Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer -A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer -A2 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 128064.36 
• Atom Count: 8386 
• Residue Count: 1120 
• Unique protein chains: 3

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.

• DOI: 10.2210/pdb1FM6/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2000-08-16 Released: 2001-02-16 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.292 
• R-Value Work: 0.250 

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

• PubMed: 10882139 
• Primary Citation of Related Structures:  
  1FM9
• Also Cited By: 3D6D, 3B3K


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
RETINOIC ACID RECEPTOR RXR-ALPHA	A, U	238	Homo sapiens	Mutation(s): 0  Gene Names: RXRA (NR2B1)
Find proteins for P19793 (Homo sapiens) Go to Gene View: RXRA Go to UniProtKB:  P19793

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA	D, X	272	Homo sapiens	Mutation(s): 0  Gene Names: PPARG (NR1C3)
Find proteins for P37231 (Homo sapiens) Go to Gene View: PPARG Go to UniProtKB:  P37231

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
STEROID RECEPTOR COACTIVATOR	B, V, E, Y	25	Homo sapiens	Mutation(s): 0  Gene Names: NCOA1 (BHLHE74, SRC1) EC: 2.3.1.48
Find proteins for Q15788 (Homo sapiens) Go to Gene View: NCOA1 Go to UniProtKB:  Q15788

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
BRL	D, X	2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL) BRL49653; ROSIGLITAZONE C18 H19 N3 O3 S YASAKCUCGLMORW-HNNXBMFYSA-N
9CR	A, U	(9cis)-retinoic acid C20 H28 O2 SHGAZHPCJJPHSC-ZVCIMWCZSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
BRL	Ki: 8 - 47 nM (100) BINDINGDB
BRL	EC50: 1 - 260 nM (100) BINDINGDB
9CR	EC50: 1.5 - 316 nM (100) BINDINGDB
9CR	IC50: 4 - 82 nM (86) BINDINGDB
BRL	IC50: 1 - 292 nM (100) BINDINGDB
9CR	Kd: 1.5 - 1810 nM (100) BINDINGDB
9CR	Ki: 3.8 - 27 nM (87) BINDINGDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.292 
• R-Value Work: 0.250 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 49.255	α = 90.00
b = 222.364	β = 98.59
c = 55.289	γ = 90.00

Software Package:

Software Name	Purpose
MAR345	data collection
AMoRE	phasing
CNS	refinement
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-08-16 
• Released Date: 2001-02-16 
• Deposition Author(s): 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.

Revision History 

• Version 1.0: 2001-02-16
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2012-12-26
  Type: Non-polymer description
• Version 1.4: 2017-10-04
  Type: Refinement description