› 4ygd

X-ray diffraction
2.51Å resolution

Crystal structure of ERGIC-53/MCFD2, monoclinic calcium-bound form 2

Released:
DOI: 10.2210/pdb4ygd/pdb
PDB entry 4ygd coloured by chain, front view.
PDB entry 4ygd coloured by chain, side view.
PDB entry 4ygd coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystallographic snapshots of the EF-hand protein MCFD2 complexed with the intracellular lectin ERGIC-53 involved in glycoprotein transport.
Satoh T, Nishio M, Suzuki K, Yagi-Utsumi M, Kamiya Y, Mizushima T, Kato K
Acta Crystallogr F Struct Biol Commun 76 216-221 (2020)
PMID: 32356523

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-155904 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Protein ERGIC-53 Chains: A, C, E, G
Molecule details ›
Chains: A, C, E, G
Length: 246 amino acids
Theoretical weight: 27.15 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P49257 (Residues: 31-269; Coverage: 50%)
Gene names: ERGIC53, F5F8D, LMAN1
Sequence domains: Legume-like lectin family
Structure domains: Jelly Rolls
Multiple coagulation factor deficiency protein 2 Chains: B, D, F, H
Molecule details ›
Chains: B, D, F, H
Length: 104 amino acids
Theoretical weight: 12.06 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8NI22 (Residues: 67-146; Coverage: 67%)
Gene names: MCFD2, SDNSF
Sequence domains: EF-hand domain pair
Structure domains: EF-hand

Ligands and Environments

2 bound ligands:
Ligand CA 16 x CA
Ligand CL 3 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P21
Unit cell:
a: 103.063Å b: 58.765Å c: 119.386Å
α: 90° β: 109.01° γ: 90°
R-values:
R R work R free
0.195 0.193 0.232
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Glycans in autophagy, endocytosis and lysosomal functions.
Reggiori et al. (2021)
1 more

1 mention without citation

Crystallographic snapshots of the EF-hand protein MCFD2 complexed with the intracellular lectin ERGIC-53 involved in glycoprotein transport.
Satoh et al. (2020)