transfer system lipoprotein TraV
e: TraB
f: Type IV conjugative transfer system lipoprotein TraV
g: TraB
h: Type IV conjugative transfer system lipoprotein TraV


Theoretical massNumber of molelcules
Total (without water)1,185,42334
Polymers1,185,42334
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area117680 Å2
ΔGint-600 kcal/mol
Surface area152320 Å2
MethodPISA

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Components

#1: Protein
TraB


Mass: 48802.102 Da / Num. of mol.: 17
Source method: isolated from a genetically manipulated source
Details: TraB / Source: (gene. exp.) Salmonella enterica (bacteria) / Production host: Escherichia coli (E. coli)
#2: Protein
Type IV conjugative transfer system lipoprotein TraV


Mass: 20928.650 Da / Num. of mol.: 17
Source method: isolated from a genetically manipulated source
Details: TraV / Source: (gene. exp.) Salmonella enterica (bacteria) / Gene: traV, GND40_003952 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A753A8N9
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 (inner ring) / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Salmonella enterica (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 1.3 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 74956 / Symmetry type: POINT

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