› 5ggi

X-ray diffraction
2.6Å resolution

Crystal structure of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in complex with Mn, UDP and Mannosyl-peptide

Released:
DOI: 10.2210/pdb5ggi/pdb
PDB entry 5ggi coloured by chain, front view.
PDB entry 5ggi coloured by chain, side view.
PDB entry 5ggi coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Carbohydrate-binding domain of the POMGnT1 stem region modulates O-mannosylation sites of α-dystroglycan.
Kuwabara N, Manya H, Yamada T, Tateno H, Kanagawa M, Kobayashi K, Akasaka-Manya K, Hirose Y, Mizuno M, Ikeguchi M, Toda T, Hirabayashi J, Senda T, Endo T, Kato R
Proc Natl Acad Sci U S A 113 9280-5 (2016)
PMID: 27493216

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
monomeric
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-165688 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 578 amino acids
Theoretical weight: 65.55 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q8WZA1 (Residues: 92-660; Coverage: 86%)
Gene names: MGAT1.2, POMGNT1, UNQ746/PRO1475
Sequence domains:
mannosyl-peptide Chains: F, G
Molecule details ›
Chains: F, G
Length: 11 amino acids
Theoretical weight: 818 Da
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand UDP 2 x UDP
Ligand MN 2 x MN
Ligand PO4 1 x PO4
Ligand MAN 2 x MAN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL32XU
Unit cell:
a: 68.162Å b: 126.539Å c: 172.865Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.201 0.199 0.238
Expression systems:
  • Homo sapiens
  • Not provided

Quick links

Citations

9 review citations

Recent advancements in understanding mammalian O-mannosylation.
Sheikh et al. (2017)
8 more

6 mentions without citation

Emerging structural insights into glycosyltransferase-mediated synthesis of glycans.
Moremen et al. (2019)
5 more