Yeast delta-COP-I mu-homology domain complexed with Dsl1 WxWx(MSE) peptide

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


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

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F, G, H
270Saccharomyces cerevisiaeMutation(s): 1 
Gene Names: RET2YFR051C
Find proteins for P43621 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P43621 
Go to UniProtKB:  P43621
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43621
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN TRANSPORT PROTEIN DSL19Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P53847 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53847 
Go to UniProtKB:  P53847
Entity Groups  
UniProt GroupP53847
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 0 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B, C, D, E
A, B, C, D, E, F, G, H
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.174 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.406α = 79.71
b = 79.298β = 87.5
c = 163.346γ = 83.6
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-11
    Type: Initial release
  • Version 1.1: 2015-12-02
    Changes: Database references
  • Version 1.2: 2016-03-02
    Changes: Data collection, Refinement description
  • Version 1.3: 2016-04-06
    Changes: Data collection