SMTL ID : 6ezn.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-mer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 8 residues within 4Å: Chain A: V.234, N.235, E.256, L.307, N.334, N.336 Chain F: R.504, M.505 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.234 Hydrogen bonds: A:N.334

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 3 residues within 4Å: Chain A: N.400, S.402, E.404 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain G: Q.32, N.60 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.3: 12 residues within 4Å: Chain F: L.78, N.539, T.541, H.542, W.598 Chain G: D.320, P.321, Y.322, R.349 Chain H: I.180, H.182, I.183 3 PLIP interactions: 1 interactions with chain G, 2 interactions with chain F Hydrogen bonds: G:D.320, G:D.320 Hydrophobic interactions: F:T.541, F:W.598

4 x CPL: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

CPL.5: 15 residues within 4Å: Chain A: W.241, Q.250, E.252, Y.409, F.410, Y.456, I.457 Chain E: T.75, A.78, F.82, V.84 Chain F: L.105, L.107, I.109 Ligands: CPL.7 10 PLIP interactions: 1 interactions with chain F, 7 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: F:L.107, A:Y.409, A:F.410, A:Y.456, A:I.457, E:F.82, E:V.84 Hydrogen bonds: A:Y.409, A:Y.409 pi-Cation interactions: A:W.241 CPL.6: 14 residues within 4Å: Chain D: M.1, I.2 Chain E: P.26, I.30, L.33, N.80, S.81, F.82, G.83, Y.85 Chain F: F.25, I.29, S.30, L.33 10 PLIP interactions: 5 interactions with chain E, 3 interactions with chain D, 2 interactions with chain F Hydrophobic interactions: E:I.30, E:L.33, E:F.82, E:F.82, F:F.25, F:L.33 Hydrogen bonds: E:S.81, D:M.1, D:M.1, D:I.2 CPL.7: 13 residues within 4Å: Chain A: Y.303 Chain D: M.1 Chain F: I.29, L.33, I.37, S.41, I.97, L.105, R.112, N.113, L.117, L.121 Ligands: CPL.5 12 PLIP interactions: 11 interactions with chain F, 1 interactions with chain A Hydrophobic interactions: F:I.29, F:L.33, F:I.37, F:I.97, F:L.105, F:L.121, F:L.121 Hydrogen bonds: F:S.41, F:N.113, F:N.113 Salt bridges: F:R.112 pi-Cation interactions: A:Y.303 CPL.10: 22 residues within 4Å: Chain B: L.119, F.123, V.124, H.127 Chain F: L.67, P.88, T.92, L.199, F.202, Y.203, S.206, Q.252, I.253 Chain G: N.380, R.385 Chain H: F.248, Y.251, G.254, T.255, S.256, I.257 Ligands: PTY.8 20 PLIP interactions: 4 interactions with chain H, 8 interactions with chain F, 7 interactions with chain B, 1 interactions with chain G Hydrophobic interactions: H:F.248, F:L.67, F:P.88, F:T.92, F:L.199, F:F.202, F:F.202, F:Y.203, F:Y.203, B:L.119, B:F.123, B:F.123, B:F.123, B:V.124 Hydrogen bonds: H:Y.251, H:I.257, G:N.380 pi-Cation interactions: H:Y.251 Salt bridges: B:H.127, B:H.127

1 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.8: 10 residues within 4Å: Chain F: N.61, S.62, F.63, T.92, F.96, H.99, L.199 Chain H: F.258, L.261 Ligands: CPL.10 8 PLIP interactions: 6 interactions with chain F, 2 interactions with chain H Hydrophobic interactions: F:F.96, F:L.199, H:F.258, H:L.261 Hydrogen bonds: F:S.62, F:F.63, F:T.92 Salt bridges: F:H.99

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.9: 3 residues within 4Å: Chain G: P.306, N.332, D.333 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wild, R. et al., Structure of the yeast oligosaccharyltransferase complex gives insight into eukaryotic N-glycosylation. Science (2018)

Release Date

2018-01-17

Peptides

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1: A
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2: B
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 3: C
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST4: D
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5: E
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3: F
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1: G
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit SWP1: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Membrane

We predict this structure to be a membrane protein.
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Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 3

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST4

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit SWP1

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