3KMR

Crystal structure of RARalpha ligand binding domain in complex with an agonist ligand (Am580) and a coactivator fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

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
  • Structures With Same Primary Citation

  • 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
A
266Homo sapiensMutation(s): 0 
Gene Names: NR1B1RARA
Find proteins for P10276 (Homo sapiens)
Go to UniProtKB:  P10276
NIH Common Fund Data Resources
PHAROS  P10276
Protein Feature View
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor coactivator 1
C
13N/AMutation(s): 0 
EC: 2.3.1.48
Find proteins for Q15788 (Homo sapiens)
Go to UniProtKB:  Q15788
NIH Common Fund Data Resources
PHAROS  Q15788
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EQN
Query on EQN

Download CCD File 
A
4-{[(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)carbonyl]amino}benzoic acid
C22 H25 N O3
SZWKGOZKRMMLAJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EQNKd:  1400   nM  BindingDB
EQNEC50:  79.43000030517578   nM  BindingDB
EQNEC50:  0.30000001192092896   nM  BindingDB
EQNEC50:  2   nM  BindingDB
EQNEC50:  4   nM  BindingDB
EQNKd:  36   nM  BindingDB
EQNEC50:  19.950000762939453   nM  BindingDB
EQNEC50:  9   nM  BindingDB
EQNEC50:  8.600000381469727   nM  BindingDB
EQNEC50:  50.119998931884766   nM  BindingDB
EQNIC50:  41   nM  BindingDB
EQNKd:  1361   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.307α = 90
b = 61.218β = 105.38
c = 49.444γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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