Crystal structure of CviR ligand-binding domain bound to the native ligand C6-HSL

Experimental Data Snapshot

  • Resolution: 1.55 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


A strategy for antagonizing quorum sensing.

Chen, G.Swem, L.R.Swem, D.L.Stauff, D.L.O'Loughlin, C.T.Jeffrey, P.D.Bassler, B.L.Hughson, F.M.

(2011) Mol Cell 42: 199-209

  • DOI: https://doi.org/10.1016/j.molcel.2011.04.003
  • Primary Citation of Related Structures:  
    3QP1, 3QP2, 3QP4, 3QP5, 3QP6, 3QP8

  • PubMed Abstract: 

    Quorum-sensing bacteria communicate via small molecules called autoinducers to coordinate collective behaviors. Because quorum sensing controls virulence factor expression in many clinically relevant pathogens, membrane-permeable quorum sensing antagonists that prevent population-wide expression of virulence genes offer a potential route to novel antibacterial therapeutics. Here, we report a strategy for inhibiting quorum-sensing receptors of the widespread LuxR family. Structure-function studies with natural and synthetic ligands demonstrate that the dimeric LuxR-type transcription factor CviR from Chromobacterium violaceum is potently antagonized by molecules that bind in place of the native acylated homoserine lactone autoinducer, provided that they stabilize a closed conformation. In such conformations, each of the two DNA-binding domains interacts with the ligand-binding domain of the opposing monomer. Consequently, the DNA-binding helices are held apart by ∼60 Å, twice the ∼30 Å separation required for operator binding. This approach may represent a general strategy for the inhibition of multidomain proteins.

  • Organizational Affiliation

    Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CviR transcriptional regulator182Chromobacterium violaceumMutation(s): 0 
Gene Names: cviR
Find proteins for D3W065 (Chromobacterium violaceum)
Explore D3W065 
Go to UniProtKB:  D3W065
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD3W065
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on HL6

Download Ideal Coordinates CCD File 
B [auth A]N-[(3S)-2-oxotetrahydrofuran-3-yl]hexanamide
C10 H17 N O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.55 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.543α = 90
b = 55.973β = 90
c = 125.223γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description