9NIA | pdb_00009nia

Crystal structure of Vibrio cholerae CqsR bound to ethanolamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 
    0.207 (Depositor), 0.207 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structure-function studies of Vibrio cholerae quorum-sensing receptor CqsR signal recognition.

Guarnaccia, A.M.Steenhaut, A.D.Olenic, S.D.Na, J.Perez, L.J.Ng, W.L.Neiditch, M.B.

(2025) PLoS Pathog 21: e1013447-e1013447

  • DOI: https://doi.org/10.1371/journal.ppat.1013447
  • Primary Citation of Related Structures:  
    9NIA, 9NIT, 9NIV, 9NJ8

  • PubMed Abstract: 

    Ethanolamine signaling through the transmembrane quorum-sensing receptor CqsR influences Vibrio cholerae niche recognition and host colonization. In this study, we present a comprehensive structure-function analysis of CqsR. Specifically, we have determined X-ray crystal structures of the CqsR periplasmic domain bound to the signaling agonist ethanolamine and its analogs, serinol and L-alaninol, as well as the ligand-free (apo) form of CqsR. The periplasmic ligand-binding domain of CqsR is a Cache domain, the most prevalent extracellular sensory module in prokaryotes. Our findings provide a rare structural comparison of ligand-bound and unbound states of a Cache domain receptor. Coupled with thermodynamic binding assays and genetic analyses, these structures elucidate the molecular basis of CqsR ligand specificity. This study not only advances the understanding of Cache domain function but also informs the identification of ligands for orphan Cache receptors and the rational design of signaling agonists and antagonists. Lastly, we discuss ligand-induced conformational changes in the CqsR Cache domains and explore the potential for the existence of additional regulatory ligands.


  • Organizational Affiliation
    • Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Newark, New Jersey, United States of America.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
histidine kinase217Vibrio cholerae C6706Mutation(s): 0 
Gene Names: VC_1831
EC: 2.7.13.3
UniProt
Find proteins for Q9KR16 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore Q9KR16 
Go to UniProtKB:  Q9KR16
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KR16
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free:  0.207 (Depositor), 0.207 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.811α = 90
b = 121.811β = 90
c = 70.711γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
PHASERphasing
HKL-3000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI121337
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)United StatesTL1TR003019

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-02
    Type: Initial release
  • Version 1.1: 2025-09-17
    Changes: Database references