4AFI

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 

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: https://doi.org/10.1016/j.devcel.2012.01.018
  • Primary Citation of Related Structures:  
    4AFI

  • 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 the VAMP7 longin domain and determines the structure of their complex ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AP-3 COMPLEX SUBUNIT DELTA-1, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7A, B173Homo sapiensMus musculus
This entity is chimeric
Mutation(s): 0 
Gene Names: AP3D1Vamp7
UniProt & NIH Common Fund Data Resources
Find proteins for P70280 (Mus musculus)
Explore P70280 
Go to UniProtKB:  P70280
Find proteins for O14617 (Homo sapiens)
Explore O14617 
Go to UniProtKB:  O14617
PHAROS:  O14617
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP70280O14617
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PR
Query on PR

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
PRASEODYMIUM ION
Pr
WCWKKSOQLQEJTE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.555α = 90
b = 63.555β = 90
c = 217.915γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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