5KEV

Vibrio parahaemolyticus VtrA/VtrC complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.265 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Bile salt receptor complex activates a pathogenic type III secretion system.

Li, P.Rivera-Cancel, G.Kinch, L.N.Salomon, D.Tomchick, D.R.Grishin, N.V.Orth, K.

(2016) Elife 5

  • DOI: 10.7554/eLife.15718
  • Primary Citation of Related Structures:  
    5KEV, 5KEW

  • PubMed Abstract: 
  • Bile is an important component of the human gastrointestinal tract with an essential role in food absorption and antimicrobial activities. Enteric bacterial pathogens have developed strategies to sense bile as an environmental cue to regulate virulence genes during infection ...

    Bile is an important component of the human gastrointestinal tract with an essential role in food absorption and antimicrobial activities. Enteric bacterial pathogens have developed strategies to sense bile as an environmental cue to regulate virulence genes during infection. We discovered that Vibrio parahaemolyticus VtrC, along with VtrA and VtrB, are required for activating the virulence type III secretion system 2 in response to bile salts. The VtrA/VtrC complex activates VtrB in the presence of bile salts. The crystal structure of the periplasmic domains of the VtrA/VtrC heterodimer reveals a β-barrel with a hydrophobic inner chamber. A co-crystal structure of VtrA/VtrC with bile salt, along with biophysical and mutational analysis, demonstrates that the hydrophobic chamber binds bile salts and activates the virulence network. As part of a family of conserved signaling receptors, VtrA/VtrC provides structural and functional insights into the evolutionarily conserved mechanism used by bacteria to sense their environment.


    Organizational Affiliation

    Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
VtrA ProteinA94Vibrio parahaemolyticus RIMD 2210633Mutation(s): 0 
Gene Names: VPA1332
UniProt
Find proteins for Q87GI4 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633))
Explore Q87GI4 
Go to UniProtKB:  Q87GI4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ87GI4
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
VtrC ProteinB144Vibrio parahaemolyticus RIMD 2210633Mutation(s): 0 
Gene Names: VPA1333
UniProt
Find proteins for Q87GI3 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633))
Explore Q87GI3 
Go to UniProtKB:  Q87GI3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ87GI3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.265 
  • Space Group: F 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 211.012α = 90
b = 211.012β = 90
c = 211.012γ = 90
Software Package:
Software NamePurpose
HKL-3000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-20
    Type: Initial release