SMTL ID : 7oci.1

Cryo-EM structure of yeast Ost6p containing oligosaccharyltransferase complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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.1: 6 residues within 4Å: Chain A: V.234, E.256, N.334, N.336 Chain F: M.505, E.509 No protein-ligand interaction detected (PLIP)

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.2: 11 residues within 4Å: Chain F: L.78, N.539, H.542 Chain G: D.320, P.321, Y.322, R.349 Chain H: I.180, H.181, H.182, I.183 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:D.320

6 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)

PEE.3: 8 residues within 4Å: Chain A: W.241, E.252, Y.409 Chain E: T.75, F.82, V.84 Chain F: N.113 Ligands: PEE.11 7 PLIP interactions: 3 interactions with chain E, 3 interactions with chain A, 1 interactions with chain F Hydrophobic interactions: E:F.82, E:F.82, E:V.84, A:Y.409 Hydrogen bonds: A:E.252, A:Y.409, F:N.113 PEE.5: 6 residues within 4Å: Chain B: M.92, L.96, C.99 Chain F: Q.277, A.280, F.284 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain B Hydrophobic interactions: F:A.280 Salt bridges: B:R.95 PEE.7: 8 residues within 4Å: Chain C: W.215, K.216, S.219 Chain F: L.224, L.227, M.228, R.230, L.381 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:L.224, F:L.224, F:L.227 Hydrogen bonds: F:R.230, F:L.381 Salt bridges: F:R.230 PEE.8: 9 residues within 4Å: Chain D: M.1, I.2, L.10 Chain E: L.33, S.81, F.82 Chain F: G.26, I.29 Ligands: AJP.9 7 PLIP interactions: 4 interactions with chain D, 1 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: D:L.10, F:I.29, E:L.33, E:F.82 Hydrogen bonds: D:M.1, D:M.1, D:I.2 PEE.11: 13 residues within 4Å: Chain A: F.410, I.453 Chain D: M.1 Chain F: I.29, L.33, V.36, L.105, I.109, R.112, N.113, L.117, L.121 Ligands: PEE.3 10 PLIP interactions: 9 interactions with chain F, 1 interactions with chain A Hydrophobic interactions: F:I.29, F:L.33, F:I.109, F:L.117, F:L.121, A:I.453 Hydrogen bonds: F:S.41, F:S.41, F:N.113 Salt bridges: F:R.112 PEE.15: 18 residues within 4Å: Chain B: F.123, V.124, H.127, N.130 Chain F: L.67, P.88, L.199, F.202, Y.203, S.206, Q.252, P.254 Chain G: N.380 Chain H: Y.251, G.254, T.255, S.256, I.257 14 PLIP interactions: 6 interactions with chain B, 5 interactions with chain F, 2 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: B:F.123, B:F.123, B:V.124, F:L.67, F:L.199, F:F.202, F:Y.203, F:Y.203 Hydrogen bonds: B:N.130, H:Y.251, H:I.257, G:N.380 Salt bridges: B:H.127, B:H.127

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

NAG.4: 3 residues within 4Å: Chain A: N.400, S.402, E.404 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.400, A:E.404 NAG.13: 3 residues within 4Å: Chain G: N.332, D.333, S.334 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:N.332, G:S.334 NAG.14: 4 residues within 4Å: Chain G: Q.32, S.33, D.58, N.60 No protein-ligand interaction detected (PLIP)

2 x AJP: Digitonin(Non-covalent)

AJP.6: 5 residues within 4Å: Chain B: N.71, F.72, F.74 Chain F: I.261, R.262 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:N.71, B:F.72, B:F.74 Hydrophobic interactions: F:R.262 AJP.9: 5 residues within 4Å: Chain D: Q.6, F.14 Chain E: L.33, F.82 Ligands: PEE.8 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:L.33, E:F.82 Hydrogen bonds: D:Q.6

1 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 4 residues within 4Å: Chain F: D.47, D.166, R.404 Ligands: V8K.12 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.47

1 x V8K: Dolichylphosphate(Non-covalent)

V8K.12: 12 residues within 4Å: Chain B: C.84, V.85 Chain F: W.208, N.216, G.271, F.273, G.274, Q.277, F.398, R.404, L.405 Ligands: MG.10 7 PLIP interactions: 6 interactions with chain F, 1 interactions with chain B Hydrophobic interactions: F:W.208, F:N.216, F:F.273, F:F.398, F:L.405, B:V.85 Salt bridges: F:R.404

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neuhaus, J.D. et al., Functional analysis of Ost3p and Ost6p containing yeast oligosaccharyltransferases. Glycobiology (2021)

Release Date

2022-02-16

Peptides

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1: A
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2: B
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST6: 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
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST6 - TM1: 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 1

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST6

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

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST6 - TM1

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