Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 34.00 kDa 
• Atom Count: 2314 
• Modelled Residue Count: 272 
• Deposited Residue Count: 294 
• Unique protein chains: 2

6ONJ

Crystal structure of PPARgamma ligand binding domain in complex with TRAP220 peptide and agonist rosiglitazone

• PDB DOI: 10.2210/pdb6ONJ/pdb

• Classification: transcription/agonist
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): No 


• Deposited: 2019-04-22 Released: 2020-03-04 
• Deposition Author(s): Shang, J., Kojetin, D.J.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.273 
• R-Value Work: 0.212 
• R-Value Observed: 0.218 

Literature

A molecular switch regulating transcriptional repression and activation of PPAR gamma.

Shang, J., Mosure, S.A., Zheng, J., Brust, R., Bass, J., Nichols, A., Solt, L.A., Griffin, P.R., Kojetin, D.J.

(2020) Nat Commun 11: 956-956

• PubMed: 32075969 
• DOI: 10.1038/s41467-020-14750-x
• Primary Citation of Related Structures:  
  6ONI, 6ONJ, 6PDZ


• PubMed Abstract: 
  

Nuclear receptor (NR) transcription factors use a conserved activation function-2 (AF-2) helix 12 mechanism for agonist-induced coactivator interaction and NR transcriptional activation. In contrast, ligand-induced corepressor-dependent NR repression appears to occur through structurally diverse mechanisms. We report two crystal structures of peroxisome proliferator-activated receptor gamma (PPARγ) in an inverse agonist/corepressor-bound transcriptionally repressive conformation. Helix 12 is displaced from the solvent-exposed active conformation and occupies the orthosteric ligand-binding pocket enabled by a conformational change that doubles the pocket volume. Paramagnetic relaxation enhancement (PRE) NMR and chemical crosslinking mass spectrometry confirm the repressive helix 12 conformation. PRE NMR also defines the mechanism of action of the corepressor-selective inverse agonist T0070907, and reveals that apo-helix 12 exchanges between transcriptionally active and repressive conformations-supporting a fundamental hypothesis in the NR field that helix 12 exchanges between transcriptionally active and repressive conformations.

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Organizational Affiliation: 

Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	A	275	Homo sapiens	Mutation(s): 0  Gene Names: PPARG, NR1C3
UniProt & NIH Common Fund Data Resources
Find proteins for P37231 (Homo sapiens) Explore P37231  Go to UniProtKB:  P37231
PHAROS:  P37231 GTEx:  ENSG00000132170

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 1, TRAP220 Coactivator Peptide	B [auth C]	19	Homo sapiens	Mutation(s): 0  Gene Names:  MED1, ARC205, CRSP1, CRSP200, DRIP205, DRIP230, PBP, PPARBP, PPARGBP, RB18A, TRAP220, TRIP2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15648 (Homo sapiens) Explore Q15648  Go to UniProtKB:  Q15648
PHAROS:  Q15648 GTEx:  ENSG00000125686

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BRL (Subject of Investigation/LOI)	C [auth A]	2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL) C18 H19 N3 O3 S YASAKCUCGLMORW-HNNXBMFYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BRL	BindingDB:  6ONJ	Ki: min: 8, max: 59 (nM) from 5 assay(s)
		Kd: min: 0.14, max: 48 (nM) from 3 assay(s)
		IC50: min: 1, max: 298 (nM) from 10 assay(s)
		EC50: min: 1, max: 1600 (nM) from 35 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.273 
• R-Value Work: 0.212 
• R-Value Observed: 0.218 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.386	α = 90
b = 85.574	β = 90
c = 121.629	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
DIALS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-04-22 
• Released Date: 2020-03-04 
Deposition Author(s): Shang, J., Kojetin, D.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	R01DK101871

Revision History  

• Version 1.0: 2020-03-04
  Type: Initial release