Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 36.82 kDa 
• Atom Count: 2450 
• Modelled Residue Count: 273 
• Deposited Residue Count: 316 
• Unique protein chains: 1

1M13

Crystal Structure of the Human Pregane X Receptor Ligand Binding Domain in Complex with Hyperforin, a Constituent of St. John's Wort

• DOI: 10.2210/pdb1M13/pdb

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


• Deposited: 2002-06-17 Released: 2003-03-04 
• Deposition Author(s): Watkins, R.E., Maglich, J.M., Moore, L.B., Wisely, G.B., Noble, S.M., Davis-Searles, P.R., Lambert, M.H., Kliewer, S.A., Redinbo, M.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.246 
• R-Value Work: 0.212 
• R-Value Observed: 0.212 

Literature

2.1 A Crystal Structure of Human PXR in Complex with the St. John's Wort Compound Hyperforin

Watkins, R.E., Maglich, J.M., Moore, L.B., Wisely, G.B., Noble, S.M., Davis-Searles, P.R., Lambert, M.H., Kliewer, S.A., Redinbo, M.R.

(2003) Biochemistry 42: 1430-1438

• PubMed: 12578355 
• DOI: 10.1021/bi0268753
• Primary Citation of Related Structures:  
  1M13


• PubMed Abstract: 
  

The nuclear xenobiotic receptor PXR is activated by a wide variety of clinically used drugs and serves as a master regulator of drug metabolism and excretion gene expression in mammals. St. John's wort is used widely in Europe and the United States to treat depression. This unregulated herbal remedy leads to dangerous drug-drug interactions, however, in patients taking oral contraceptives, antivirals, or immunosuppressants. Such interactions are caused by the activation of the human PXR by hyperforin, the psychoactive agent in St. John's wort. In this study, we show that hyperforin induces the expression of numerous drug metabolism and excretion genes in primary human hepatocytes. We present the 2.1 A crystal structure of hyperforin in complex with the ligand binding domain of human PXR. Hyperforin induces conformational changes in PXR's ligand binding pocket relative to structures of human PXR elucidated previously and increases the size of the pocket by 250 A(3). We find that the mutation of individual aromatic residues within the ligand binding cavity changes PXR's response to particular ligands. Taken together, these results demonstrate that PXR employs structural flexibility to expand the chemical space it samples and that the mutation of specific residues within the ligand binding pocket of PXR tunes the receptor's response to ligands.

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Organizational Affiliation: 

Department of Chemistry, The University of North Carolina at Chapel Hill, North Carolina 27599, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orphan Nuclear Receptor PXR	A	316	Homo sapiens	Mutation(s): 0  Gene Names: NR1I2 or PXR, NR1I2, PXR
Find proteins for O75469 (Homo sapiens) Explore O75469  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
HYF	A	4-HYDROXY-5-ISOBUTYRYL-6-METHYL-1,3,7-TRIS-(3-METHYL-BUT-2-ENYL)-6-(4-METHYL-PENT-3-ENYL)-BICYCLO[3.3.1]NON-3-ENE-2,9-DIONE C35 H52 O4 IWBJJCOKGLUQIZ-OJCNYLSASA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
HYF	Kd:  27   nM  Binding MOAD
HYF	Kd :  27   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.246 
• R-Value Work: 0.212 
• R-Value Observed: 0.212 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.372	α = 90
b = 91.372	β = 90
c = 85.645	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-06-17 
• Released Date: 2003-03-04 
Deposition Author(s): Watkins, R.E., Maglich, J.M., Moore, L.B., Wisely, G.B., Noble, S.M., Davis-Searles, P.R., Lambert, M.H., Kliewer, S.A., Redinbo, M.R.

Revision History  

• Version 1.0: 2003-03-04
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance