SMTL ID : 6c26.1

The Cryo-EM structure of a eukaryotic oligosaccharyl transferase complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x NAG- NAG- BMA- BMA- BMA- BMA- BMA: beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-2)-[beta-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-BMA-BMA-BMA-BMA.1: 10 residues within 4Å: Chain A: L.78, N.539, T.541, H.542 Chain G: H.181, H.182 Chain H: D.320, P.321, Y.322, R.349 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:R.349

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: 5 residues within 4Å: Chain A: R.504, M.505, E.509 Chain B: E.256, N.336 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.509

8 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.3: 8 residues within 4Å: Chain A: I.37, S.41, R.112, N.113, L.117, L.121 Chain B: Y.303 Ligands: EGY.6 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.121, A:L.121 Hydrogen bonds: A:S.41, A:N.113 Salt bridges: A:R.112 pi-Cation interactions: B:Y.303 EGY.4: 7 residues within 4Å: Chain A: L.58, F.63, T.92, H.99 Chain G: F.258 Ligands: EGY.7, EGY.10 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain G Hydrogen bonds: A:N.61, A:H.99 Salt bridges: A:H.99 Hydrophobic interactions: G:F.258 EGY.5: 7 residues within 4Å: Chain A: F.258, I.261, R.262, M.267 Chain E: R.69, N.71, F.74 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:N.71 Salt bridges: E:R.69 Hydrophobic interactions: A:I.261 EGY.6: 10 residues within 4Å: Chain A: I.109 Chain B: W.241, Q.250, E.252, Y.409 Chain C: T.75, F.82, V.84 Ligands: EGY.3, EGY.8 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: B:Y.409 Salt bridges: B:E.252 pi-Cation interactions: B:W.241 Hydrophobic interactions: C:V.84, A:I.109 EGY.7: 14 residues within 4Å: Chain A: M.192, C.196 Chain B: M.472, N.473, V.474, T.475 Chain E: R.109, A.112, V.116 Chain G: F.244, L.272, S.275, T.276 Ligands: EGY.4 8 PLIP interactions: 3 interactions with chain E, 3 interactions with chain B, 2 interactions with chain G Hydrophobic interactions: E:A.112, E:V.116, G:F.244, G:L.272 Salt bridges: E:R.109 Hydrogen bonds: B:N.473, B:V.474, B:T.475 EGY.8: 8 residues within 4Å: Chain A: F.25, I.29 Chain C: L.22, S.81, F.82, Y.85 Chain D: I.2 Ligands: EGY.6 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: C:F.82, A:F.25, D:I.2 EGY.9: 7 residues within 4Å: Chain A: L.224, M.228, R.230, F.378 Chain F: I.214, S.215, R.217 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain F Hydrophobic interactions: A:L.224, A:F.378 Hydrogen bonds: A:R.230, F:R.217 EGY.10: 13 residues within 4Å: Chain A: L.67, T.92, F.202, Y.203, S.206, I.253 Chain E: V.124, H.127 Chain G: Y.251, T.255, I.257 Chain H: N.380 Ligands: EGY.4 7 PLIP interactions: 4 interactions with chain A, 2 interactions with chain E, 1 interactions with chain H Hydrophobic interactions: A:T.92, A:F.202, A:Y.203, A:Y.203, E:V.124 Salt bridges: E:H.127 Hydrogen bonds: H:N.380

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

NAG.11: 1 residues within 4Å: Chain H: N.60 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bai, L. et al., The atomic structure of a eukaryotic oligosaccharyltransferase complex. Nature (2018)

Release Date

2018-01-31

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
1

C
5

D
4

E
2

F
3

G
C

H
B

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 1

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST4

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 3

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit SWP1

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1

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