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 

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This is version 1.6 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, RARalpha helix H12 adopts an antagonist position ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (RETINOID X RECEPTOR-ALPHA)A233Mus musculusMutation(s): 1 
Gene Names: Rxra, Nr2b1
UniProt
Find proteins for P28700 (Mus musculus)
Explore P28700 
Go to UniProtKB:  P28700
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28700
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (RETINOIC ACID RECEPTOR-ALPHA)B235Homo sapiensMutation(s): 0 
Gene Names: RARA, NR1B1
UniProt & NIH Common Fund Data Resources
Find proteins for P10276 (Homo sapiens)
Explore P10276 
Go to UniProtKB:  P10276
PHAROS:  P10276
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10276
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 Ideal Coordinates CCD File 
D [auth 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 Ideal Coordinates CCD File 
C [auth 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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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.6: 2021-11-03
    Changes: Database references, Derived calculations