3W67

Crystal structure of mouse alpha-tocopherol transfer protein in complex with alpha-tocopherol and phosphatidylinositol-(3,4)-bisphosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 
    0.260 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.213 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 3PTClick on this verticalbar to view detailsBest fitted VIVClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Impaired alpha-TTP-PIPs interaction underlies familial vitamin E deficiency

Kono, N.Ohto, U.Hiramatsu, T.Urabe, M.Uchida, Y.Satow, Y.Arai, H.

(2013) Science 340: 1106-1110

  • DOI: https://doi.org/10.1126/science.1233508
  • Primary Citation of Related Structures:  
    3W67, 3W68

  • PubMed Abstract: 

    α-Tocopherol (vitamin E) transfer protein (α-TTP) regulates the secretion of α-tocopherol from liver cells. Missense mutations of some arginine residues at the surface of α-TTP cause severe vitamin E deficiency in humans, but the role of these residues is unclear. Here, we found that wild-type α-TTP bound phosphatidylinositol phosphates (PIPs), whereas the arginine mutants did not. In addition, PIPs in the target membrane promoted the intermembrane transfer of α-tocopherol by α-TTP. The crystal structure of the α-TTP-PIPs complex revealed that the disease-related arginine residues interacted with phosphate groups of the PIPs and that the PIPs binding caused the lid of the α-tocopherol-binding pocket to open. Thus, PIPs have a role in promoting the release of a ligand from a lipid-transfer protein.


  • Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-tocopherol transfer protein
A, B, C, D
266Mus musculusMutation(s): 0 
Gene Names: Ttpa
UniProt
Find proteins for Q8BWP5 (Mus musculus)
Explore Q8BWP5 
Go to UniProtKB:  Q8BWP5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8BWP5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3PT
Query on 3PT

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D]
(2R)-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6S)-2,3,6-trihydroxy-4,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dibutanoate
C17 H33 O19 P3
DHAFWWKSHUBGAH-DXOPXGNRSA-N
VIV
Query on VIV

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
K [auth D]
(2R)-2,5,7,8-TETRAMETHYL-2-[(4R,8R)-4,8,12-TRIMETHYLTRIDECYL]CHROMAN-6-OL
C29 H50 O2
GVJHHUAWPYXKBD-IEOSBIPESA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
VIV BindingDB:  3W67 Kd: 2420 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free:  0.260 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.213 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.285α = 100.24
b = 69.665β = 109.72
c = 87.183γ = 100.46
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 3PTClick on this verticalbar to view detailsBest fitted VIVClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-01
    Type: Initial release
  • Version 1.1: 2013-09-04
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description