4YGC

Crystal structure of ERGIC-53/MCFD2, monoclinic calcium-bound form 1

Summary for 4YGC

• Entry DOI: 10.2210/pdb4ygc/pdb
• Related: 4YGB 4YGD 4YGE
• Descriptor: Protein ERGIC-53, Multiple coagulation factor deficiency protein 2, CALCIUM ION, ... (5 entities in total)
• Functional Keywords: beta-sandwich, ef-hand, cargo receptor, calcium binding, er, ergic, protein transport
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 8
• Total formula weight: 157624.72

Authors

Satoh, T.,Nishio, M.,Yagi-Utsumi, M.,Suzuki, K.,Anzai, T.,Mizushima, T.,Kamiya, Y.,Kato, K. (deposition date: 2015-02-26, release date: 2016-04-06, Last modification date: 2024-11-06)

Primary citation

Satoh, T.,Nishio, M.,Suzuki, K.,Yagi-Utsumi, M.,Kamiya, Y.,Mizushima, T.,Kato, K.
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

PubMed Abstract: 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-53) interacts with N-linked glycans on cargo glycoproteins, whereas MCFD2 recognizes polypeptide segments of cargo glycoproteins. Crystal structures of ERGIC-53 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-53-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.

PubMed: 32356523
DOI: 10.1107/S2053230X20005452

Experimental method

X-RAY DIFFRACTION (2.4 Å)