Skip to main content

 7OIU | pdb_00007oiu

Inner Membrane Complex (IMC) protomer structure (TrwM/VirB3, TrwK/VirB4, TrwG/VirB8tails) from the fully-assembled R388 type IV secretion system determined by cryo-EM.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7OIU

This is version 1.3 of the entry. See complete history. 

Literature

Cryo-EM structure of a type IV secretion system.

Mace, K., Vadakkepat, A.K., Redzej, A., Lukoyanova, N., Oomen, C., Braun, N., Ukleja, M., Lu, F., Costa, T.R.D., Orlova, E.V., Baker, D., Cong, Q., Waksman, G.

(2022) Nature 607: 191-196

  • DOI: https://doi.org/10.1038/s41586-022-04859-y
  • Primary Citation Related Structures: 
    7O3J, 7O3T, 7O3V, 7O41, 7O42, 7O43, 7OIU, 7Q1V

  • PubMed Abstract: 

    Bacterial conjugation is the fundamental process of unidirectional transfer of DNAs, often plasmid DNAs, from a donor cell to a recipient cell 1 . It is the primary means by which antibiotic resistance genes spread among bacterial populations 2,3 . In Gram-negative bacteria, conjugation is mediated by a large transport apparatus-the conjugative type IV secretion system (T4SS)-produced by the donor cell and embedded in both its outer and inner membranes. The T4SS also elaborates a long extracellular filament-the conjugative pilus-that is essential for DNA transfer 4,5 . Here we present a high-resolution cryo-electron microscopy (cryo-EM) structure of a 2.8 megadalton T4SS complex composed of 92 polypeptides representing 8 of the 10 essential T4SS components involved in pilus biogenesis. We added the two remaining components to the structural model using co-evolution analysis of protein interfaces, to enable the reconstitution of the entire system including the pilus. This structure describes the exceptionally large protein-protein interaction network required to assemble the many components that constitute a T4SS and provides insights on the unique mechanism by which they elaborate pili.


  • Organizational Affiliation: 
    • Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, London, UK. k.mace@mail.cryst.bbk.ac.uk.

Macromolecule Content 

  • Total Structure Weight: 277.23 kDa 
  • Atom Count: 12,744 
  • Modeled Residue Count: 1,683 
  • Deposited Residue Count: 2,443 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TrwM proteinA [auth C]104Escherichia coliMutation(s): 0 
Gene Names: trwM
Membrane Entity: Yes 
UniProt
Find proteins for O50329 (Escherichia coli)
Explore O50329 
Go to UniProtKB:  O50329
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO50329
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
TrwK proteinB [auth A],
C [auth B]
823Escherichia coliMutation(s): 0 
Gene Names: trwK
EC: 3.6.4.6
Membrane Entity: Yes 
UniProt
Find proteins for O50330 (Escherichia coli)
Explore O50330 
Go to UniProtKB:  O50330
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO50330
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
TrwG protein
D, E, F
231Escherichia coliMutation(s): 0 
Gene Names: trwG
Membrane Entity: Yes 
UniProt
Find proteins for O50335 (Escherichia coli)
Explore O50335 
Go to UniProtKB:  O50335
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO50335
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom098302
Wellcome TrustUnited Kingdom217089
Wellcome TrustUnited Kingdom202679/Z/16/Z
Wellcome TrustUnited Kingdom206166/Z/17/Z

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-22
    Type: Initial release
  • Version 1.1: 2022-07-06
    Changes: Database references
  • Version 1.2: 2022-07-20
    Changes: Database references
  • Version 1.3: 2024-07-10
    Changes: Data collection