5FJZ

Yeast delta-COP-I mu-homology domain complexed with Dsl1 WxWxV peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Basis for the Binding of Tryptophan-Based Motifs by Delta-Cop.

Suckling, R.J.Poon, P.P.Travis, S.M.Majoul, I.V.Hughson, F.M.Evans, P.R.Duden, R.Owen, D.J.

(2015) Proc Natl Acad Sci U S A 112: 14242

  • DOI: 10.1073/pnas.1506186112
  • Primary Citation of Related Structures:  
    5FJX, 5FJW, 5FK0, 5FJZ

  • PubMed Abstract: 
  • Coatomer consists of two subcomplexes: the membrane-targeting, ADP ribosylation factor 1 (Arf1):GTP-binding βγδζ-COP F-subcomplex, which is related to the adaptor protein (AP) clathrin adaptors, and the cargo-binding αβ'ε-COP B-subcomplex. We present ...

    Coatomer consists of two subcomplexes: the membrane-targeting, ADP ribosylation factor 1 (Arf1):GTP-binding βγδζ-COP F-subcomplex, which is related to the adaptor protein (AP) clathrin adaptors, and the cargo-binding αβ'ε-COP B-subcomplex. We present the structure of the C-terminal μ-homology domain of the yeast δ-COP subunit in complex with the WxW motif from its binding partner, the endoplasmic reticulum-localized Dsl1 tether. The motif binds at a site distinct from that used by the homologous AP μ subunits to bind YxxΦ cargo motifs with its two tryptophan residues sitting in compatible pockets. We also show that the Saccharomyces cerevisiae Arf GTPase-activating protein (GAP) homolog Gcs1p uses a related WxxF motif at its extreme C terminus to bind to δ-COP at the same site in the same way. Mutations designed on the basis of the structure in conjunction with isothermal titration calorimetry confirm the mode of binding and show that mammalian δ-COP binds related tryptophan-based motifs such as that from ArfGAP1 in a similar manner. We conclude that δ-COP subunits bind Wxn(1-6)[WF] motifs within unstructured regions of proteins that influence the lifecycle of COPI-coated vesicles; this conclusion is supported by the observation that, in the context of a sensitizing domain deletion in Dsl1p, mutating the tryptophan-based motif-binding site in yeast causes defects in both growth and carboxypeptidase Y trafficking/processing.


    Organizational Affiliation

    Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom; duden@bio.uni-luebeck.de djo30@cam.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
COATOMER SUBUNIT DELTAABCD270Saccharomyces cerevisiaeMutation(s): 1 
Find proteins for P43621 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P43621 
Go to UniProtKB:  P43621
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN TRANSPORT PROTEIN DSL1PQRS9Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P53847 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53847 
Go to UniProtKB:  P53847
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.81α = 90
b = 72.81β = 90
c = 343.29γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-11-11
    Type: Initial release
  • Version 1.1: 2015-12-02
    Changes: Database references