5FJX

Yeast delta-COP-I mu-homology domain complexed with Gcs1 WxxF peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.202 

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:  
    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 ...

    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
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
COATOMER SUBUNIT DELTAA, B, C270Saccharomyces cerevisiaeMutation(s): 1 
UniProt
Find proteins for P43621 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P43621 
Go to UniProtKB:  P43621
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ADP-RIBOSYLATION FACTOR GTPASE-ACTIVATING PROTEIN GCS1D, E8Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P35197 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P35197 
Go to UniProtKB:  P35197
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		A, B, CL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.765α = 90
b = 84.855β = 90
c = 148.64γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data

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