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 ...

    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
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(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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9CR
Query on 9CR
Download CCD File 
A, 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
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
REAKd:  1.5   nM  Binding MOAD
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 

  • 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