1FM6

THE 2.1 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF THE HETERODIMER OF THE HUMAN RXRALPHA AND PPARGAMMA LIGAND BINDING DOMAINS RESPECTIVELY BOUND WITH 9-CIS RETINOIC ACID AND ROSIGLITAZONE AND CO-ACTIVATOR PEPTIDES.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.250 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Asymmetry in the PPARgamma/RXRalpha crystal structure reveals the molecular basis of heterodimerization among nuclear receptors.

Gampe Jr., R.T., Montana, V.G., Lambert, M.H., Miller, A.B., Bledsoe, R.K., Milburn, M.V., Kliewer, S.A., Willson, T.M., Xu, H.E.

(2000) Mol Cell 5: 545-555

  • DOI: 10.1016/s1097-2765(00)80448-7
  • Primary Citation of Related Structures:  
    1FM6, 1FM9

  • PubMed Abstract: 

    • The nuclear receptor PPARgamma/RXRalpha heterodimer regulates glucose and lipid homeostasis and is the target for the antidiabetic drugs GI262570 and the thiazolidinediones (TZDs). We report the crystal structures of the PPARgamma and RXRalpha LBDs compl ...

    The nuclear receptor PPARgamma/RXRalpha heterodimer regulates glucose and lipid homeostasis and is the target for the antidiabetic drugs GI262570 and the thiazolidinediones (TZDs). We report the crystal structures of the PPARgamma and RXRalpha LBDs complexed to the RXR ligand 9-cis-retinoic acid (9cRA), the PPARgamma agonist rosiglitazone or GI262570, and coactivator peptides. The PPARgamma/RXRalpha heterodimer is asymmetric, with each LBD deviated approximately 10 degrees from the C2 symmetry, allowing the PPARgamma AF-2 helix to interact with helices 7 and 10 of RXRalpha. The heterodimer interface is composed of conserved motifs in PPARgamma and RXRalpha that form a coiled coil along helix 10 with additional charge interactions from helices 7 and 9. The structures provide a molecular understanding of the ability of RXR to heterodimerize with many nuclear receptors and of the permissive activation of the PPARgamma/RXRbeta heterodimer by 9cRA.

    Organizational Affiliation: 

    Glaxo Wellcome Research and Development, Research Triangle Park, North Carolina 27709, USA.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RETINOIC ACID RECEPTOR RXR-ALPHA A, U238Homo sapiensMutation(s): 0 
Gene Names: RXRA, NR2B1
Find proteins for P19793 (Homo sapiens)
Explore P19793 
Go to UniProtKB:  P19793
NIH Common Fund Data Resources
PHAROS:  P19793
GTEx:  ENSG00000186350
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA D, X272Homo sapiensMutation(s): 0 
Gene Names: PPARG, NR1C3
Find proteins for P37231 (Homo sapiens)
Explore P37231 
Go to UniProtKB:  P37231
NIH Common Fund Data Resources
PHAROS:  P37231
GTEx:  ENSG00000132170
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
STEROID RECEPTOR COACTIVATOR B, E, V, Y25N/AMutation(s): 0 
Find proteins for Q15788 (Homo sapiens)
Explore Q15788 
Go to UniProtKB:  Q15788
NIH Common Fund Data Resources
PHAROS:  Q15788
GTEx:  ENSG00000084676
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BRL
Query on BRL
Download Ideal Coordinates CCD File 
D, X
2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL)
C18 H19 N3 O3 S
YASAKCUCGLMORW-HNNXBMFYSA-N		 Ligand Interaction
9CR
Query on 9CR
Download Ideal Coordinates CCD File 
A, U
(9cis)-retinoic acid
C20 H28 O2
SHGAZHPCJJPHSC-ZVCIMWCZSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
9CRKd:  14   nM  BindingDB
9CREC50:  200   nM  BindingDB
BRLKi:  47   nM  BindingDB
9CRKd:  13   nM  BindingDB
BRLIC50:  38   nM  BindingDB
9CRKi:  11   nM  BindingDB
9CREC50:  1.5   nM  BindingDB
9CRKi:  14   nM  BindingDB
9CRKd:  8   nM  BindingDB
9CREC50:  316   nM  BindingDB
BRLEC50:  240   nM  BindingDB
9CRKi:  13   nM  BindingDB
9CRKd:  9   nM  BindingDB
BRLEC50:  1   nM  BindingDB
BRLEC50:  260   nM  BindingDB
BRLKi:  27   nM  BindingDB
BRLEC50:  300   nM  BindingDB
BRLEC50:  316   nM  BindingDB
BRLEC50:  326   nM  BindingDB
9CRKi:  8.399999618530273   nM  BindingDB
BRLEC50:  332   nM  BindingDB
BRLEC50:  396   nM  BindingDB
9CRKi:  27   nM  BindingDB
BRLEC50:  39   nM  BindingDB
BRLEC50:  40   nM  BindingDB
9CREC50:  4.5   nM  BindingDB
9CRKd:  50   nM  BindingDB
9CRKd:  30   nM  BindingDB
BRLEC50:  52   nM  BindingDB
9CRIC50:  82   nM  BindingDB
9CREC50:  6   nM  BindingDB
9CRIC50:  29   nM  BindingDB
9CRIC50:  32   nM  BindingDB
9CREC50:  13   nM  BindingDB
9CREC50:  29   nM  BindingDB
BRLEC50:  83   nM  BindingDB
BRLEC50:  87   nM  BindingDB
BRLEC50:  89   nM  BindingDB
BRLEC50:  95   nM  BindingDB
BRLEC50:  100   nM  BindingDB
BRLEC50:  114   nM  BindingDB
BRLEC50:  117   nM  BindingDB
BRLEC50:  120   nM  BindingDB
9CREC50:  10   nM  BindingDB
9CRKi:  9   nM  BindingDB
9CRKi:  12   nM  BindingDB
9CRKd:  240   nM  BindingDB
BRLEC50:  10   nM  BindingDB
9CRKi:  8   nM  BindingDB
9CRKd:  14   nM  BindingDB
9CRKd:  32   nM  BindingDB
9CRKd:  12   nM  BindingDB
BRLEC50:  30   nM  BindingDB
9CREC50:  2.5999999046325684   nM  BindingDB
9CRKi:  7.400000095367432   nM  BindingDB
BRLEC50:  20   nM  BindingDB
9CRKd:  1.5   nM  BindingDB
BRLIC50:  1   nM  BindingDB
9CRKd:  16   nM  BindingDB
BRLIC50:  292   nM  BindingDB
BRLKd:  1.2000000476837158   nM  BindingDB
9CRKd:  15   nM  BindingDB
BRLIC50:  298   nM  BindingDB
9CREC50:  4.300000190734863   nM  BindingDB
9CRKd:  35   nM  BindingDB
9CRKd:  4   nM  BindingDB
9CREC50:  120   nM  BindingDB
BRLIC50:  159   nM  BindingDB
9CREC50:  200   nM  BindingDB
9CRIC50:  12   nM  BindingDB
9CRKd:  3   nM  BindingDB
9CRKd:  15   nM  BindingDB
BRLIC50:  112   nM  BindingDB
9CREC50:  100   nM  BindingDB
9CRKi:  3.799999952316284   nM  BindingDB
BRLIC50:  103   nM  BindingDB
BRLKi:  8   nM  BindingDB
BRLEC50:  4   nM  BindingDB
9CRKd:  11   nM  BindingDB
9CREC50:  110   nM  BindingDB
BRLEC50:  1100   nM  BindingDB
9CRKd:  1810   nM  BindingDB
9CREC50:  250   nM  BindingDB
BRLKd:  0.14000000059604645   nM  BindingDB
9CREC50:  140   nM  BindingDB
9CRKd:  1560   nM  BindingDB
9CREC50:  128   nM  BindingDB
BRLIC50:  76   nM  BindingDB
BRLEC50:  1600   nM  BindingDB
9CREC50:  195   nM  BindingDB
9CRIC50:  4   nM  BindingDB
9CREC50:  124   nM  BindingDB
9CREC50:  219   nM  BindingDB
9CREC50:  120   nM  BindingDB
BRLEC50:  8   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.250 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.255α = 90
b = 222.364β = 98.59
c = 55.289γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
MAR345data collection
HKL-2000data scaling

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-02-16
    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: 2012-12-26
    Changes: Non-polymer description
  • Version 1.4: 2017-10-04
    Changes: Refinement description