4RHA

Structure of the C-terminal domain of outer-membrane protein OmpA from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 

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:  
    3OON, 4RHA, 5VES

  • 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 one of these major OM proteins ...

    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

    Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois, 60439.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Outer membrane protein AA, B146Salmonella enterica subsp. enterica serovar Typhimurium str. 14028SMutation(s): 0 
Gene Names: ompA
UniProt
Find proteins for A0A0H2UKZ3 (Salmonella typhimurium (strain 14028s / SGSC 2262))
Explore A0A0H2UKZ3 
Go to UniProtKB:  A0A0H2UKZ3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, BL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.627α = 90
b = 58.627β = 90
c = 72.746γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000phasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-29
    Type: Initial release
  • Version 1.1: 2015-02-04
    Changes: Database references, Other, Source and taxonomy, Structure summary
  • Version 1.2: 2015-03-25
    Changes: Other
  • Version 1.3: 2017-11-22
    Changes: Refinement description
  • Version 1.4: 2019-12-04
    Changes: Database references, Derived calculations