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: 3.00 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.290 

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
  • Structures With Same Primary Citation

  • 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 U S A 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: human, PPARA, NR1C1, PPAR
Find proteins for Q07869 (Homo sapiens)
Go to UniProtKB:  Q07869
NIH Common Fund Data Resources
PHAROS  Q07869
GTEx  ENSG00000186951
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NUCLEAR RECEPTOR CO-REPRESSOR 2
E, F, G, H
19N/AMutation(s): 0 
Find proteins for Q9Y618 (Homo sapiens)
Go to UniProtKB:  Q9Y618
NIH Common Fund Data Resources
PHAROS  Q9Y618
GTEx  ENSG00000196498
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
471
Query on 471
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: 3.00 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.290 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.409α = 90
b = 112.773β = 90
c = 123.954γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNXrefinement
MAR345data collection
SCALEPACKdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-02-20
    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: 2013-09-18
    Changes: Derived calculations
  • Version 1.4: 2017-02-01
    Changes: Structure summary
  • Version 1.5: 2017-10-11
    Changes: Refinement description