4J79

Crystal structure of beta'-COP/PEDVspike complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

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Literature

Rules for the recognition of dilysine retrieval motifs by coatomer.

Ma, W., Goldberg, J.

(2013) EMBO J 32: 926-937

  • DOI: 10.1038/emboj.2013.41
  • Primary Citation of Related Structures:  
    4J82, 4J84, 4J86, 4J87, 4J81, 4J8B, 4J8G, 4J79, 4J73, 4J77

  • PubMed Abstract: 

    • Cytoplasmic dilysine motifs on transmembrane proteins are captured by coatomer α-COP and β'-COP subunits and packaged into COPI-coated vesicles for Golgi-to-ER retrieval. Numerous ER/Golgi proteins contain K(x)Kxx motifs, but the rules for their recognition are unclear ...

    Cytoplasmic dilysine motifs on transmembrane proteins are captured by coatomer α-COP and β'-COP subunits and packaged into COPI-coated vesicles for Golgi-to-ER retrieval. Numerous ER/Golgi proteins contain K(x)Kxx motifs, but the rules for their recognition are unclear. We present crystal structures of α-COP and β'-COP bound to a series of naturally occurring retrieval motifs-encompassing KKxx, KxKxx and non-canonical RKxx and viral KxHxx sequences. Binding experiments show that α-COP and β'-COP have generally the same specificity for KKxx and KxKxx, but only β'-COP recognizes the RKxx signal. Dilysine motif recognition involves lysine side-chain interactions with two acidic patches. Surprisingly, however, KKxx and KxKxx motifs bind differently, with their lysine residues transposed at the binding patches. We derive rules for retrieval motif recognition from key structural features: the reversed binding modes, the recognition of the C-terminal carboxylate group which enforces lysine positional context, and the tolerance of the acidic patches for non-lysine residues.

    Organizational Affiliation: 

    Memorial Sloan-Kettering Cancer Center, Howard Hughes Medical Institute and the Structural Biology Program, New York, NY, USA.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Coatomer subunit beta' A301Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P41811 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P41811 
Go to UniProtKB:  P41811
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Spike glycoprotein B6Porcine epidemic diarrhea virusMutation(s): 0 
Find proteins for Q91AV1 (Porcine epidemic diarrhea virus (strain CV777))
Explore Q91AV1 
Go to UniProtKB:  Q91AV1
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.1α = 90
b = 51.18β = 101.75
c = 85.25γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2013-02-12 
  • Released Date: 2013-03-27 
    • Deposition Author(s): Ma, W., Goldberg, J.

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-27
    Type: Initial release
  • Version 1.1: 2013-04-17
    Changes: Database references