Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 4-mer -A4 

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

Macromolecule Content

• Total Structure Weight: 136082.34 
• Atom Count: 8611 
• Residue Count: 1200 
• Unique protein chains: 2

4J5X

Crystal Structure of the SR12813-bound PXR/RXRalpha LBD Heterotetramer Complex

• DOI: 10.2210/pdb4J5X/pdb

• Classification: Retinoic acid-binding protein
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2013-02-10 Released: 2013-08-21 
• Deposition Author(s): Wallace, B.D., Betts, L., Redinbo, M.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.298 
• R-Value Work: 0.245 

Literature

Structural and Functional Analysis of the Human Nuclear Xenobiotic Receptor PXR in Complex with RXRalpha.

Wallace, B.D., Betts, L., Talmage, G., Pollet, R.M., Holman, N.S., Redinbo, M.R.

(2013) J.Mol.Biol. 425: 2561-2577

• PubMed: 23602807 
• DOI: 10.1016/j.jmb.2013.04.012
• Primary Citation of Related Structures:  
  4J5W


• PubMed Abstract: 
  

The human nuclear xenobiotic receptor PXR recognizes a range of potentially harmful drugs and endobiotic chemicals but must complex with the nuclear receptor RXRα to control the expression of numerous drug metabolism genes. To date, the structural basis and functional consequences of this interaction have remained unclear. Here we present 2.8-Å-resolution crystal structures of the heterodimeric complex formed between the ligand-binding domains of human PXR and RXRα. These structures establish that PXR and RXRα form a heterotetramer unprecedented in the nuclear receptor family of ligand-regulated transcription factors. We further show that both PXR and RXRα bind to the transcriptional coregulator SRC-1 with higher affinity when they are part of the PXR/RXRα heterotetramer complex than they do when each ligand-binding domain is examined alone. Furthermore, we purify the full-length forms of each receptor from recombinant bacterial expression systems and characterize their interactions with a range of direct and everted repeat DNA elements. Taken together, these data advance our understanding of PXR, the master regulator of drug metabolism gene expression in humans, in its functional partnership with RXRα.

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Organizational Affiliation: 

Department of Chemistry, Biochemistry and Microbiology, University of North Carolina at Chapel Hill, 250 Bell Tower Drive, Chapel Hill, NC 27599, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Retinoic acid receptor RXR-alpha, Nuclear receptor coactivator 1	D, C	264	Homo sapiens	Mutation(s): 0  Gene Names: RXRA (NR2B1), NCOA1 (BHLHE74, SRC1) EC: 2.3.1.48
Find proteins for P19793 (Homo sapiens) Go to Gene View: RXRA Go to UniProtKB:  P19793
Find proteins for Q15788 (Homo sapiens) Go to Gene View: NCOA1 Go to UniProtKB:  Q15788

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Nuclear receptor subfamily 1 group I member 2, Nuclear receptor coactivator 1	A, B	336	Homo sapiens	Mutation(s): 0  Gene Names: NR1I2 (PXR), NCOA1 (BHLHE74, SRC1) EC: 2.3.1.48
Find proteins for O75469 (Homo sapiens) Go to Gene View: NR1I2 Go to UniProtKB:  O75469
Find proteins for Q15788 (Homo sapiens) Go to Gene View: NCOA1 Go to UniProtKB:  Q15788

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SRL	A, B	[2-(3,5-DI-TERT-BUTYL-4-HYDROXY-PHENYL)-1-(DIETHOXY-PHOSPHORYL)-VINYL]-PHOSPHONIC ACID DIETHLYL ESTER SR12813 C24 H42 O7 P2 YQLJDECYQDRSBI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.298 
• R-Value Work: 0.245 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 70.090	α = 90.00
b = 120.300	β = 90.00
c = 175.790	γ = 90.00

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
JBluIce-EPICS	data collection
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-02-10 
• Released Date: 2013-08-21 
• Deposition Author(s): Wallace, B.D., Betts, L., Redinbo, M.R.

Revision History 

• Version 1.0: 2013-08-21
  Type: Initial release
• Version 1.1: 2017-08-16
  Type: Source and taxonomy
• Version 1.2: 2017-11-15
  Type: Refinement description