9E2V | pdb_00009e2v

Cryo-EM map of homodecameric TraT

• PDB DOI: https://doi.org/10.2210/pdb9E2V/pdb
• EM Map EMD-47469: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-10-23 Released: 2025-04-16 
• Deposition Author(s): Lundgren, C.A.K., Lea, S., Deme, J.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Structure of the conjugation surface exclusion protein TraT.

Chen, N., Bukys, A., Lundgren, C.A.K., Deme, J.C., El Sayyed, H., Kapanidis, A.N., Lea, S.M., Berks, B.C.

(2025) Commun Biol 8: 1702-1702

• PubMed: 41299015 
• DOI: https://doi.org/10.1038/s42003-025-09102-8
• Primary Citation of Related Structures:  
  9E2V


• PubMed Abstract: 
  

  Conjugal transfer of plasmids between bacteria is a major route for the spread of antimicrobial resistance. Many conjugative plasmids encode exclusion systems that inhibit redundant conjugation. In incompatibility group F (IncF) plasmids surface exclusion is mediated by the outer membrane protein TraT. Here we report the cryoEM structure of the TraT exclusion protein complex from the canonical F plasmid of Escherichia coli. TraT is a hollow homodecamer shaped like a chef's hat. In contrast to most outer membrane proteins, TraT spans the outer membrane using transmembrane α-helices. We develop a microscopy-based conjugation assay to probe the effects of directed mutagenesis on TraT. Our analysis provides no support for the idea that TraT has specific interactions with partner proteins. Instead, we infer that TraT is most likely to function by physical interference with conjugation. This work provides structural insight into a natural inhibitor of microbial gene transfer.

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Organizational Affiliation: 
• Department of Biochemistry, University of Oxford, Oxford, UK.
Biological Physics Research Group, Department of Physics, University of Oxford, Oxford, UK.
Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK.
Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA. [e-mail].
Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA. [e-mail].
Department of Biochemistry, University of Oxford, Oxford, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C10  (Explore in 3D)
Global Stoichiometry: Homo 10-mer - A10 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 276.68 kDa 
• Atom Count: 16,910 
• Modeled Residue Count: 2,260 
• Deposited Residue Count: 2,610 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TraT complement resistance protein	A, B, C, D, E, F, G, H, I, J	261	Escherichia coli K-12	Mutation(s): 0  Gene Names: traT, ECOK12F101
UniProt
Find proteins for P13979 (Escherichia coli (strain K12)) Explore P13979  Go to UniProtKB:  P13979

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	dev_5246

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-16 
Deposition Author(s): Lundgren, C.A.K., Lea, S., Deme, J.

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Funding Organization	Location	Grant Number
Other government		--

Revision History  

• Version 1.0: 2025-04-16
  Type: Initial release
  
• Version 1.1: 2025-12-10
  Changes: Data collection, Database references