Crystal structure of the pED208 TraM N-terminal domain

Experimental Data Snapshot

  • Resolution: 1.30 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Structural basis of cooperative DNA recognition by the plasmid conjugation factor, TraM.

Wong, J.J.Lu, J.Edwards, R.A.Frost, L.S.Glover, J.N.

(2011) Nucleic Acids Res 39: 6775-6788

  • DOI: https://doi.org/10.1093/nar/gkr296
  • Primary Citation of Related Structures:  
    3OMY, 3ON0

  • PubMed Abstract: 

    The conjugative transfer of F-like plasmids such as F, R1, R100 and pED208, between bacterial cells requires TraM, a plasmid-encoded DNA-binding protein. TraM tetramers bridge the origin of transfer (oriT) to a key component of the conjugative pore, the coupling protein TraD. Here we show that TraM recognizes a high-affinity DNA-binding site, sbmA, as a cooperative dimer of tetramers. The crystal structure of the TraM-sbmA complex from the plasmid pED208 shows that binding cooperativity is mediated by DNA kinking and unwinding, without any direct contact between tetramers. Sequence-specific DNA recognition is carried out by TraM's N-terminal ribbon-helix-helix (RHH) domains, which bind DNA in a staggered arrangement. We demonstrate that both DNA-binding specificity, as well as selective interactions between TraM and the C-terminal tail of its cognate TraD mediate conjugation specificity within the F-like family of plasmids. The ability of TraM to cooperatively bind DNA without interaction between tetramers leaves the C-terminal TraM tetramerization domains free to make multiple interactions with TraD, driving recruitment of the plasmid to the conjugative pore.

  • Organizational Affiliation

    Department of Biochemistry, School of Molecular and Systems Medicine, University of Alberta, Edmonton, AB T6G 2H7, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein traM
A, B
52Escherichia coliMutation(s): 0 
Gene Names: traM
Find proteins for P33788 (Escherichia coli)
Explore P33788 
Go to UniProtKB:  P33788
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33788
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.30 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.069α = 90
b = 54.069β = 90
c = 67.268γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-05-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-09-07
    Changes: Database references
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description