1XIU

Crystal structure of the agonist-bound ligand-binding domain of Biomphalaria glabrata RXR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of a Novel Tetrameric Complex of Agonist-bound Ligand-binding Domain of Biomphalaria glabrata Retinoid X Receptor.

de Groot, A.de Rosny, E.Juillan-Binard, C.Ferrer, J.-L.Laudet, V.Pierce, R.J.Pebay-Peyroula, E.Fontecilla-Camps, J.-C.Borel, F.

(2005) J.Mol.Biol. 354: 841-853

  • DOI: 10.1016/j.jmb.2005.09.090

  • PubMed Abstract: 
  • Nuclear receptors form an important class of transcription regulators in metazoans. To learn more about the evolution of these proteins, we have initiated structural studies on nuclear receptor ligand-binding domains from various animals. Here we pre ...

    Nuclear receptors form an important class of transcription regulators in metazoans. To learn more about the evolution of these proteins, we have initiated structural studies on nuclear receptor ligand-binding domains from various animals. Here we present the crystal structure of the ligand-binding domain (LBD) of the retinoid X receptor (RXR) from the mollusc Biomphalaria glabrata. The structure reveals a novel tetrameric association in which each monomer is complexed to the human RXR ligand 9-cis retinoic acid and to a human co-activator-derived peptide. The ligand and the co-activator peptide are bound in essentially the same manner as observed in previously reported human RXR LBD structures, suggesting that the mechanisms of RXR-mediated transcription regulation are very similar in mollusc and human. The structure shows further that binding of ligand and co-activator peptide does not necessarily lead to the typical holo-conformation in which helix 12 (H12) folds back and packs against the LBD. Within a canonical dimer, only one monomer is in this closed agonist conformation. The other monomer is in an open conformation with H12 protruding from the LBD core, occupying the H12 interaction groove of another open monomer in an adjacent dimer in a domain swapping fashion, thus resulting in a tetrameric association. Additional tetramer interfaces are formed between H11 of the closed LBD and H6 of the open LBD. This novel holo-tetramer configuration may have a biological role in activating genes whose promoters are poorly recognised by dimers but much more efficiently by the corresponding tetramers.


    Organizational Affiliation

    Laboratoire de Cristallographie et Cristallogenèse des Protéines, Institut de Biologie Structurale 'Jean-Pierre Ebel' (UMR 5075, CEA-CNRS-UJF), 41 rue Jules Horowitz, 38027 Grenoble cedex 1, France. nicolaas.degroot@cea.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RXR-like protein
A, B
230Biomphalaria glabrataMutation(s): 0 
Gene Names: RXR
Find proteins for Q8T5C6 (Biomphalaria glabrata)
Go to UniProtKB:  Q8T5C6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor coactivator 1
E, F
15Homo sapiensMutation(s): 0 
Gene Names: NCOA1 (BHLHE74, SRC1)
EC: 2.3.1.48
Find proteins for Q15788 (Homo sapiens)
Go to Gene View: NCOA1
Go to UniProtKB:  Q15788
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9CR
Query on 9CR

Download SDF File 
Download CCD File 
A, B
(9cis)-retinoic acid
C20 H28 O2
SHGAZHPCJJPHSC-ZVCIMWCZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.193 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 87.100α = 90.00
b = 87.100β = 90.00
c = 320.400γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
MOLREPphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-09-13
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2016-11-16
    Type: Non-polymer description