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 9FSM | pdb_00009fsm

Cryo-EM structure of the decameric TraT surface exclusion lipoprotein from Klebsiella pneumoniae (pKpQIL plasmid)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9FSM

This is version 1.1 of the entry. See complete history. 

Literature

Cryo-EM structure and evolutionary history of the conjugation surface exclusion protein TraT.

Seddon, C., David, S., Wong, J.L.C., Ishimoto, N., He, S., Bradshaw, J., Low, W.W., Frankel, G., Beis, K.

(2025) Nat Commun 16: 659-659

  • DOI: https://doi.org/10.1038/s41467-025-55834-w
  • Primary Citation Related Structures: 
    9FS5, 9FSM

  • PubMed Abstract: 

    Conjugation plays a major role in dissemination of antimicrobial resistance genes. Following transfer of IncF-like plasmids, recipients become refractory to a second wave of conjugation with the same plasmid via entry (TraS) and surface (TraT) exclusion mechanisms. Here, we show that TraT from the pKpQIL and F plasmids (TraT pKpQIL and TraT F ) exhibits plasmid surface exclusion specificity. The cryo-EM structures of TraT pKpQIL and TraT F reveal that they oligomerise into decameric champagne bottle cork-like structures, which are anchored to the outer membrane via a diacylglycerol and palmitic acid modified α-helical barrel domain. Unexpectedly, we identify chromosomal TraT homologues from multiple Gram-negative phyla which form numerous divergent lineages in a phylogenetic tree of TraT sequences. Plasmid-associated TraT sequences are found in multiple distinct lineages, including two separate clades incorporating TraT from Enterobacteriaceae IncF/F-like and Legionellaceae F-like plasmids. These findings suggest that different plasmid backbones have acquired and co-opted TraT on independent occasions.


  • Organizational Affiliation: 
    • Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.

Macromolecule Content 

  • Total Structure Weight: 246.15 kDa 
  • Atom Count: 17,060 
  • Modeled Residue Count: 2,260 
  • Deposited Residue Count: 2,260 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TraT complement resistance protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
226Klebsiella pneumoniaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for W1DJ50 (Klebsiella pneumoniae IS43)
Explore W1DJ50 
Go to UniProtKB:  W1DJ50
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW1DJ50
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGA
(Subject of Investigation/LOI)

Query on DGA



Download:Ideal Coordinates CCD File
K [auth A]
L [auth B]
M [auth C]
N [auth D]
O [auth E]
K [auth A],
L [auth B],
M [auth C],
N [auth D],
O [auth E],
P [auth F],
Q [auth G],
R [auth H],
S [auth I],
T [auth J]
DIACYL GLYCEROL
C39 H76 O5
UHUSDOQQWJGJQS-QNGWXLTQSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M011178/1

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-11
    Type: Initial release
  • Version 1.1: 2025-06-11
    Changes: Data collection, Database references