1FM9

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 GI262570 AND CO-ACTIVATOR PEPTIDES.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.5 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
  • Structures With Same Primary Citation

  • 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 c ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RETINOIC ACID RECEPTOR RXR-ALPHA
A
238Homo sapiensMutation(s): 0 
Gene Names: RXRANR2B1
Find proteins for P19793 (Homo sapiens)
Go to UniProtKB:  P19793
NIH Common Fund Data Resources
PHAROS  P19793
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA
D
272Homo sapiensMutation(s): 0 
Gene Names: PPARGNR1C3
Find proteins for P37231 (Homo sapiens)
Go to UniProtKB:  P37231
NIH Common Fund Data Resources
PHAROS  P37231
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
STEROID RECEPTOR COACTIVATOR
B, E
25N/AMutation(s): 0 
Find proteins for Q15788 (Homo sapiens)
Go to UniProtKB:  Q15788
NIH Common Fund Data Resources
PHAROS  Q15788
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
570
Query on 570

Download CCD File 
D
2-(2-BENZOYL-PHENYLAMINO)-3-{4-[2-(5-METHYL-2-PHENYL-OXAZOL-4-YL)-ETHOXY]-PHENYL}-PROPIONIC ACID
C34 H30 N2 O5
ZZCHHVUQYRMYLW-HKBQPEDESA-N
 Ligand Interaction
9CR
Query on 9CR

Download CCD File 
A
(9cis)-retinoic acid
C20 H28 O2
SHGAZHPCJJPHSC-ZVCIMWCZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
570Ki :  1   nM  PDBBind
9CREC50:  120   nM  BindingDB
9CRKd:  15   nM  BindingDB
9CREC50:  110   nM  BindingDB
9CRKi:  14   nM  BindingDB
9CREC50:  6   nM  BindingDB
9CRKd:  50   nM  BindingDB
9CRKi:  11   nM  BindingDB
9CRKi:  13   nM  BindingDB
9CRIC50:  82   nM  BindingDB
9CREC50:  10   nM  BindingDB
9CREC50:  13   nM  BindingDB
9CREC50:  200   nM  BindingDB
570EC50:  0.3400000035762787   nM  BindingDB
9CRKd:  11   nM  BindingDB
9CRKd:  8   nM  BindingDB
570Ki:  1.1699999570846558   nM  BindingDB
9CRKd:  9   nM  BindingDB
9CREC50:  316   nM  BindingDB
9CRKi:  8.399999618530273   nM  BindingDB
9CREC50:  1.5   nM  BindingDB
9CRKd:  14   nM  BindingDB
9CRKd:  13   nM  BindingDB
570IC50:  217   nM  BindingDB
9CRIC50:  32   nM  BindingDB
9CRIC50:  29   nM  BindingDB
9CREC50:  4.5   nM  BindingDB
570EC50:  0.3499999940395355   nM  BindingDB
9CRKd:  35   nM  BindingDB
9CRKd:  30   nM  BindingDB
9CREC50:  29   nM  BindingDB
570Ki:  1   nM  Binding MOAD
9CRKi:  3.799999952316284   nM  BindingDB
9CRKi:  9   nM  BindingDB
9CREC50:  2.5999999046325684   nM  BindingDB
9CREC50:  124   nM  BindingDB
570EC50:  5   nM  BindingDB
9CRKd:  3   nM  BindingDB
9CRKd:  16   nM  BindingDB
9CREC50:  100   nM  BindingDB
570EC50:  6   nM  BindingDB
9CRKd:  14   nM  BindingDB
9CREC50:  120   nM  BindingDB
9CRKd:  15   nM  BindingDB
9CRKd:  32   nM  BindingDB
9CRKd:  12   nM  BindingDB
9CRIC50:  12   nM  BindingDB
9CRKd:  1560   nM  BindingDB
9CRKd:  4   nM  BindingDB
9CREC50:  195   nM  BindingDB
9CRKd:  1810   nM  BindingDB
9CREC50:  250   nM  BindingDB
9CRKi:  8   nM  BindingDB
9CREC50:  219   nM  BindingDB
9CRIC50:  4   nM  BindingDB
9CREC50:  140   nM  BindingDB
9CRKi:  12   nM  BindingDB
570EC50:  0.6000000238418579   nM  BindingDB
570EC50:  1.5   nM  BindingDB
9CREC50:  200   nM  BindingDB
9CRKi:  7.400000095367432   nM  BindingDB
570Ki:  1.100000023841858   nM  BindingDB
9CREC50:  128   nM  BindingDB
9CRKd:  240   nM  BindingDB
570EC50:  4   nM  BindingDB
9CREC50:  4.300000190734863   nM  BindingDB
9CRKd:  1.5   nM  BindingDB
570IC50:  25   nM  BindingDB
9CRKi:  27   nM  BindingDB
570EC50:  3   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.239 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.143α = 90
b = 54.046β = 90
c = 211.149γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
CNSrefinement
MAR345data collection
HKL-2000data scaling
X-PLORphasing

Structure Validation

View Full Validation Report



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
  • Version 1.5: 2018-01-31
    Changes: Experimental preparation