Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer -A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 53301.05 
• Atom Count: 3586 
• Residue Count: 468 
• Unique protein chains: 2

1DKF

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

• DOI: 10.2210/pdb1DKF/pdb

• Classification: HORMONE/GROWTH FACTOR RECEPTOR
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 1 


• Deposited: 1999-12-07 Released: 2000-04-19 
• Deposition Author(s): Bourguet, W., Vivat, V., Wurtz, J.M., Chambon, P., Gronemeyer, H., Moras, D., Structural Proteomics in Europe (SPINE)

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Experimental Data Snapshot

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

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: 10882070 


• 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 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN (RETINOID X RECEPTOR-ALPHA)	A	233	Mus musculus	Mutation(s): 1  Gene Names: Rxra (Nr2b1)
Find proteins for P28700 (Mus musculus) Go to UniProtKB:  P28700

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN (RETINOIC ACID RECEPTOR-ALPHA)	B	235	Homo sapiens	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
OLA	A	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N
BMS	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

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 = 116.600	α = 90.00
b = 116.600	β = 90.00
c = 207.800	γ = 120.00

Software Package:

Software Name	Purpose
AMoRE	phasing
SCALEPACK	data scaling
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-12-07 
• Released Date: 2000-04-19 
• Deposition Author(s): Bourguet, W., Vivat, V., Wurtz, J.M., Chambon, P., Gronemeyer, H., Moras, D., Structural Proteomics in Europe (SPINE)

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