7SZI | pdb_00007szi

Cryo-EM structure of OmpK36-TraN mating pair stabilization proteins from carbapenem-resistant Klebsiella pneumoniae


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7SZI

This is version 1.3 of the entry. See complete history

Literature

Mating pair stabilization mediates bacterial conjugation species specificity.

Low, W.W.Wong, J.L.C.Beltran, L.C.Seddon, C.David, S.Kwong, H.S.Bizeau, T.Wang, F.Pena, A.Costa, T.R.D.Pham, B.Chen, M.Egelman, E.H.Beis, K.Frankel, G.

(2022) Nat Microbiol 7: 1016-1027

  • DOI: https://doi.org/10.1038/s41564-022-01146-4
  • Primary Citation Related Structures: 
    7SZI

  • PubMed Abstract: 

    Bacterial conjugation mediates contact-dependent transfer of DNA from donor to recipient bacteria, thus facilitating the spread of virulence and resistance plasmids. Here we describe how variants of the plasmid-encoded donor outer membrane (OM) protein TraN cooperate with distinct OM receptors in recipients to mediate mating pair stabilization and efficient DNA transfer. We show that TraN from the plasmid pKpQIL (Klebsiella pneumoniae) interacts with OmpK36, plasmids from R100-1 (Shigella flexneri) and pSLT (Salmonella Typhimurium) interact with OmpW, and the prototypical F plasmid (Escherichia coli) interacts with OmpA. Cryo-EM analysis revealed that TraN pKpQIL interacts with OmpK36 through the insertion of a β-hairpin in the tip of TraN into a monomer of the OmpK36 porin trimer. Combining bioinformatic analysis with AlphaFold structural predictions, we identified a fourth TraN structural variant that mediates mating pair stabilization by binding OmpF. Accordingly, we devised a classification scheme for TraN homologues on the basis of structural similarity and their associated receptors: TraNα (OmpW), TraNβ (OmpK36), TraNγ (OmpA), TraNδ (OmpF). These TraN-OM receptor pairings have real-world implications as they reflect the distribution of resistance plasmids within clinical Enterobacteriaceae isolates, demonstrating the importance of mating pair stabilization in mediating conjugation species specificity. These findings will allow us to predict the distribution of emerging resistance plasmids in high-risk bacterial pathogens.


  • Organizational Affiliation
    • MRC Centre for Molecular Microbiology and Infection, Imperial College, London, UK.

Macromolecule Content 

  • Total Structure Weight: 115.08 kDa 
  • Atom Count: 8,089 
  • Modeled Residue Count: 1,038 
  • Deposited Residue Count: 1,044 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
OmpK36
A, B, C
345Klebsiella pneumoniaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D6QLY0 (Klebsiella pneumoniae)
Explore D6QLY0 
Go to UniProtKB:  D6QLY0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD6QLY0
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
TraN9Klebsiella pneumoniaeMutation(s): 0 
UniProt
Find proteins for A0A2X1SF68 (Klebsiella pneumoniae)
Explore A0A2X1SF68 
Go to UniProtKB:  A0A2X1SF68
Entity Groups
UniProt GroupA0A2X1SF68
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19
RECONSTRUCTIONcryoSPARC3.2.0

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States5T32AI007046-45
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM122510

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-08
    Type: Initial release
  • Version 1.1: 2022-07-06
    Changes: Database references
  • Version 1.2: 2022-07-13
    Changes: Database references
  • Version 1.3: 2024-10-23
    Changes: Data collection, Structure summary