3OON

The structure of an outer membrance protein from Borrelia burgdorferi B31


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Insights into PG-binding, conformational change, and dimerization of the OmpA C-terminal domains from Salmonella enterica serovar Typhimurium and Borrelia burgdorferi.

Tan, K.Deatherage Kaiser, B.L.Wu, R.Cuff, M.Fan, Y.Bigelow, L.Jedrzejczak, R.P.Adkins, J.N.Cort, J.R.Babnigg, G.Joachimiak, A.

(2017) Protein Sci. 26: 1738-1748

  • DOI: 10.1002/pro.3209
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Salmonella enterica serovar Typhimurium can induce both humoral and cell-mediated responses when establishing itself in the host. These responses are primarily stimulated against the lipopolysaccharide and major outer membrane (OM) proteins. OmpA is ...

    Salmonella enterica serovar Typhimurium can induce both humoral and cell-mediated responses when establishing itself in the host. These responses are primarily stimulated against the lipopolysaccharide and major outer membrane (OM) proteins. OmpA is one of these major OM proteins. It comprises a N-terminal eight-stranded β-barrel transmembrane domain and a C-terminal domain (OmpA CTD ). The OmpA CTD and its homologs are believed to bind to peptidoglycan (PG) within the periplasm, maintaining bacterial osmotic homeostasis and modulating the permeability and integrity of the OM. Here we present the first crystal structures of the OmpA CTD from two pathogens: S. typhimurium (STOmpA CTD ) in open and closed forms and causative agent of Lyme Disease Borrelia burgdorferi (BbOmpA CTD ), in closed form. In the open form of STOmpA CTD , an aspartate residue from a long β2-α3 loop points into the binding pocket, suggesting that an anion group such as a carboxylate group from PG is favored at the binding site. In the closed form of STOmpA CTD and in the structure of BbOmpA CTD , a sulfate group from the crystallization buffer is tightly bound at the binding site. The differences between the closed and open forms of STOmpA CTD , suggest a large conformational change that includes an extension of α3 helix by ordering a part of β2-α3 loop. We propose that the sulfate anion observed in these structures mimics the carboxylate group of PG when bound to STOmpA CTD suggesting PG-anchoring mechanism. In addition, the binding of PG or a ligand mimic may enhance dimerization of STOmpA CTD , or possibly that of full length STOmpA.


    Organizational Affiliation

    Center for Structural Genomics of Infectious Diseases, University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois, 60637.,Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois, 60439.,National Security Directorate, Pacific Northwest National Laboratory, Richland, Washington, 99352.,Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, 99352.,Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois, 60439.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Outer membrane protein (Tpn50)
A
123Borrelia burgdorferi (strain ATCC 35210 / B31 / CIP 102532 / DSM 4680)Mutation(s): 0 
Find proteins for O51189 (Borrelia burgdorferi (strain ATCC 35210 / B31 / CIP 102532 / DSM 4680))
Go to UniProtKB:  O51189
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.212 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 52.089α = 90.00
b = 74.784β = 90.00
c = 66.760γ = 90.00
Software Package:
Software NamePurpose
ARPmodel building
SHELXDphasing
HKL-3000data reduction
HKL-3000phasing
REFMACrefinement
SBC-Collectdata collection
HKL-3000data scaling
MLPHAREphasing
WARPmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2015-04-08
    Type: Structure summary
  • Version 1.3: 2017-11-08
    Type: Refinement description
  • Version 1.4: 2019-12-04
    Type: Database references, Derived calculations