6OHU

Structure of EBP and tamoxifen


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.526 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.273 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis for human sterol isomerase in cholesterol biosynthesis and multidrug recognition.

Long, T.Hassan, A.Thompson, B.M.McDonald, J.G.Wang, J.Li, X.

(2019) Nat Commun 10: 2452-2452

  • DOI: 10.1038/s41467-019-10279-w
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 3-β-hydroxysteroid-Δ <sup>8 </sup>, Δ <sup>7 </sup>-isomerase, known as Emopamil-Binding Protein (EBP), is an endoplasmic reticulum membrane protein involved in cholesterol biosynthesis, autophagy, oligodendrocyte formation. The mutation on EBP can c ...

    3-β-hydroxysteroid-Δ 8 , Δ 7 -isomerase, known as Emopamil-Binding Protein (EBP), is an endoplasmic reticulum membrane protein involved in cholesterol biosynthesis, autophagy, oligodendrocyte formation. The mutation on EBP can cause Conradi-Hunermann syndrome, an inborn error. Interestingly, EBP binds an abundance of structurally diverse pharmacologically active compounds, causing drug resistance. Here, we report two crystal structures of human EBP, one in complex with the anti-breast cancer drug tamoxifen and the other in complex with the cholesterol biosynthesis inhibitor U18666A. EBP adopts an unreported fold involving five transmembrane-helices (TMs) that creates a membrane cavity presenting a pharmacological binding site that accommodates multiple different ligands. The compounds exploit their positively-charged amine group to mimic the carbocationic sterol intermediate. Mutagenesis studies on specific residues abolish the isomerase activity and decrease the multidrug binding capacity. This work reveals the catalytic mechanism of EBP-mediated isomerization in cholesterol biosynthesis and how this protein may act as a multi-drug binder.


    Organizational Affiliation

    Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA. xiaochun.li@utsouthwestern.edu.,Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.,State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA. xiaochun.li@utsouthwestern.edu.,Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-beta-hydroxysteroid-Delta(8),Delta(7)-isomerase
A, B, C
238Homo sapiensMutation(s): 0 
Gene Names: EBP
EC: 5.3.3.5
Find proteins for Q15125 (Homo sapiens)
Go to Gene View: EBP
Go to UniProtKB:  Q15125
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CTX
Query on CTX

Download SDF File 
Download CCD File 
A, B, C
(Z)-2-[4-(1,2)-DIPHENYL-1-BUTENYL)-PHENOXY]-N,N-DIMETHYLETHANAMINE
TRANS FORM OF TAMOXIFEN
C26 H29 N O
NKANXQFJJICGDU-QPLCGJKRSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.526 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.273 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 192.837α = 90.00
b = 66.829β = 90.00
c = 98.678γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data scaling
PHENIXphasing
PHENIXrefinement
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2019-04-06 
  • Released Date: 2019-06-19 
  • Deposition Author(s): Long, T., Li, X.

Revision History 

  • Version 1.0: 2019-06-19
    Type: Initial release