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

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Basic information

Entry
Database: PDB / ID: 7oko
TitleStructure of the outer-membrane core complex (outer ring) from a conjugative type IV secretion system
Components
  • TraB
  • Type IV conjugative transfer system lipoprotein TraV
  • Type-F conjugative transfer system secretin TraK
KeywordsMEMBRANE PROTEIN / Type IV secretion system / F plasmid / outer-membrane core complex / conjugation
Function / homology
Function and homology information


Pilus assembly TraK / Type-F conjugative transfer system secretin TraK / : / TraK N-terminal domain / TraK C-terminal domain / Type IV conjugative transfer system protein TraV / Type IV conjugative transfer system lipoprotein (TraV) / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Type-F conjugative transfer system secretin TraK / Type IV conjugative transfer system lipoprotein TraV
Similarity search - Component
Biological speciesSalmonella enterica (bacteria)
Salmonella enterica subsp. salamae serovar 58:l
z13
z28:z6
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 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 8, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
AA: Type IV conjugative transfer system lipoprotein TraV
AB: Type IV conjugative transfer system lipoprotein TraV
AC: TraB
0: Type IV conjugative transfer system lipoprotein TraV
1: Type IV conjugative transfer system lipoprotein TraV
2: TraB
3: Type-F conjugative transfer system secretin TraK
4: Type-F conjugative transfer system secretin TraK
5: Type IV conjugative transfer system lipoprotein TraV
6: Type IV conjugative transfer system lipoprotein TraV
7: TraB
8: Type-F conjugative transfer system secretin TraK
9: Type-F conjugative transfer system secretin TraK
A: Type-F conjugative transfer system secretin TraK
B: Type-F conjugative transfer system secretin TraK
C: Type IV conjugative transfer system lipoprotein TraV
D: Type IV conjugative transfer system lipoprotein TraV
E: TraB
F: Type-F conjugative transfer system secretin TraK
G: Type-F conjugative transfer system secretin TraK
H: Type IV conjugative transfer system lipoprotein TraV
I: Type IV conjugative transfer system lipoprotein TraV
J: TraB
K: Type-F conjugative transfer system secretin TraK
L: Type-F conjugative transfer system secretin TraK
M: Type IV conjugative transfer system lipoprotein TraV
N: Type IV conjugative transfer system lipoprotein TraV
O: TraB
P: Type-F conjugative transfer system secretin TraK
Q: Type-F conjugative transfer system secretin TraK
R: Type IV conjugative transfer system lipoprotein TraV
S: Type IV conjugative transfer system lipoprotein TraV
T: TraB
U: Type-F conjugative transfer system secretin TraK
V: Type-F conjugative transfer system secretin TraK
W: Type IV conjugative transfer system lipoprotein TraV
X: Type IV conjugative transfer system lipoprotein TraV
Y: TraB
Z: Type-F conjugative transfer system secretin TraK
a: Type-F conjugative transfer system secretin TraK
b: Type IV conjugative transfer system lipoprotein TraV
c: Type IV conjugative transfer system lipoprotein TraV
d: TraB
e: Type-F conjugative transfer system secretin TraK
f: Type-F conjugative transfer system secretin TraK
g: Type IV conjugative transfer system lipoprotein TraV
h: Type IV conjugative transfer system lipoprotein TraV
i: TraB
j: Type-F conjugative transfer system secretin TraK
k: Type-F conjugative transfer system secretin TraK
l: Type IV conjugative transfer system lipoprotein TraV
m: Type IV conjugative transfer system lipoprotein TraV
n: TraB
o: Type-F conjugative transfer system secretin TraK
p: Type-F conjugative transfer system secretin TraK
q: Type IV conjugative transfer system lipoprotein TraV
r: Type IV conjugative transfer system lipoprotein TraV
s: TraB
t: Type-F conjugative transfer system secretin TraK
u: Type-F conjugative transfer system secretin TraK
v: Type IV conjugative transfer system lipoprotein TraV
w: Type IV conjugative transfer system lipoprotein TraV
x: TraB
y: Type-F conjugative transfer system secretin TraK
z: Type-F conjugative transfer system secretin TraK


Theoretical massNumber of molelcules
Total (without water)1,164,93865
Polymers1,164,93865
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area165080 Å2
ΔGint-904 kcal/mol
Surface area317380 Å2
MethodPISA

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Components

#1: Protein ...
Type IV conjugative transfer system lipoprotein TraV / TraV


Mass: 20928.650 Da / Num. of mol.: 26
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica (bacteria) / Gene: traV, GND40_003952 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A753A8N9
#2: Protein/peptide
TraB


Mass: 1128.233 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica (bacteria) / Production host: Escherichia coli (E. coli)
#3: Protein ...
Type-F conjugative transfer system secretin TraK


Mass: 23312.551 Da / Num. of mol.: 26
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. salamae serovar 58:l,z13,z28:z6 (bacteria)
Gene: traK, G4J24_003123 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A734HNY4

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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 (outer ring) / Type: COMPLEX / Entity ID: #1-#2 / 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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 298235 / Symmetry type: POINT

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