1MV9

Crystal Structure of the human RXR alpha ligand binding domain bound to the eicosanoid DHA (Docosa Hexaenoic Acid) and a coactivator peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular Recognition of Agonist Ligands by RXRs

Egea, P.F.Mitschler, A.Moras, D.

(2002) MOL.ENDOCRINOL. 16: 987-997

  • DOI: 10.1210/mend.16.5.0823
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The nuclear receptor RXR is an obligate partner in many signal transduction pathways. We report the high-resolution structures of two complexes of the human RXRalpha ligand-binding domain specifically bound to two different and chemically unrelated a ...

    The nuclear receptor RXR is an obligate partner in many signal transduction pathways. We report the high-resolution structures of two complexes of the human RXRalpha ligand-binding domain specifically bound to two different and chemically unrelated agonist compounds: docosa hexaenoic acid, a natural derivative of eicosanoic acid, present in mammalian cells and recently identified as a potential endogenous RXR ligand in the mouse brain, and the synthetic ligand BMS 649. In both structures the RXR-ligand-binding domain forms homodimers and exhibits the active conformation previously observed with 9-cis-RA. Analysis of the differences in ligand-protein contacts (predominantly van der Waals forces) and binding cavity geometries and volumes for the several agonist-bound RXR structures clarifies the structural features important for ligand recognition. The L-shaped ligand-binding pocket adapts to the diverse ligands, especially at the level of residue N306, which might thus constitute a new target for drug-design. Despite its highest affinity 9-cis-RA displays the lowest number of ligand-protein contacts. These structural results support the idea that docosa hexaenoic acid and related fatty acids could be natural agonists of RXRs and question the real nature of the endogenous ligand(s) in mammalian cells.


    Organizational Affiliation

    Laboratoire de Biologie et Génomique Structurales, Université Louis Pasteur, Parc d'Innovation BP163, 67404 Illkirch cedex, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RXR retinoid X receptor
A
240Homo sapiensMutation(s): 0 
Gene Names: RXRA (NR2B1)
Find proteins for P19793 (Homo sapiens)
Go to Gene View: RXRA
Go to UniProtKB:  P19793
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor coactivator 2
B
13Homo sapiensMutation(s): 0 
Gene Names: NCOA2 (BHLHE75, SRC2, TIF2)
Find proteins for Q15596 (Homo sapiens)
Go to Gene View: NCOA2
Go to UniProtKB:  Q15596
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HXA
Query on HXA

Download SDF File 
Download CCD File 
A
DOCOSA-4,7,10,13,16,19-HEXAENOIC ACID
C22 H32 O2
MBMBGCFOFBJSGT-KUBAVDMBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.201 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 64.361α = 90.00
b = 64.361β = 90.00
c = 112.740γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SCALEPACKdata scaling
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-10-16
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance