Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 28.80 kDa 
• Atom Count: 2317 
• Residue Count: 236 
• Unique protein chains: 1

1EXA

ENANTIOMER DISCRIMINATION ILLUSTRATED BY CRYSTAL STRUCTURES OF THE HUMAN RETINOIC ACID RECEPTOR HRARGAMMA LIGAND BINDING DOMAIN: THE COMPLEX WITH THE ACTIVE R-ENANTIOMER BMS270394.

• DOI: 10.2210/pdb1EXA/pdb

• Classification: GENE REGULATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-05-02 Released: 2000-06-09 
• Deposition Author(s): Klaholz, B.P., Mitschler, A., Belema, M., Zusi, C., Moras, D., Structural Proteomics in Europe (SPINE)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 0.250 
• R-Value Work: 0.209 

Literature

Enantiomer discrimination illustrated by high-resolution crystal structures of the human nuclear receptor hRARgamma.

Klaholz, B.P., Mitschler, A., Belema, M., Zusi, C., Moras, D.

(2000) Proc Natl Acad Sci U S A 97: 6322-6327

• PubMed: 10841540 
• DOI: 10.1073/pnas.97.12.6322
• Primary Citation of Related Structures:  
  1EXA, 1EXX


• PubMed Abstract: 
  

The human retinoic acid receptor (hRAR) is a member of the nuclear receptor superfamily that regulates the transcription of target genes in a ligand-dependent manner. The three hRAR isotypes are targets for retinoids that are used in the treatment of various diseases, including breast cancer and skin diseases. Drug efficiency and safety depend on the pharmacological activity of enantiomers, which can differ because of the chiral environment generated by the target. We report the crystal structures of the hRARgamma ligand-binding domain bound to two enantiomers, the active BMS270394 and the inactive BMS270395, solved at 1.6 A and 1.7 A resolution, respectively. The crystal structures reveal that in both enantiomers, the hydroxyl moiety attached to the chiral center forms a hydrogen bond to the Met-272 sulfur atom, thus imposing a conformation of BMS270395 that differs significantly from that observed for BMS270394 and other known retinoids. BMS270395 adopts an energetically unfavorable conformation, accounting for its inactivity; in contrast, the conformation of BMS270394 is close to an energy minimum. Our high-resolution data allow rationalization of enantiomer discrimination by the receptor and provide a model system for the pharmacological properties of enantiomeric pairs.

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Related Citations: 

• Conformational adaptation of agonists to the human nuclear receptor hRARgamma.
  Klaholz, B.P., Renaud, J.-P., Mitschler, A., Zusi, C., Chambon, P., Gronemeyer, H., Moras, D.
  (1998) Nat Struct Biol 5: 199

• Structural basis for isotype selectivity of the human retinoic acid nuclear receptor.
  Klaholz, B.P., Mitschler, A., Moras, D.
  (2000) To be published --: --

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Organizational Affiliation: 

Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique, Cedex, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RETINOIC ACID RECEPTOR GAMMA-2	A	246	Homo sapiens	Mutation(s): 0  Gene Names: RARG, NR1B3
Find proteins for P13631 (Homo sapiens) Explore P13631  Go to UniProtKB:  P13631
NIH Common Fund Data Resources
PHAROS  P13631 GTEx  ENSG00000172819

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LMU	A	DODECYL-ALPHA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-YHBSTRCHSA-N
394	A	R-3-FLUORO-4-[2-HYDROXY-2-(5,5,8,8-TETRAMETHYL-5,6,7,8,-TETRAHYDRO-NAPHTALEN-2-YL)-ACETYLAMINO]-BENZOIC ACID C23 H26 F N O4 AANFHDFOMFRLLR-LJQANCHMSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
394	Kd:  528   nM  BindingDB
394	Ki:  1.5   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 0.250 
• R-Value Work: 0.209 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.672	α = 90
b = 59.672	β = 90
c = 155.545	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-05-02 
• Released Date: 2000-06-09 
Deposition Author(s): Klaholz, B.P., Mitschler, A., Belema, M., Zusi, C., Moras, D., Structural Proteomics in Europe (SPINE)

Revision History 

• Version 1.0: 2000-06-09
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance