› 6ezn

Electron Microscopy
3.3Å resolution

Cryo-EM structure of the yeast oligosaccharyltransferase (OST) complex

Released:
DOI: 10.2210/pdb6ezn/pdb
PDB entry 6ezn coloured by chain, front view.
PDB entry 6ezn coloured by chain, side view.
PDB entry 6ezn coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Molecular basis for glycan recognition and reaction priming of eukaryotic oligosaccharyltransferase.
Ramírez AS, de Capitani M, Pesciullesi G, Kowal J, Bloch JS, Irobalieva RN, Reymond JL, Aebi M, Locher KP
Nat Commun 13 7296 (2022)
PMID: 36435935
Related structures: EMD-4161

Function and Biology Details

Reaction catalysed: 
Dolichyl diphosphooligosaccharide + [protein]-L-asparagine = dolichyl diphosphate + a glycoprotein with the oligosaccharide chain attached by N-beta-D-glycosyl linkage to a protein L-asparagine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-152647 (preferred)
Entry contents:
8 distinct polypeptide molecules
Macromolecules (11 distinct):
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 Chain: A
Molecule details ›
Chain: A
Length: 476 amino acids
Theoretical weight: 54.12 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P41543 (Residues: 1-476; Coverage: 100%)
Gene names: J1404, NLT1, OST1, YJL002C
Sequence domains: Ribophorin I
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2 Chain: B
Molecule details ›
Chain: B
Length: 130 amino acids
Theoretical weight: 14.71 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P46964 (Residues: 1-130; Coverage: 100%)
Gene names: OST2, YOR103C, YOR3211C
Sequence domains: DAD family
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 3 Chain: C
Molecule details ›
Chain: C
Length: 350 amino acids
Theoretical weight: 39.52 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P48439 (Residues: 1-350; Coverage: 100%)
Gene names: OST3, YOR085W, YOR3124W
Sequence domains: OST3 / OST6 family, transporter family
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST4 Chain: D
Molecule details ›
Chain: D
Length: 36 amino acids
Theoretical weight: 3.99 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q99380 (Residues: 1-36; Coverage: 100%)
Gene names: OST4, YDL232W
Sequence domains: Oligosaccaryltransferase
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5 Chain: E
Molecule details ›
Chain: E
Length: 86 amino acids
Theoretical weight: 9.53 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q92316 (Residues: 1-86; Coverage: 100%)
Gene names: OST5, YGL226BC, YGL226C-A
Sequence domains: Oligosaccharyltransferase subunit 5
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3 Chain: F
Molecule details ›
Chain: F
Length: 718 amino acids
Theoretical weight: 81.6 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P39007 (Residues: 1-718; Coverage: 100%)
Gene names: STT3, YGL022W
Sequence domains:
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1 Chain: G
Molecule details ›
Chain: G
Length: 430 amino acids
Theoretical weight: 49.44 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P33767 (Residues: 1-430; Coverage: 100%)
Gene names: WBP1, YEL002C
Sequence domains: Oligosaccharyltransferase 48 kDa subunit beta
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit SWP1 Chain: H
Molecule details ›
Chain: H
Length: 286 amino acids
Theoretical weight: 31.68 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q02795 (Residues: 1-286; Coverage: 100%)
Gene names: SWP1, YM9375.19, YMR149W
Sequence domains: Oligosaccharyltransferase subunit Ribophorin II

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
3 bound ligands:
Ligand CPL 4 x CPL
Ligand PTY 1 x PTY
Ligand NAG 1 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.3Å
Relevant EMDB volumes: EMD-4161

Quick links

Citations

1 review citation

The role of N-glycosylation modification in the pathogenesis of liver cancer.
Hu et al. (2023)
2 other articles

10 mentions without citation

Structural Insight into the Mechanism of N-Linked Glycosylation by Oligosaccharyltransferase.
Mohanty et al. (2020)
9 more