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 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.6 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: https://doi.org/10.1038/415813a
  • Primary Citation of Related Structures:  
    1KKQ

  • 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-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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR
A, B, C, D
269Homo sapiensMutation(s): 0 
Gene Names: human
UniProt & NIH Common Fund Data Resources
Find proteins for Q07869 (Homo sapiens)
Explore Q07869 
Go to UniProtKB:  Q07869
PHAROS:  Q07869
GTEx:  ENSG00000186951 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07869
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NUCLEAR RECEPTOR CO-REPRESSOR 2
E, F, G, H
19N/AMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y618 (Homo sapiens)
Explore Q9Y618 
Go to UniProtKB:  Q9Y618
PHAROS:  Q9Y618
GTEx:  ENSG00000196498 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y618
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
471
Query on 471

Download Ideal Coordinates CCD File 
I [auth A],
J [auth B],
K [auth C],
L [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
471 PDBBind:  1KKQ IC50: 240 (nM) from 1 assay(s)
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

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.6: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description