Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 133.21 kDa 
• Atom Count: 9606 
• Modelled Residue Count: 1152 
• Deposited Residue Count: 1152 
• Unique protein chains: 2

1KKQ

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

• DOI: 10.2210/pdb1KKQ/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2001-12-10 Released: 2002-02-20 
• Deposition Author(s): Xu, H.E., Stanley, T.B., Montana, V.G., Lambert, M.H., Shearer, B.G., Cobb, J.E., McKee, D.D., Galardi, C.M., Nolte, R.T., Parks, D.J.

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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 

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

• PubMed: 11845213 
• DOI: 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.

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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

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Organizational Affiliation: 

Nuclear Receptor Discovery Research, GlaxoSmithKline, Research Triangle Park, NC 27709, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR	A, B, C, D	269	Homo sapiens	Mutation(s): 0  Gene Names: human, PPARA, NR1C1, PPAR
Find proteins for Q07869 (Homo sapiens) Explore Q07869  Go to UniProtKB:  Q07869
NIH Common Fund Data Resources
PHAROS:  Q07869 GTEx:  ENSG00000186951

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NUCLEAR RECEPTOR CO-REPRESSOR 2	E, F, G, H	19	N/A	Mutation(s): 0
Find proteins for Q9Y618 (Homo sapiens) Explore Q9Y618  Go to UniProtKB:  Q9Y618
NIH Common Fund Data Resources
PHAROS:  Q9Y618 GTEx:  ENSG00000196498

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
471	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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
471	IC50 :  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 = 103.409	α = 90
b = 112.773	β = 90
c = 123.954	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNX	refinement
MAR345	data collection
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-12-10 
• Released Date: 2002-02-20 
Deposition Author(s): Xu, H.E., Stanley, T.B., Montana, V.G., Lambert, M.H., Shearer, B.G., Cobb, J.E., McKee, D.D., Galardi, C.M., Nolte, R.T., Parks, D.J.

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