› 5kij

X-ray diffraction
1.65Å resolution

Crystal structure of the class I human endoplasmic reticulum 1,2-alpha-mannosidase and Man9GlcNAc2-PA complex

Released:
DOI: 10.2210/pdb5kij/pdb
PDB entry 5kij coloured by chain, front view.
PDB entry 5kij coloured by chain, side view.
PDB entry 5kij coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Substrate recognition and catalysis by GH47 α-mannosidases involved in Asn-linked glycan maturation in the mammalian secretory pathway.
Xiang Y, Karaveg K, Moremen KW
Proc Natl Acad Sci U S A 113 E7890-E7899 (2016)
PMID: 27856750

Function and Biology Details

Reaction catalysed: 
(1a) Man(9)GlcNAc(2)-[protein] + H(2)O = Man(8)GlcNAc(2)-[protein] (isomer 8A(1,2,3)B(1,2)) + beta-D-mannopyranose
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193855 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase Chain: A
Molecule details ›
Chain: A
Length: 452 amino acids
Theoretical weight: 52.03 KDa
Source organism: Homo sapiens
Expression system: Komagataella pastoris
UniProt:
  • Canonical: Q9UKM7 (Residues: 245-696; Coverage: 65%)
Gene names: MAN1B1, UNQ747/PRO1477
Sequence domains: Glycosyl hydrolase family 47
Structure domains: Glycosyltransferase

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
4 bound ligands:
Ligand LA 1 x LA
Ligand SO4 2 x SO4
Ligand BU1 4 x BU1
Ligand 1PS 1 x 1PS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P1
Unit cell:
a: 50.625Å b: 53.83Å c: 56.118Å
α: 89.65° β: 63.6° γ: 62.7°
R-values:
R R work R free
0.184 0.182 0.222
Expression system: Komagataella pastoris

Quick links

Citations

1 review citation

Modulation of ERQC and ERAD: A Broad-Spectrum Spanner in the Works of Cancer Cells?
Tax et al. (2019)
16 other articles

5 mentions without citation

Exploitation of glycosylation in enveloped virus pathobiology.
Watanabe et al. (2019)
4 more