3HVL

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

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

  • DOI: 10.1093/protein/gzn017
  • Primary Citation of Related Structures:  

  • 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 protei ...

    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.

    Organizational Affiliation: 

    Structural Chemistry Department, Schering-Plough Research Institute, Kenilworth, NJ 07033, USA. wenyan.wang@spcorp.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pregnane X receptor, Linker, Steroid receptor coactivator 1
A, B
344Homo sapiensMutation(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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SRL
Query on SRL
Download SDF File 
Download CCD File 
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
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 85.440α = 90.00
b = 88.840β = 90.00
c = 105.390γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata reduction
BUSTER-TNTrefinement
CrystalCleardata scaling
BUSTER-TNTphasing
CrystalCleardata collection

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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