Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 79.38 kDa 
• Atom Count: 5056 
• Residue Count: 576 
• Unique protein chains: 1

3HVL

Tethered PXR-LBD/SRC-1p complexed with SR-12813

• DOI: 10.2210/pdb3HVL/pdb
• Entry: 3HVL supersedes: 3CTC

• Classification: Transcription, Transferase
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-06-16 Released: 2009-08-04 
• Deposition Author(s): Lesburg, C.A., Wang, W., Prosise, W.W., Chen, J., Taremi, S.S., Le, H.V., Madison, V., Cui, X., Thomas, A., Cheng, K.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.265 
• R-Value Work: 0.220 
• R-Value Observed: 0.223 

Literature

Construction and characterization of a fully active PXR/SRC-1 tethered protein with increased stability

Wang, W., Prosise, W.W., Chen, J., Taremi, S.S., Le, H.V., Madison, V., Cui, X., Thomas, A., Cheng, K.C., Lesburg, C.A.

(2008) Protein Eng Des Sel 21: 425-433

• PubMed: 18456871 
• DOI: 10.1093/protein/gzn017
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The nuclear xenobiotic receptor PXR is a ligand-inducible transcription factor regulating drug-metabolizing enzymes and transporters and a master switch mediating potentially adverse drug-drug interactions. In addition to binding a coactivator protein such as SRC-1, the C-terminal ligand-binding domain (LBD) is solely responsible for ligand recognition and thus the ligand-dependent downstream effects. In an effort to facilitate structural studies of PXR to understand and abolish the interactions between PXR and its ligands, several recombinant PXR/SRC-1 constructs were designed and evaluated for expression, stability and activity. Expression strategies employing either dual expression or translationally coupled bicistronic expression were found to be unsuitable for producing stable PXR in a stochiometric complex with a peptide derived from SRC-1 (SRC-1p). A single polypeptide chain encompassing PXR and SRC-1p tethered with a peptidyl linker was designed to promote intramolecular complex formation. This tethered protein was overexpressed as a soluble protein and required no additional SRC-1p for further stabilization. X-ray crystal structures in the presence and absence of the known PXR agonist SR-12813 were determined to high resolution. In addition, a circular dichroism-based binding assay was developed to allow rapid evaluation of PXR ligand affinity, making this tethered protein a convenient and effective reagent for the rational attenuation of drug-induced PXR-mediated metabolism.

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Organizational Affiliation: 

Structural Chemistry Department, Schering-Plough Research Institute, Kenilworth, NJ 07033, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Pregnane X receptor, Linker, Steroid receptor coactivator 1	A, B	344	Homo sapiens	Mutation(s): 0  Gene Names: NR1I2, PXR EC: 2.3.1.48
Find proteins for Q15788 (Homo sapiens) Go to UniProtKB:  Q15788
NIH Common Fund Data Resources
PHAROS  Q15788 GTEx  ENSG00000084676
Find proteins for O75469 (Homo sapiens) Go to UniProtKB:  O75469
NIH Common Fund Data Resources
PHAROS  O75469 GTEx  ENSG00000144852

Small Molecules

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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
SRL	EC50:  80   nM  BindingDB
SRL	EC50:  440   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.265 
• R-Value Work: 0.220 
• R-Value Observed: 0.223 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.44	α = 90
b = 88.84	β = 90
c = 105.39	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
BUSTER-TNT	refinement
CrystalClear	data reduction
CrystalClear	data scaling
BUSTER-TNT	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-06-16 
• Released Date: 2009-08-04 
Deposition Author(s): Lesburg, C.A., Wang, W., Prosise, W.W., Chen, J., Taremi, S.S., Le, H.V., Madison, V., Cui, X., Thomas, A., Cheng, K.C.
• This entry supersedes: 3CTC

Revision History 

• Version 1.0: 2009-08-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-04-02
  Changes: Source and taxonomy
• Version 1.3: 2017-08-16
  Changes: Refinement description, Source and taxonomy