PDBsum entry 4j86

Protein transport

PDB id: 4j86

Contents

Protein chains

301 a.a.

Ligands

THR-PHE-LYS-LYS-THR-ASN ×2

Waters ×705

PDB id:

4j86

Name:

Protein transport

Title:

Crystal structure of beta'-cop/ywbp1 complex

Structure:

Coatomer subunit beta'. Chain: a, b. Synonym: beta'-coat protein, beta'-cop. Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit wbp1. Chain: c, d. Fragment: unp residues 425-430. Synonym: oligosaccharyl transferase subunit wbp1, oligosaccharyl transferase subunit beta.

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Synthetic: yes. Organism_taxid: 4932

Resolution:

1.48Å R-factor: 0.163 R-free: 0.188

Authors:

W.Ma,J.Goldberg

Key ref:

W.Ma and J.Goldberg (2013). Rules for the recognition of dilysine retrieval motifs by coatomer. Embo J, 32, 926-937. PubMed id: 23481256 DOI: 10.1038/emboj.2013.41

Date:

14-Feb-13 Release date: 27-Mar-13

Protein chains

P41811  (COPB2_YEAST) -  Coatomer subunit beta' from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 889 a.a.

Struc: 301 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1038/emboj.2013.41

Embo J 32:926-937 (2013)

PubMed id: 23481256

Rules for the recognition of dilysine retrieval motifs by coatomer.

W.Ma, J.Goldberg.

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.