Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.05 kDa 
• Atom Count: 2814 
• Modelled Residue Count: 306 
• Deposited Residue Count: 307 
• Unique protein chains: 2

4J79

Crystal structure of beta'-COP/PEDVspike complex

• PDB DOI: 10.2210/pdb4J79/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Saccharomyces cerevisiae, Porcine epidemic diarrhea virus
• Mutation(s): No 


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

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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 

Literature

Rules for the recognition of dilysine retrieval motifs by coatomer.

Ma, W., Goldberg, J.

(2013) EMBO J 32: 926-937

• PubMed: 23481256 
• DOI: 10.1038/emboj.2013.41
• Primary Citation of Related Structures:  
  4J73, 4J77, 4J78, 4J79, 4J81, 4J82, 4J84, 4J86, 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coatomer subunit beta'	A	301	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P41811 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P41811  Go to UniProtKB:  P41811

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	B	6	Porcine epidemic diarrhea virus	Mutation(s): 0
UniProt
Find proteins for Q91AV1 (Porcine epidemic diarrhea virus (strain CV777)) Explore Q91AV1  Go to UniProtKB:  Q91AV1

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 = 75.1	α = 90
b = 51.18	β = 101.75
c = 85.25	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-02-12 
• 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
  Changes: Database references