SMTL ID : 6s7o.1

Cryo-EM structure of human oligosaccharyltransferase complex OST-A

Coordinates

PDB Format

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: 4 residues within 4Å: Chain A: R.75, R.513, E.518, N.537 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-(1-6)-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.2: 11 residues within 4Å: Chain A: L.80, N.548, T.550, H.551 Chain F: I.526, Q.527, H.528, L.529 Chain G: D.361, P.362, F.363 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain A Hydrogen bonds: G:D.361 Hydrophobic interactions: A:T.550

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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: 13 residues within 4Å: Chain A: I.501 Chain E: V.291, Y.292, N.299, V.300, S.301, T.302, S.303, H.304, L.305, L.306, M.314, E.315 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:H.304, E:S.303, E:L.305 Hydrophobic interactions: E:V.291, E:L.305

9 x KZB: (2~{S},3~{R},4~{R},5~{S},6~{S})-2-(hydroxymethyl)-6-[(1~{S},2~{R},3~{R},4~{R},5'~{S},6~{S},7~{R},8~{S},9~{R},12~{R},13~{R},15~{S},16~{S},18~{R})-5',7,9,13-tetramethyl-3,15-bis(oxidanyl)spiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosane-6,2'-oxane]-16-yl]oxy-oxane-3,4,5-triol(Non-covalent)

KZB.4: 13 residues within 4Å: Chain A: Y.244, T.248, V.262, F.271 Chain D: F.42, C.45, L.46, G.49, F.53, F.56, L.57, F.60, I.61 10 PLIP interactions: 7 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:F.42, D:F.53, D:F.56, D:F.56, D:L.57, D:F.60, D:I.61, A:Y.244, A:T.248, A:V.262 KZB.5: 9 residues within 4Å: Chain A: F.126, V.130, H.133, F.174, Y.181, K.185, W.194 Ligands: EGY.7, EGY.12 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.130, A:Y.181, A:W.194 KZB.6: 4 residues within 4Å: Chain A: H.101, V.102, F.105, F.106 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:H.101, A:V.102, A:F.105, A:F.105, A:F.106 KZB.14: 4 residues within 4Å: Chain E: T.403, F.404, L.440 Ligands: KZB.15 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:T.403, E:F.404, E:F.404, E:F.404, E:L.440 KZB.15: 5 residues within 4Å: Chain E: L.441, A.444, A.445, I.448 Ligands: KZB.14 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:A.444, E:I.448 KZB.18: 5 residues within 4Å: Chain F: L.587, Y.591 Chain G: F.433 Ligands: KZB.19, KZB.22 3 PLIP interactions: 1 interactions with chain G, 2 interactions with chain F Hydrophobic interactions: G:F.433, F:L.587, F:Y.591 KZB.19: 6 residues within 4Å: Chain F: L.581, A.584, A.585, Q.596 Ligands: KZB.18, KZB.20 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:L.581 KZB.20: 7 residues within 4Å: Chain F: L.589, V.592, Q.596, L.597, Q.601, Y.605 Ligands: KZB.19 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:L.589, F:V.592, F:L.597, F:Y.605 KZB.22: 4 residues within 4Å: Chain F: Y.591 Chain G: Y.426, A.430 Ligands: KZB.18 4 PLIP interactions: 2 interactions with chain G, 2 interactions with chain F Hydrophobic interactions: G:Y.426, G:Y.426 Hydrogen bonds: F:Y.591, F:Y.591

7 x EGY: (4R,7R)-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-7-[(undecanoyloxy)methyl]-3,5,8-trioxa-4lambda~5~-phosphadocosan-1-aminium(Non-covalent)

EGY.7: 15 residues within 4Å: Chain A: K.19, L.20, L.23, S.24, V.28, I.129, Y.132, H.133, K.136 Chain C: M.30, F.37, V.41 Ligands: KZB.5, EGY.11, EGY.12 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:L.23, A:V.28, A:I.129, C:F.37, C:F.37 Hydrogen bonds: A:Y.132 Salt bridges: A:K.19, A:H.133, A:K.136 EGY.8: 12 residues within 4Å: Chain A: L.221, L.224, V.225, T.229, R.231, F.379, L.382, T.395 Chain H: P.28, S.29, A.30, V.33 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain H Hydrophobic interactions: A:L.221, A:L.224, A:F.379, H:P.28 Salt bridges: A:R.231 Hydrogen bonds: H:S.29 EGY.11: 12 residues within 4Å: Chain B: M.1, I.2 Chain C: L.26, M.30, L.71, W.74, V.75, G.76, Y.78 Chain E: D.290 Ligands: EGY.7, EGY.16 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B, 1 interactions with chain E Hydrophobic interactions: C:L.26, C:L.71, C:W.74, B:I.2 Salt bridges: E:D.290 EGY.12: 8 residues within 4Å: Chain A: F.126 Chain C: E.40, V.41 Chain E: L.449, Y.456, V.457 Ligands: KZB.5, EGY.7 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.126 EGY.13: 14 residues within 4Å: Chain D: R.92, A.95, D.96, F.99 Chain E: F.461, S.462, I.463 Chain F: L.606, S.611, T.613, F.614, G.617, N.618, L.621 8 PLIP interactions: 3 interactions with chain D, 2 interactions with chain E, 3 interactions with chain F Hydrophobic interactions: D:A.95, E:I.463, F:L.606, F:F.614, F:F.614 Salt bridges: D:R.92, D:R.92 Hydrogen bonds: E:I.463 EGY.16: 11 residues within 4Å: Chain A: V.38, S.43, I.99, L.103, R.113, N.114, F.118 Chain B: M.1 Chain E: Y.292, R.294 Ligands: EGY.11 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:V.38, A:I.99, A:I.99, A:L.103, A:L.103, A:F.118, A:F.118, A:F.118 Hydrogen bonds: A:S.43, A:N.114 Salt bridges: A:R.113, E:R.294 pi-Cation interactions: E:Y.292 EGY.21: 15 residues within 4Å: Chain A: F.65, Y.66, H.69, I.94, F.203, Y.204, S.207, Q.253 Chain D: N.110 Chain F: Y.593, W.594, N.598, M.599 Chain G: H.415, R.420 8 PLIP interactions: 5 interactions with chain A, 1 interactions with chain D, 1 interactions with chain G, 1 interactions with chain F Hydrophobic interactions: A:F.65, A:I.94, A:F.203, A:Y.204, A:Y.204 Hydrogen bonds: D:N.110, F:M.599 Salt bridges: G:H.415

2 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 4 residues within 4Å: Chain A: D.167, N.168, E.169, R.405 No protein-ligand interaction detected (PLIP) MG.17: 3 residues within 4Å: Chain C: V.79 Chain E: E.376, E.438 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.438

1 x KZE: [(3~{R},6~{Z},10~{Z},14~{Z},18~{Z})-3,7,11,15,19,23-hexamethyltetracosa-6,10,14,18,22-pentaenyl] dihydrogen phosphate(Non-covalent)

KZE.10: 12 residues within 4Å: Chain A: W.209, G.211, F.214, N.217, W.326, R.329, F.330, L.333, T.395, F.399, R.405, L.406 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.214, A:F.214, A:N.217, A:W.326, A:F.330, A:F.330, A:F.330, A:T.395, A:F.399, A:L.406, A:L.406 Salt bridges: A:R.329, A:R.405

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ramirez, A.S. et al., Cryo-electron microscopy structures of human oligosaccharyltransferase complexes OST-A and OST-B. Science (2019)

Release Date

2019-12-18

Peptides

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A: A
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4: B
Transmembrane protein 258: C
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1: D
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1: E
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2: F
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit: G
Oligosaccharyltransferase complex subunit OSTC: 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 STT3A

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4

Transmembrane protein 258

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit

Oligosaccharyltransferase complex subunit OSTC

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