4YGB image
Deposition Date 2015-02-26
Release Date 2016-04-06
Last Version Date 2024-10-23
Entry Detail
PDB ID:
4YGB
Title:
Crystal structure of ERGIC-53/MCFD2, monoclinic calcium-free form
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.60 Å
R-Value Free:
0.19
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Protein ERGIC-53
Gene (Uniprot):LMAN1
Chain IDs:A, C
Chain Length:246
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Multiple coagulation factor deficiency protein 2
Gene (Uniprot):MCFD2
Chain IDs:B, D
Chain Length:104
Number of Molecules:2
Biological Source:Homo sapiens
Primary Citation
Crystallographic snapshots of the EF-hand protein MCFD2 complexed with the intracellular lectin ERGIC-53 involved in glycoprotein transport.
Acta Crystallogr.,Sect.F 76 216 221 (2020)
PMID: 32356523 DOI: 10.1107/S2053230X20005452

Abstact

The transmembrane intracellular lectin ER-Golgi intermediate compartment protein 53 (ERGIC-53) and the soluble EF-hand multiple coagulation factor deficiency protein 2 (MCFD2) form a complex that functions as a cargo receptor, trafficking various glycoproteins between the endoplasmic reticulum (ER) and the Golgi apparatus. It has been demonstrated that the carbohydrate-recognition domain (CRD) of ERGIC-53 (ERGIC-53CRD) interacts with N-linked glycans on cargo glycoproteins, whereas MCFD2 recognizes polypeptide segments of cargo glycoproteins. Crystal structures of ERGIC-53CRD complexed with MCFD2 and mannosyl oligosaccharides have revealed protein-protein and protein-sugar binding modes. In contrast, the polypeptide-recognition mechanism of MCFD2 remains largely unknown. Here, a 1.60 Å resolution crystal structure of the ERGIC-53CRD-MCFD2 complex is reported, along with three other crystal forms. Comparison of these structures with those previously reported reveal that MCFD2, but not ERGIC-53-CRD, exhibits significant conformational plasticity that may be relevant to its accommodation of various polypeptide ligands.

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