6DGP | pdb_00006dgp

Crystal Structure of Human PPARgamma Ligand Binding Domain in Complex with TRAP220 Coactivator Peptide

• PDB DOI: https://doi.org/10.2210/pdb6DGP/pdb

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


• Deposited: 2018-05-17 Released: 2019-05-22 
• 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: 3.10 Å
• R-Value Free: 
  0.294 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Human PPARgamma Ligand Binding Domain in Complex with TRAP220 Coactivator Peptide

Shang, J., Kojetin, D.J.

To be published.

Biological Assembly 1  

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

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 72.7 kDa 
• Atom Count: 4,346 
• Modeled Residue Count: 542 
• Deposited Residue Count: 632 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	A, B	297	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
TRAP220 Coactivator Peptide (Mediator of RNA polymerase II transcription subunit 1)	C, D	19	Homo sapiens	Mutation(s): 0  Gene Names: MED1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.294 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.09	α = 90
b = 54.73	β = 90.05
c = 123.471	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-05-22 
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: 2019-05-22
  Type: Initial release
  
• Version 1.1: 2019-12-25
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description