1KKQ

Crystal structure of the human PPAR-alpha ligand-binding domain in complex with an antagonist GW6471 and a SMRT corepressor motif


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.258 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Structural basis for antagonist-mediated recruitment of nuclear co-repressors by PPARalpha.

Xu, H.E.Stanley, T.B.Montana, V.G.Lambert, M.H.Shearer, B.G.Cobb, J.E.McKee, D.D.Galardi, C.M.Plunket, K.D.Nolte, R.T.Parks, D.J.Moore, J.T.Kliewer, S.A.Willson, T.M.Stimmel, J.B.

(2002) Nature 415: 813-817

  • DOI: 10.1038/415813a

  • PubMed Abstract: 
  • Repression of gene transcription by nuclear receptors is mediated by interactions with co-repressor proteins such as SMRT and N-CoR, which in turn recruit histone deacetylases to the chromatin. Aberrant interactions between nuclear receptors and co-r ...

    Repression of gene transcription by nuclear receptors is mediated by interactions with co-repressor proteins such as SMRT and N-CoR, which in turn recruit histone deacetylases to the chromatin. Aberrant interactions between nuclear receptors and co-repressors contribute towards acute promyelocytic leukaemia and thyroid hormone resistance syndrome. The binding of co-repressors to nuclear receptors occurs in the unliganded state, and can be stabilized by antagonists. Here we report the crystal structure of a ternary complex containing the peroxisome proliferator-activated receptor-alpha ligand-binding domain bound to the antagonist GW6471 and a SMRT co-repressor motif. In this structure, the co-repressor motif adopts a three-turn alpha-helix that prevents the carboxy-terminal activation helix (AF-2) of the receptor from assuming the active conformation. Binding of the co-repressor motif is further reinforced by the antagonist, which blocks the AF-2 helix from adopting the active position. Biochemical analyses and structure-based mutagenesis indicate that this mode of co-repressor binding is highly conserved across nuclear receptors.


    Related Citations: 
    • Structural determinants of ligand binding selectivity between the peroxisome proliferator-activated receptors
      Xu, H.E.,Lambert, M.H.,Montana, V.G.,Willson, T.M.
      (2001) Proc.Natl.Acad.Sci.USA 98: 13919


    Organizational Affiliation

    Nuclear Receptor Discovery Research, GlaxoSmithKline, Research Triangle Park, NC 27709, USA. ex11957@gsk.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR
A, B, C, D
269Homo sapiensMutation(s): 0 
Gene Names: PPARA (NR1C1, PPAR)
Find proteins for Q07869 (Homo sapiens)
Go to Gene View: PPARA
Go to UniProtKB:  Q07869
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NUCLEAR RECEPTOR CO-REPRESSOR 2
E, F, G, H
19Homo sapiensMutation(s): 0 
Gene Names: NCOR2 (CTG26)
Find proteins for Q9Y618 (Homo sapiens)
Go to Gene View: NCOR2
Go to UniProtKB:  Q9Y618
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
471
Query on 471

Download SDF File 
Download CCD File 
A, B, C, D
N-((2S)-2-({(1Z)-1-METHYL-3-OXO-3-[4-(TRIFLUOROMETHYL) PHENYL]PROP-1-ENYL}AMINO)-3-{4-[2-(5-METHYL-2-PHENYL-1,3-OXAZOL-4-YL)ETHOXY]PHENYL}PROPYL)PROPANAMIDE
C35 H36 F3 N3 O4
TYEFSRMOUXWTDN-DYQICHDWSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
471IC50: 240 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.258 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 103.409α = 90.00
b = 112.773β = 90.00
c = 123.954γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
MAR345data collection
SCALEPACKdata scaling
CNXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-02-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2013-09-18
    Type: Derived calculations
  • Version 1.4: 2017-02-01
    Type: Structure summary
  • Version 1.5: 2017-10-11
    Type: Refinement description