1DKF

CRYSTAL STRUCTURE OF A HETERODIMERIC COMPLEX OF RAR AND RXR LIGAND-BINDING DOMAINS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Crystal structure of a heterodimeric complex of RAR and RXR ligand-binding domains.

Bourguet, W.Vivat, V.Wurtz, J.M.Chambon, P.Gronemeyer, H.Moras, D.

(2000) Mol.Cell 5: 289-298


  • PubMed Abstract: 
  • The crystal structure of a heterodimer between the ligand-binding domains (LBDs) of the human RARalpha bound to a selective antagonist and the constitutively active mouse RXRalphaF318A mutant shows that, pushed by a bulky extension of the ligand, RAR ...

    The crystal structure of a heterodimer between the ligand-binding domains (LBDs) of the human RARalpha bound to a selective antagonist and the constitutively active mouse RXRalphaF318A mutant shows that, pushed by a bulky extension of the ligand, RARalpha helix H12 adopts an antagonist position. The unexpected presence of a fatty acid in the ligand-binding pocket of RXRalpha(F318A is likely to account for its apparent "constitutivity." Specific conformational changes suggest the structural basis of pure and partial antagonism. The RAR-RXR heterodimer interface is similar to that observed in most nuclear receptor (NR) homodimers. A correlative analysis of 3D structures and sequences provides a novel view on dimerization among members of the nuclear receptor superfamily.


    Organizational Affiliation

    Institut de Génétique et de Biologie Moléculaire et Cellulaire, CRNS/INSERM/Université Louis Pasteur/Collège de France, Illkirch, Strasbourg.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (RETINOID X RECEPTOR-ALPHA)
A
233Mus musculusMutation(s): 1 
Gene Names: Rxra (Nr2b1)
Find proteins for P28700 (Mus musculus)
Go to UniProtKB:  P28700
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (RETINOIC ACID RECEPTOR-ALPHA)
B
235Homo sapiensMutation(s): 0 
Gene Names: RARA (NR1B1)
Find proteins for P10276 (Homo sapiens)
Go to Gene View: RARA
Go to UniProtKB:  P10276
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLA
Query on OLA

Download SDF File 
Download CCD File 
A
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
BMS
Query on BMS

Download SDF File 
Download CCD File 
B
4-[(4,4-DIMETHYL-1,2,3,4-TETRAHYDRO-[1,2']BINAPTHALENYL-7-CARBONYL)-AMINO]-BENZOIC ACID
C29 H26 N2 O3
WBEIHCAWTAWTBK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.203 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 116.600α = 90.00
b = 116.600β = 90.00
c = 207.800γ = 120.00
Software Package:
Software NamePurpose
AMoREphasing
SCALEPACKdata scaling
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-04-19
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description
  • Version 1.4: 2018-04-04
    Type: Data collection
  • Version 1.5: 2018-04-11
    Type: Data collection