5JI0 | pdb_00005ji0

PPARgamma-RXRalpha(S427F) heterodimer in complex with SRC-1, rosiglitazone, and 9-cis-retanoic acid

• PDB DOI: https://doi.org/10.2210/pdb5JI0/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-04-21 Released: 2017-04-26 
• Deposition Author(s): Bloudoff, K., Larsen, N.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 
  0.246 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Literature

PPARgamma-RXRalpha(S427F) heterodimer in complex with SRC-1, rosiglitazone, and 9-cis-retanoic acid

Korpal, M., Zhu, P., Bloudoff, K., Larsen, N.A., Fekkes, P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 64.57 kDa 
• Atom Count: 4,370 
• Modeled Residue Count: 513 
• Deposited Residue Count: 569 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinoic acid receptor RXR-alpha	A	242	Homo sapiens	Mutation(s): 1  Gene Names: RXRA, NR2B1
UniProt & NIH Common Fund Data Resources
Find proteins for P19793 (Homo sapiens) Explore P19793  Go to UniProtKB:  P19793
PHAROS:  P19793 GTEx:  ENSG00000186350

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	B [auth D]	273	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor coactivator 1	C [auth E], D [auth F]	27	Homo sapiens	Mutation(s): 2  EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens) Explore Q15788  Go to UniProtKB:  Q15788
PHAROS:  Q15788 GTEx:  ENSG00000084676

Small Molecules

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

Binding Affinity Annotations
ID	Source	Binding Affinity
9CR	BindingDB:  5JI0	Ki: min: 3.8, max: 583 (nM) from 12 assay(s)
		Kd: min: 1.5, max: 1810 (nM) from 20 assay(s)
		IC50: min: 4, max: 82 (nM) from 5 assay(s)
		EC50: min: 1.5, max: 316 (nM) from 25 assay(s)
BRL	BindingDB:  5JI0	Ki: min: 8, max: 59 (nM) from 7 assay(s)
		Kd: min: 1.2, max: 3380 (nM) from 4 assay(s)
		IC50: min: 7.7, max: 6.00e+4 (nM) from 14 assay(s)
		EC50: min: 0.1, max: 730 (nM) from 47 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free:  0.246 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.88	α = 90
b = 66.527	β = 90
c = 165.927	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-26 
Deposition Author(s): Bloudoff, K., Larsen, N.A.

Revision History  

• Version 1.0: 2017-04-26
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Structure summary