6TQR

The crystal structure of the MSP domain of human VAP-A in complex with the Phospho-FFAT motif of STARD3.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

FFAT motif phosphorylation controls formation and lipid transfer function of inter-organelle contacts.

Di Mattia, T.Martinet, A.Ikhlef, S.McEwen, A.G.Nomine, Y.Wendling, C.Poussin-Courmontagne, P.Voilquin, L.Eberling, P.Ruffenach, F.Cavarelli, J.Slee, J.Levine, T.P.Drin, G.Tomasetto, C.Alpy, F.

(2020) EMBO J 39: e104369-e104369

  • DOI: https://doi.org/10.15252/embj.2019104369
  • Primary Citation of Related Structures:  
    6TQR, 6TQS, 6TQT, 6TQU

  • PubMed Abstract: 

    Organelles are physically connected in membrane contact sites. The endoplasmic reticulum possesses three major receptors, VAP-A, VAP-B, and MOSPD2, which interact with proteins at the surface of other organelles to build contacts. VAP-A, VAP-B, and MOSPD2 contain an MSP domain, which binds a motif named FFAT (two phenylalanines in an acidic tract). In this study, we identified a non-conventional FFAT motif where a conserved acidic residue is replaced by a serine/threonine. We show that phosphorylation of this serine/threonine is critical for non-conventional FFAT motifs (named Phospho-FFAT) to be recognized by the MSP domain. Moreover, structural analyses of the MSP domain alone or in complex with conventional and Phospho-FFAT peptides revealed new mechanisms of interaction. Based on these new insights, we produced a novel prediction algorithm, which expands the repertoire of candidate proteins with a Phospho-FFAT that are able to create membrane contact sites. Using a prototypical tethering complex made by STARD3 and VAP, we showed that phosphorylation is instrumental for the formation of ER-endosome contacts, and their sterol transfer function. This study reveals that phosphorylation acts as a general switch for inter-organelle contacts.


  • Organizational Affiliation

    Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vesicle-associated membrane protein-associated protein A
A, B, C, D
213Homo sapiensMutation(s): 0 
Gene Names: VAPAVAP33
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P0L0 (Homo sapiens)
Explore Q9P0L0 
Go to UniProtKB:  Q9P0L0
PHAROS:  Q9P0L0
GTEx:  ENSG00000101558 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9P0L0
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
StAR-related lipid transfer protein 3
E, F
17Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q14849 (Homo sapiens)
Explore Q14849 
Go to UniProtKB:  Q14849
PHAROS:  Q14849
GTEx:  ENSG00000131748 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14849
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.14α = 89.46
b = 43.78β = 92.91
c = 83.64γ = 105.13
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-19-CE44-0003
French National Research AgencyFranceANR-10-INSB-05-01
French National Research AgencyFranceANR-10-LABX-0030-INRT
French National Research AgencyFranceANR-10-IDEX-0002-02.

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-18
    Type: Initial release
  • Version 1.1: 2020-12-16
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description