3KMZ

Crystal structure of RARalpha ligand binding domain in complex with the inverse agonist BMS493 and a corepressor fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A unique secondary-structure switch controls constitutive gene repression by retinoic acid receptor.

le Maire, A.Teyssier, C.Erb, C.Grimaldi, M.Alvarez, S.de Lera, A.R.Balaguer, P.Gronemeyer, H.Royer, C.A.Germain, P.Bourguet, W.

(2010) Nat.Struct.Mol.Biol. 17: 801-807

  • DOI: 10.1038/nsmb.1855
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In the absence of ligand, some nuclear receptors, including retinoic acid receptor (RAR), act as transcriptional repressors by recruiting corepressor complexes to target genes. This constitutive repression is crucial in metazoan reproduction, develop ...

    In the absence of ligand, some nuclear receptors, including retinoic acid receptor (RAR), act as transcriptional repressors by recruiting corepressor complexes to target genes. This constitutive repression is crucial in metazoan reproduction, development and homeostasis. However, its specific molecular determinants had remained obscure. Using structural, biochemical and cell-based assays, we show that the basal repressive activity of RAR is conferred by an extended beta-strand that forms an antiparallel beta-sheet with specific corepressor residues. Agonist binding induces a beta-strand-to-alpha-helix transition that allows for helix H11 formation, which in turn provokes corepressor release, repositioning of helix H12 and coactivator recruitment. Several lines of evidence suggest that this structural switch could be implicated in the intrinsic repressor function of other nuclear receptors. Finally, we report on the molecular mechanism by which inverse agonists strengthen corepressor interaction and enhance gene silencing by RAR.


    Organizational Affiliation

    Institut National de la Santé et de la Recherche Médicale, U554, Montpellier, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Retinoic acid receptor alpha
B, A
266Homo sapiensMutation(s): 0 
Gene Names: RARA (NR1B1)
Find proteins for P10276 (Homo sapiens)
Go to Gene View: RARA
Go to UniProtKB:  P10276
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor corepressor 1
C, D
19Homo sapiensMutation(s): 0 
Gene Names: NCOR1 (KIAA1047)
Find proteins for O75376 (Homo sapiens)
Go to Gene View: NCOR1
Go to UniProtKB:  O75376
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EQO
Query on EQO

Download SDF File 
Download CCD File 
A, B
4-{(E)-2-[5,5-dimethyl-8-(phenylethynyl)-5,6-dihydronaphthalen-2-yl]ethenyl}benzoic acid
C29 H24 O2
YCADIXLLWMXYKW-CMDGGOBGSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
C, D
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EQOIC50: 114 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.172 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 104.831α = 90.00
b = 105.625β = 89.92
c = 53.382γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
ProDCdata collection
MOSFLMdata reduction
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-06-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance