7O3J | pdb_00007o3j

O-layer structure (TrwH/VirB7, TrwF/VirB9CTD, TrwE/VirB10CTD) of the outer membrane core complex from the fully-assembled R388 type IV secretion system determined by cryo-EM.

• PDB DOI: https://doi.org/10.2210/pdb7O3J/pdb
• EM Map EMD-12707: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTM


• Deposited: 2021-04-01 Released: 2022-06-22 
• Deposition Author(s): Mace, K., Vadakkepat, A.K., Lukoyanova, N., Waksman, G.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

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

• PubMed: 35732732 
• 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.

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Organizational Affiliation: 
• Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, London, UK. [e-mail].
Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, London, UK.
strucTEM Microscopic Services, Gammelsdorf, Germany.
National Center For Biotechnology CNB-CSIC, Madrid, Spain.
MRC Center for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, UK.
University of Washington, Molecular Engineering and Sciences, Seattle, WA, USA.
University of Washington, Molecular Engineering and Sciences, Seattle, WA, USA. [e-mail].
Eugene McDermott Center for Human Growth and Development University of Texas Southwestern Medical Center, Houston, TX, USA. [e-mail].
Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, London, UK. [e-mail].
Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C14  (Explore in 3D)
Global Stoichiometry: Hetero 42-mer - A14B14C14 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 1,081.95 kDa 
• Atom Count: 38,458 
• Modeled Residue Count: 5,054 
• Deposited Residue Count: 9,912 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TrwE protein	A, BA [auth b], D, EA [auth e], G, HA [auth h], J, KA [auth k], M, NA [auth n], P, S, V, Y	395	Escherichia coli	Mutation(s): 0  Gene Names: trwE Membrane Entity: Yes
UniProt
Find proteins for O50337 (Escherichia coli) Explore O50337  Go to UniProtKB:  O50337

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TrwF protein	B, CA [auth c], E, FA [auth f], H, IA [auth i], K, LA [auth l], N, OA [auth o], Q, T, W, Z	266	Escherichia coli	Mutation(s): 0  Gene Names: trwF Membrane Entity: Yes
UniProt
Find proteins for O50336 (Escherichia coli) Explore O50336  Go to UniProtKB:  O50336

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
TrwH protein	AA [auth a], C, DA [auth d], F, GA [auth g], I, JA [auth j], L, MA [auth m], O, PA [auth p], R, U, X	47	Escherichia coli	Mutation(s): 0  Gene Names: trwH Membrane Entity: Yes
UniProt
Find proteins for O50334 (Escherichia coli) Explore O50334  Go to UniProtKB:  O50334

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-06-22 
Deposition Author(s): Mace, K., Vadakkepat, A.K., Lukoyanova, N., Waksman, G.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	098302
Wellcome Trust	United Kingdom	217089
Wellcome Trust	United Kingdom	202679/Z/16/Z
Wellcome Trust	United Kingdom	206166/Z/17/Z

Revision History  

• 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: 2024-10-23
  Changes: Data collection, Refinement description, Structure summary