SMTL ID : 6s7t.1

Cryo-EM structure of human oligosaccharyltransferase complex OST-B

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x ALA- ALA- ASN- ALA- THR- ALA- ALA: PEPTIDE(Non-covalent)

ALA-ALA-ASN-ALA-THR-ALA-ALA.1: 16 residues within 4Å: Chain A: E.101, F.102, D.103, R.214, S.402, V.403, S.404, E.405, Q.407, W.604, W.605, D.606, N.623, G.669, K.674, W.677 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.102, A:W.677 Hydrogen bonds: A:D.103, A:R.214, A:S.402, A:S.404, A:S.404, A:S.404, A:E.405, A:E.405, A:W.604, A:D.606, A:D.606, A:N.623

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: R.592, E.597, N.616 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.641 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.3: 14 residues within 4Å: Chain A: L.134, N.627, S.629, H.630, L.633 Chain F: I.526, Q.527, H.528, L.529 Chain G: R.359, I.360, D.361, P.362, F.363 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain G Hydrophobic interactions: A:L.633 Hydrogen bonds: G:D.361

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.5: 15 residues within 4Å: Chain A: F.95, E.96, T.577, R.578, I.580 Chain E: V.291, N.299, V.300, S.301, S.303, H.304, L.305, L.306, E.315 Ligands: EGY.6 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:V.291 Hydrogen bonds: E:S.303, E:L.305, E:H.304

10 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.6: 10 residues within 4Å: Chain A: F.85, V.92, I.93, F.95, S.97, D.168, F.172 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.5, EGY.15, EGY.22 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.85, A:D.168, A:F.172, A:F.172, A:F.172 EGY.7: 7 residues within 4Å: Chain A: L.114, G.118, F.119, I.148, L.152, W.155, I.156 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.148, A:L.152, A:W.155, A:W.155, A:I.156 Hydrogen bonds: A:F.119 EGY.8: 7 residues within 4Å: Chain A: W.248, C.251, S.255 Chain D: R.92 Chain F: F.614 Ligands: KZB.12, EGY.18 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain F, 1 interactions with chain D Hydrophobic interactions: A:W.248, F:F.614 Salt bridges: D:R.92 EGY.9: 11 residues within 4Å: Chain A: V.279, L.282, M.283, Q.284, R.285, I.433, L.445, I.448 Chain H: K.216, W.219, A.223 10 PLIP interactions: 4 interactions with chain H, 6 interactions with chain A Hydrophobic interactions: H:W.219, H:W.219, H:A.223, A:V.279, A:V.279, A:I.433, A:L.445, A:I.448 Salt bridges: H:K.216, A:R.285 EGY.10: 10 residues within 4Å: Chain A: S.70, F.74, I.183 Chain C: F.37, V.41, S.43, R.48 Chain E: T.452, Y.456, V.457 9 PLIP interactions: 4 interactions with chain A, 2 interactions with chain E, 3 interactions with chain C Hydrophobic interactions: A:F.74, A:F.74, A:F.74, A:I.183, E:T.452, E:Y.456, C:F.37 Hydrogen bonds: C:S.43 Salt bridges: C:R.48 EGY.11: 6 residues within 4Å: Chain A: F.278, L.282, Q.284, A.361, F.365 Ligands: 0K3.14 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.278, A:L.282, A:L.282, A:A.361, A:F.365 Hydrogen bonds: A:Q.284 EGY.15: 9 residues within 4Å: Chain B: M.1 Chain C: L.26, L.71, W.74, V.75, Y.78 Chain E: D.290 Ligands: EGY.6, EGY.22 5 PLIP interactions: 1 interactions with chain E, 3 interactions with chain C, 1 interactions with chain B Salt bridges: E:D.290 Hydrophobic interactions: C:L.71, C:W.74, C:V.75 Hydrogen bonds: B:M.1 EGY.18: 12 residues within 4Å: Chain D: R.92, A.95, L.98, F.99 Chain E: F.461, S.462, I.463 Chain F: F.579, L.606, F.614, L.621 Ligands: EGY.8 8 PLIP interactions: 3 interactions with chain F, 4 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: F:F.579, F:L.606, F:L.621, D:A.95, D:L.98 Salt bridges: D:R.92, D:R.92 Hydrogen bonds: E:I.463 EGY.22: 10 residues within 4Å: Chain A: S.97, L.160, I.162, D.168 Chain C: L.72, V.75 Chain E: R.294, Y.400 Ligands: EGY.6, EGY.15 7 PLIP interactions: 2 interactions with chain C, 2 interactions with chain E, 3 interactions with chain A Hydrophobic interactions: C:L.72, C:V.75, E:Y.400, A:L.160, A:I.162 Hydrogen bonds: E:R.294 Salt bridges: A:D.168 EGY.26: 19 residues within 4Å: Chain A: F.119, Y.120, L.123, I.148, F.257, Y.258, S.261, I.308, P.309 Chain D: L.106, N.110 Chain F: Y.593, W.594, L.597, N.598, M.599, F.600, L.603 Chain G: H.415 9 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D, 3 interactions with chain F, 1 interactions with chain G Hydrophobic interactions: A:L.123, A:F.257, A:F.257, A:I.308, D:L.106, F:L.603 Hydrogen bonds: F:Y.593, F:M.599 Salt bridges: G:H.415

13 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.12: 9 residues within 4Å: Chain A: L.180, I.183, L.187, R.190, F.232, Y.235, K.239, W.248 Ligands: EGY.8 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.180, A:I.183, A:L.187, A:F.232, A:F.232, A:Y.235, A:W.248 KZB.16: 4 residues within 4Å: Chain C: L.21, F.63, F.66 Chain I: P.274 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain I Hydrophobic interactions: C:L.21, C:F.63, C:F.66, I:P.274 KZB.17: 4 residues within 4Å: Chain A: W.68, L.71 Chain C: F.31, A.34 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:A.34, A:W.68, A:L.71 KZB.19: 8 residues within 4Å: Chain A: I.316, R.317, L.371, Y.376, I.377 Chain D: T.50, F.53 Chain F: E.534 6 PLIP interactions: 1 interactions with chain F, 3 interactions with chain A, 2 interactions with chain D Hydrogen bonds: F:E.534 Hydrophobic interactions: A:I.316, A:L.371, A:Y.376, D:F.53, D:F.53 KZB.20: 7 residues within 4Å: Chain D: L.13, Y.16, L.17, K.25, D.28 Chain F: R.562, I.563 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain F Hydrophobic interactions: D:L.13, D:Y.16, D:L.17, D:K.25, F:I.563, F:I.563 Hydrogen bonds: D:Y.16, D:K.25, F:R.562 KZB.21: 14 residues within 4Å: Chain A: K.288, Y.291, Q.332, A.335, F.336, Y.339, D.342 Chain D: F.67, V.71, R.74, I.75, N.78, Q.80, N.81 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:F.67, D:F.67, D:V.71, D:I.75, A:A.335, A:Y.339, A:Y.339 Hydrogen bonds: D:R.74, D:Q.80 KZB.23: 6 residues within 4Å: Chain E: F.404, L.434, Q.437, L.440, L.441 Ligands: KZB.24 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:L.434, E:L.440, E:L.440 KZB.24: 4 residues within 4Å: Chain E: T.403, A.444, A.445 Ligands: KZB.23 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:T.403, E:A.444 KZB.27: 5 residues within 4Å: Chain F: L.587, Y.591 Chain G: F.433 Ligands: KZB.29, KZB.30 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain G Hydrophobic interactions: F:L.587, F:Y.591, G:F.433 KZB.28: 7 residues within 4Å: Chain F: A.585, V.592, L.597, Q.601, Y.605, L.609 Ligands: KZB.29 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:A.585, F:V.592, F:L.597, F:Y.605, F:L.609 Hydrogen bonds: F:Y.605 KZB.29: 7 residues within 4Å: Chain F: L.581, A.584, A.585, G.588, V.592 Ligands: KZB.27, KZB.28 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:L.581 KZB.30: 6 residues within 4Å: Chain F: L.550, W.594 Chain G: F.421, Y.426, A.430 Ligands: KZB.27 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain G Hydrophobic interactions: F:L.550, F:W.594, G:F.421, G:A.430 Hydrogen bonds: G:Y.426 KZB.31: 8 residues within 4Å: Chain F: F.557, I.561, A.565, N.566, V.567 Chain G: F.440, I.441, I.444 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:V.567

2 x MG: MAGNESIUM ION(Non-covalent)

MG.13: 2 residues within 4Å: Chain A: R.459 Ligands: 0K3.14 No protein-ligand interaction detected (PLIP) MG.25: 3 residues within 4Å: Chain C: V.79 Chain E: E.376, E.438 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:E.376, E:E.438

1 x 0K3: (2Z,6Z,10Z,14Z,18Z,22Z,26Z)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-octaen-1-yl dihydrogen phosphate(Non-covalent)

0K3.14: 19 residues within 4Å: Chain A: W.263, G.264, F.268, N.271, L.275, F.278, A.323, V.364, F.365, V.368, R.383, F.384, L.387, S.449, F.453, R.459, L.460 Ligands: EGY.11, MG.13 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:W.263, A:F.268, A:N.271, A:L.275, A:L.275, A:F.278, A:A.323, A:V.364, A:V.368, A:L.387, A:F.453, A:F.453, A:L.460 Salt bridges: A:R.383

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 STT3B: 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
Magnesium transporter protein 1: H
Malectin: I

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

Membrane

We predict this structure to be a membrane protein.
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Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B

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

Magnesium transporter protein 1

Malectin

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