1DKF

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.203 
  • R-Value Observed: 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

  • DOI: 10.1016/s1097-2765(00)80424-4
  • Primary Citation of Related Structures:  
    1DKF

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (RETINOID X RECEPTOR-ALPHA)A233Mus musculusMutation(s): 1 
Gene Names: RxraNr2b1
Find proteins for P28700 (Mus musculus)
Explore P28700 
Go to UniProtKB:  P28700
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (RETINOIC ACID RECEPTOR-ALPHA)B235Homo sapiensMutation(s): 0 
Gene Names: RARANR1B1
Find proteins for P10276 (Homo sapiens)
Explore P10276 
Go to UniProtKB:  P10276
NIH Common Fund Data Resources
PHAROS  P10276
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BMS
Query on BMS

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
OLA
Query on OLA

Download CCD File 
A
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.6α = 90
b = 116.6β = 90
c = 207.8γ = 120
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

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