4J86

Crystal structure of beta'-COP/yWbp1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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:  4J73, 4J77, 4J78, 4J79, 4J81, 4J82, 4J84, 4J87, 4J8B, 4J8G

  • 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 reco ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Coatomer subunit beta'
A, B
301Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SEC27
Find proteins for P41811 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P41811
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1
C, D
6N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.163 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 73.976α = 90.00
b = 50.648β = 99.46
c = 83.576γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-02-14 
  • Released Date: 2013-03-27 
  • Deposition Author(s): Ma, W., Goldberg, J.

Revision History 

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