Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 20.61 kDa 
• Atom Count: 1522 
• Modelled Residue Count: 178 
• Deposited Residue Count: 182 
• Unique protein chains: 1

3QP2

Crystal structure of CviR ligand-binding domain bound to C8-HSL

• DOI: 10.2210/pdb3QP2/pdb

• Classification: TRANSCRIPTION
• Organism(s): Chromobacterium violaceum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-02-11 Released: 2011-03-30 
• Deposition Author(s): Chen, G., Swem, L., Swem, D., Stauff, D., O'Loughlin, C., Jeffrey, P., Bassler, B., Hughson, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.223 
• R-Value Work: 0.201 
• R-Value Observed: 0.202 

Literature

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

• PubMed: 21504831 
• DOI: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CviR transcriptional regulator	A	182	Chromobacterium violaceum	Mutation(s): 0  Gene Names: cviR
UniProt
Find proteins for D3W065 (Chromobacterium violaceum) Explore D3W065  Go to UniProtKB:  D3W065

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HTF (Subject of Investigation/LOI)	B [auth A]	N-(2-OXOTETRAHYDROFURAN-3-YL)OCTANAMIDE C12 H21 N O3 JKEJEOJPJVRHMQ-JTQLQIEISA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.223 
• R-Value Work: 0.201 
• R-Value Observed: 0.202 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.58	α = 90
b = 55.907	β = 90
c = 124.988	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2011-02-11 
• Released Date: 2011-03-30 
Deposition Author(s): Chen, G., Swem, L., Swem, D., Stauff, D., O'Loughlin, C., Jeffrey, P., Bassler, B., Hughson, F.

Revision History  

• Version 1.0: 2011-03-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance