SMTL ID : 8agb.1

Structure of yeast oligosaccharylransferase complex with lipid-linked oligosaccharide bound

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- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-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.1: 14 residues within 4Å: Chain A: L.78, W.538, N.539, T.541, H.542, I.545 Chain F: I.180, H.181, H.182, I.183 Chain G: D.320, P.321, Y.322, R.349 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain A Hydrogen bonds: G:D.320, G:D.320, G:D.320, G:R.349, G:R.349 Hydrophobic interactions: A:I.545

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.2: 8 residues within 4Å: Chain A: R.504, M.505, E.509 Chain E: V.234, Y.254, E.256, L.307, N.336 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:E.509 Hydrophobic interactions: E:V.234

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

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

1 x NDG- NAG- BMA- MAN- MAN- MAN- GLC- GLC- GLC- MAN- MAN: alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-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-alpha-D-glucopyranose

NDG-NAG-BMA-MAN-MAN-MAN-GLC-GLC-GLC-MAN-MAN.4: 20 residues within 4Å: Chain A: D.47, G.84, F.255, F.258, Y.521, N.535, N.536, T.537, W.538, N.540, T.541 Chain D: F.72, P.73, F.74, N.75, N.130 Chain G: Y.383, P.384, I.389 Ligands: ELU.8 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:W.538, A:T.541, A:T.541, A:T.541, D:N.75, D:N.130, A:D.47

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

CPL.5: 14 residues within 4Å: Chain A: L.33, V.36, I.97, L.105, L.107, I.109, R.112, N.113, V.114, L.117, L.121 Chain B: M.1 Chain E: Y.303 Ligands: CPL.10 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:L.33, A:L.33, A:I.97, A:L.105, A:L.107, A:I.109, A:L.117, A:L.117, A:L.121, A:L.121 Hydrogen bonds: A:N.113, A:N.113 Salt bridges: A:R.112 pi-Cation interactions: E:Y.303 CPL.9: 17 residues within 4Å: Chain A: F.25, G.26, I.29, S.30 Chain B: M.1, I.2 Chain C: L.22, L.33, T.74, T.75, A.78, N.80, S.81, F.82, G.83, Y.85 Ligands: CPL.10 12 PLIP interactions: 3 interactions with chain A, 5 interactions with chain C, 1 interactions with chain E, 3 interactions with chain B Hydrophobic interactions: A:F.25, A:I.29, A:I.29, C:L.33, C:L.33, C:T.74, C:F.82, C:F.82 Salt bridges: E:D.301 Hydrogen bonds: B:M.1, B:M.1, B:I.2 CPL.10: 11 residues within 4Å: Chain A: L.105, L.107, I.109 Chain C: T.75, F.82, V.84 Chain E: W.241, Q.250, Y.409 Ligands: CPL.5, CPL.9 8 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C, 4 interactions with chain E Hydrophobic interactions: A:L.107, C:T.75, C:F.82, C:V.84 Hydrogen bonds: E:Y.409, E:Y.409 Salt bridges: E:E.252 pi-Cation interactions: E:W.241 CPL.14: 24 residues within 4Å: Chain A: L.67, P.88, T.92, F.96, L.199, F.202, Y.203, S.206, Q.252, I.253, P.254 Chain D: I.120, F.123, H.127 Chain F: F.244, F.248, Y.251, Y.252, T.255, S.256, I.257 Chain G: N.380, R.385 Ligands: PTY.11 10 PLIP interactions: 2 interactions with chain D, 3 interactions with chain A, 4 interactions with chain F, 1 interactions with chain G Hydrophobic interactions: D:I.120, D:F.123, A:F.96, A:L.199, A:I.253, F:F.244, F:F.248 Hydrogen bonds: F:I.257, G:N.380 pi-Cation interactions: F:Y.251

2 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.6: 9 residues within 4Å: Chain A: L.227, M.228, R.230, F.378, L.381, L.394 Chain H: S.216, R.217, W.220 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain H Hydrophobic interactions: A:L.227, A:F.378, A:F.378, A:L.381, A:L.394, H:W.220 Salt bridges: A:R.230, H:R.217 PTY.11: 12 residues within 4Å: Chain A: S.62, F.63, T.92, A.95, F.96, H.99 Chain F: F.258, L.261, F.262, S.264, L.265 Ligands: CPL.14 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain F Hydrophobic interactions: A:F.63, A:F.96, F:L.261, F:L.261, F:F.262, F:L.265, F:L.265 Hydrogen bonds: A:F.63 Salt bridges: A:H.99

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.7: 3 residues within 4Å: Chain A: D.47, D.166 Ligands: ELU.8 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.166, A:D.166

1 x ELU: phosphono [(3~{R},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,10,14-trienyl] hydrogen phosphate(Non-covalent)

ELU.8: 11 residues within 4Å: Chain A: E.168, W.208, G.209, V.212, F.213, N.216, L.394, F.398, R.404 Ligands: NDG-NAG-BMA-MAN-MAN-MAN-GLC-GLC-GLC-MAN-MAN.4, MN.7 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.212, A:F.213, A:N.216, A:L.394, A:F.398 Hydrogen bonds: A:E.168, A:G.209 Salt bridges: A:R.404, A:R.404

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

NAG.12: 2 residues within 4Å: Chain G: N.332, D.333 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:N.332, G:D.333 NAG.13: 2 residues within 4Å: Chain G: S.33, N.60 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ramirez, A.S. et al., Molecular basis for glycan recognition and reaction priming of eukaryotic oligosaccharyltransferase. Nat Commun (2022)

Release Date

2022-12-07

Peptides

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

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST4

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit SWP1

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 3

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