Crystal structure of human VAT-1

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.222 

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Structural basis for interorganelle phospholipid transport mediated by VAT-1.

Watanabe, Y.Tamura, Y.Kakuta, C.Watanabe, S.Endo, T.

(2020) J Biol Chem 295: 3257-3268

  • DOI: https://doi.org/10.1074/jbc.RA119.011019
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Eukaryotic cells are compartmentalized to form organelles, whose functions rely on proper phospholipid and protein transport. Here we determined the crystal structure of human VAT-1, a cytosolic soluble protein that was suggested to transfer phosphatidylserine, at 2.2 Å resolution. We found that VAT-1 transferred not only phosphatidylserine but also other acidic phospholipids between membranes in vitro Structure-based mutational analyses showed the presence of a possible lipid-binding cavity at the interface between the two subdomains, and two tyrosine residues in the flexible loops facilitated phospholipid transfer, likely by functioning as a gate to this lipid-binding cavity. We also found that a basic and hydrophobic loop with two tryptophan residues protruded from the molecule and facilitated binding to the acidic-lipid membranes, thereby achieving efficient phospholipid transfer.

  • Organizational Affiliation

    Department of Bioscience, Graduate School of Agriculture, Ehime University, Matsuyama, Ehime 790-8566, Japan; Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto 603-8555, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Synaptic vesicle membrane protein VAT-1 homolog
A, B, C, D
357Homo sapiensMutation(s): 0 
Gene Names: VAT1
EC: 1
UniProt & NIH Common Fund Data Resources
Find proteins for Q99536 (Homo sapiens)
Explore Q99536 
Go to UniProtKB:  Q99536
PHAROS:  Q99536
GTEx:  ENSG00000108828 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99536
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.155α = 90
b = 131.72β = 90
c = 174.027γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-12
    Type: Initial release
  • Version 1.1: 2020-03-18
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description