1G5Y

THE 2.0 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF THE RXRALPHA LIGAND BINDING DOMAIN TETRAMER IN THE PRESENCE OF A NON-ACTIVATING RETINOIC ACID ISOMER.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.231 

wwPDB Validation   3D Report Full Report



Literature

Structural basis for autorepression of retinoid X receptor by tetramer formation and the AF-2 helix.

Gampe Jr., R.T.Montana, V.G.Lambert, M.H.Wisely, G.B.Milburn, M.V.Xu, H.E.

(2000) Genes Dev 14: 2229-2241

  • DOI: 10.1101/gad.802300
  • Primary Citation of Related Structures:  
    1G1U, 1G5Y

  • PubMed Abstract: 
  • The 9-cis-retinoic acid receptors (RXRalpha, RXRbeta, and RXRgamma) are nuclear receptors that play key roles in multiple hormone-signaling pathways. Biochemical data indicate that, in the absence of ligand, RXR can exist as an inactive tetramer and ...

    The 9-cis-retinoic acid receptors (RXRalpha, RXRbeta, and RXRgamma) are nuclear receptors that play key roles in multiple hormone-signaling pathways. Biochemical data indicate that, in the absence of ligand, RXR can exist as an inactive tetramer and that its dissociation, induced by ligand, is important for receptor activation. In this article we report the inactivated tetramer structures of the RXRalpha ligand-binding domain (LBD), either in the absence of or in the presence of a nonactivating ligand. These structures reveal that the RXR LBD tetramer forms a compact, disc-shaped complex, consisting of two symmetric dimers that are packed along helices 3 and 11. In each monomer, the AF-2 helix protrudes away from the core domain and spans into the coactivator binding site in the adjacent monomer of the symmetric dimer. In this configuration, the AF-2 helix physically excludes the binding of coactivators and suggests an autorepression mechanism that is mediated by the AF-2 helix within the tetramer. The RXR-tetramer interface is assembled from amino acids that are conserved across several closely related receptors, including the HNF4s and COUP transcription factors, and may therefore provide a model for understanding structure and regulation of this subfamily of nuclear receptors.


    Related Citations: 
    • Asymmetry in the PPARalpha/RXRalpha Crystal Structure Reveals the Molecular Basis of Heterodimerization among Nuclear Receptors
      Gampe Jr., R.T., Montana, V.G., Lambert, M.H., Miller, A.B., Bledsoe, R.K., Milburn, M.V., Kliewer, S.A., Willson, T.M., Xu, H.E.
      (2000) Mol Cell 5: 545

    Organizational Affiliation

    GlaxoWellcome Research and Development, Research Triangle Park, North Carolina 27709, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RETINOIC ACID RECEPTOR RXR-ALPHAABCD238Homo sapiensMutation(s): 0 
Gene Names: RXRANR2B1
Find proteins for P19793 (Homo sapiens)
Explore P19793 
Go to UniProtKB:  P19793
NIH Common Fund Data Resources
PHAROS  P19793
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
REA
Query on REA

Download CCD File 
B, C
RETINOIC ACID
C20 H28 O2
SHGAZHPCJJPHSC-YCNIQYBTSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
9CRKd:  14   nM  BindingDB
9CRKd:  32   nM  BindingDB
9CRKd:  1.5   nM  BindingDB
9CRKd:  16   nM  BindingDB
9CRKd:  15   nM  BindingDB
9CRKd:  240   nM  BindingDB
9CREC50:  2.5999999046325684   nM  BindingDB
9CRKi:  9   nM  BindingDB
9CRIC50:  12   nM  BindingDB
9CREC50:  29   nM  BindingDB
9CRKi:  8   nM  BindingDB
9CRKi:  7.400000095367432   nM  BindingDB
9CRKi:  3.799999952316284   nM  BindingDB
9CRKd:  12   nM  BindingDB
9CRKi:  12   nM  BindingDB
9CREC50:  4.300000190734863   nM  BindingDB
9CREC50:  128   nM  BindingDB
9CREC50:  195   nM  BindingDB
9CRKd:  1560   nM  BindingDB
9CREC50:  140   nM  BindingDB
9CRKd:  1810   nM  BindingDB
9CRKd:  4   nM  BindingDB
9CREC50:  219   nM  BindingDB
9CREC50:  124   nM  BindingDB
9CRKi:  27   nM  BindingDB
9CREC50:  100   nM  BindingDB
9CRIC50:  4   nM  BindingDB
9CRKd:  3   nM  BindingDB
9CREC50:  120   nM  BindingDB
9CREC50:  200   nM  BindingDB
9CRKi:  11   nM  BindingDB
9CRKd:  11   nM  BindingDB
9CREC50:  110   nM  BindingDB
9CREC50:  120   nM  BindingDB
9CREC50:  1.5   nM  BindingDB
9CRKd:  15   nM  BindingDB
9CREC50:  200   nM  BindingDB
9CRKd:  13   nM  BindingDB
9CRKd:  14   nM  BindingDB
9CREC50:  250   nM  BindingDB
9CRKd:  8   nM  BindingDB
9CREC50:  316   nM  BindingDB
9CRKi:  14   nM  BindingDB
9CRKd:  9   nM  BindingDB
9CRKi:  13   nM  BindingDB
9CREC50:  13   nM  BindingDB
9CRIC50:  82   nM  BindingDB
9CRKi:  8.399999618530273   nM  BindingDB
9CREC50:  10   nM  BindingDB
9CRKd:  35   nM  BindingDB
9CREC50:  6   nM  BindingDB
9CRIC50:  29   nM  BindingDB
9CRKd:  50   nM  BindingDB
9CRKd:  30   nM  BindingDB
9CREC50:  4.5   nM  BindingDB
9CRIC50:  32   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.231 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.052α = 90
b = 99.701β = 96.7
c = 96.281γ = 90
Software Package:
Software NamePurpose
MAR345data collection
HKL-2000data reduction
CNSrefinement
CNXrefinement
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-05-02
    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
  • Version 1.4: 2017-10-04
    Changes: Refinement description
  • Version 1.5: 2018-04-04
    Changes: Data collection
  • Version 2.0: 2018-04-25
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary