4AFI

Complex between Vamp7 longin domain and fragment of delta-adaptin from AP3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis of the Intracellular Sorting of the Snare Vamp7 by the Ap3 Adaptor Complex

Kent, H.M.Evans, P.R.Schaefer, I.B.Gray, S.R.Sanderson, C.M.Luzio, J.P.Peden, A.A.Owen, D.J.

(2012) Dev.Cell 22: 979

  • DOI: 10.1016/j.devcel.2012.01.018

  • PubMed Abstract: 
  • VAMP7 is involved in the fusion of late endocytic compartments with other membranes. One possible mechanism of VAMP7 delivery to these late compartments is via the AP3 trafficking adaptor. We show that the linker of the δ-adaptin subunit of AP3 binds ...

    VAMP7 is involved in the fusion of late endocytic compartments with other membranes. One possible mechanism of VAMP7 delivery to these late compartments is via the AP3 trafficking adaptor. We show that the linker of the δ-adaptin subunit of AP3 binds the VAMP7 longin domain and determines the structure of their complex. Mutation of residues on both partners abolishes the interaction in vitro and in vivo. The binding of VAMP7 to δ-adaptin requires the VAMP7 SNARE motif to be engaged in SNARE complex formation and hence AP3 must transport VAMP7 when VAMP7 is part of a cis-SNARE complex. The absence of δ-adaptin causes destabilization of the AP3 complex in mouse mocha fibroblasts and mislocalization of VAMP7. The mislocalization can be rescued by transfection with wild-type δ-adaptin but not by δ-adaptin containing mutations that abolish VAMP7 binding, despite in all cases intact AP3 being present and LAMP1 trafficking being rescued.


    Organizational Affiliation

    Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AP-3 COMPLEX SUBUNIT DELTA-1, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7
A, B
173Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: Vamp7 (Sybl1), AP3D1
Find proteins for P70280 (Mus musculus)
Go to UniProtKB:  P70280
Find proteins for O14617 (Homo sapiens)
Go to Gene View: AP3D1
Go to UniProtKB:  O14617
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PR
Query on PR

Download SDF File 
Download CCD File 
A, B
PRASEODYMIUM ION
Pr
WCWKKSOQLQEJTE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.231 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 63.555α = 90.00
b = 63.555β = 90.00
c = 217.915γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-30
    Type: Initial release
  • Version 1.1: 2012-08-22
    Type: Database references
  • Version 1.2: 2017-03-15
    Type: Source and taxonomy