1FBY

CRYSTAL STRUCTURE OF THE HUMAN RXR ALPHA LIGAND BINDING DOMAIN BOUND TO 9-CIS RETINOIC ACID

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Crystal structure of the human RXRalpha ligand-binding domain bound to its natural ligand: 9-cis retinoic acid.

Egea, P.F., Mitschler, A., Rochel, N., Ruff, M., Chambon, P., Moras, D.

(2000) EMBO J 19: 2592-2601

  • DOI: 10.1093/emboj/19.11.2592
  • Primary Citation of Related Structures:  
    1FBY

  • PubMed Abstract: 

    • The pleiotropic effects of active retinoids are transduced by their cognate nuclear receptors, retinoid X receptors (RXRs) and retinoic acid receptors (RARs), which act as transcriptional regulators activated by two stereoisomers of retinoic acid (RA): 9-cis RA (9-cRA) and all-trans RA (a-tRA) ...

    The pleiotropic effects of active retinoids are transduced by their cognate nuclear receptors, retinoid X receptors (RXRs) and retinoic acid receptors (RARs), which act as transcriptional regulators activated by two stereoisomers of retinoic acid (RA): 9-cis RA (9-cRA) and all-trans RA (a-tRA). Among nuclear receptors, RXR occupies a central position and plays a crucial role in many intracellular signalling pathways as a ubiquitous heterodimerization partner with numerous other members of this superfamily. Whereas RARs bind both isomers, RXRs exclusively bind 9-cRA. The crystal structure of the ligand-binding domain (LBD) of human RXRalpha bound to 9-cRA reveals the molecular basis of this ligand selectivity and allows a comparison of both apo and holo forms of the same nuclear receptor. In the crystal, the receptor is monomeric and exhibits a canonical agonist conformation without direct contacts between the ligand and the transactivation helix H12. Comparison with the unliganded RXRalpha LBD structure reveals the molecular mechanisms of ligand-induced conformational changes and allows us to describe at the atomic level how these changes generate the proper protein interface involved in nuclear receptor-coactivator interaction.

    Organizational Affiliation: 

    Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP/Collège de France, BP 163-67404 Illkirch Cedex, CU de Strasbourg, France.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RETINOIC ACID RECEPTOR RXR-ALPHAA, B239Homo sapiensMutation(s): 0 
Gene Names: RXRA, NR2B1
Find proteins for P19793 (Homo sapiens)
Explore P19793 
Go to UniProtKB:  P19793
NIH Common Fund Data Resources
PHAROS:  P19793
GTEx:  ENSG00000186350
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9CR
Query on 9CR
Download Ideal Coordinates CCD File 
 C [auth A], D [auth B](9cis)-retinoic acid
C20 H28 O2
SHGAZHPCJJPHSC-ZVCIMWCZSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
9CRKd:  240   nM  BindingDB
9CRKd:  12   nM  BindingDB
9CRKi:  12   nM  BindingDB
9CRKi:  8   nM  BindingDB
9CRKd:  1.5   nM  BindingDB
9CREC50:  219   nM  BindingDB
9CRKi:  9   nM  BindingDB
9CREC50:  100   nM  BindingDB
9CREC50:  128   nM  BindingDB
9CREC50:  140   nM  BindingDB
9CREC50:  120   nM  BindingDB
9CRKd:  3   nM  BindingDB
9CRKd:  32   nM  BindingDB
9CRIC50:  82   nM  BindingDB
9CREC50:  10   nM  BindingDB
9CRKi:  27   nM  BindingDB
9CREC50:  13   nM  BindingDB
9CRKd:  1.5   nM  Binding MOAD
9CRKi:  7.400000095367432   nM  BindingDB
9CREC50:  29   nM  BindingDB
9CREC50:  2.5999999046325684   nM  BindingDB
9CRKi:  13   nM  BindingDB
9CREC50:  4.300000190734863   nM  BindingDB
9CRKi:  14   nM  BindingDB
9CRKd:  14   nM  BindingDB
9CRKi:  11   nM  BindingDB
9CRKd:  11   nM  BindingDB
9CREC50:  120   nM  BindingDB
9CRIC50:  4   nM  BindingDB
9CREC50:  110   nM  BindingDB
9CREC50:  6   nM  BindingDB
9CREC50:  200   nM  BindingDB
9CRKd:  50   nM  BindingDB
9CRKd:  4   nM  BindingDB
9CRIC50:  32   nM  BindingDB
9CREC50:  200   nM  BindingDB
9CREC50:  124   nM  BindingDB
9CRKd:  30   nM  BindingDB
9CRIC50:  29   nM  BindingDB
9CRIC50:  12   nM  BindingDB
9CREC50:  4.5   nM  BindingDB
9CRKd:  35   nM  BindingDB
9CREC50:  195   nM  BindingDB
9CRKd:  1560   nM  BindingDB
9CRKd:  1810   nM  BindingDB
9CREC50:  250   nM  BindingDB
9CRKi:  3.799999952316284   nM  BindingDB
9CRKd:  9   nM  BindingDB
9CRKd:  8   nM  BindingDB
9CRKd:  15   nM  BindingDB
9CREC50:  316   nM  BindingDB
9CRKd:  15   nM  BindingDB
9CRKd:  16   nM  BindingDB
9CREC50:  1.5   nM  BindingDB
9CRKd:  13   nM  BindingDB
9CRKi:  8.399999618530273   nM  BindingDB
9CRKd:  14   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.228 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.325α = 90
b = 86.358β = 90
c = 90.527γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-07-28
    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: 2016-11-09
    Changes: Non-polymer description