SMTL ID : 8age.1

Structure of yeast oligosaccharylransferase complex with acceptor peptide bound

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

TYR-ALA-ASN-ALA-THR-SER-ALA.1: 15 residues within 4Å: Chain A: F.46, D.47, R.159, S.347, V.348, S.349, E.350, W.516, W.517, D.518, N.535, K.586, W.589 Chain H: Q.263 Ligands: 323.21 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.46 Hydrogen bonds: A:D.47, A:R.159, A:S.347, A:S.349, A:S.349, A:E.350, A:W.516, A:D.518, A:N.535

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: 13 residues within 4Å: Chain A: L.78, W.538, N.539, T.541, H.542, I.545 Chain F: H.181, H.182, I.183 Chain G: D.320, P.321, Y.322, R.349 6 PLIP interactions: 4 interactions with chain G, 2 interactions with chain A Hydrogen bonds: G:D.320, G:D.320, G:Y.322, G:R.349, G:R.349 Hydrophobic interactions: A:T.541, A:I.545

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.3: 4 residues within 4Å: Chain A: M.505 Chain E: E.256, L.307, N.336 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain E: N.400 No protein-ligand interaction detected (PLIP)

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

MN.5: 2 residues within 4Å: Chain A: D.47, D.166 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.47, A:D.166

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

CPL.6: 14 residues within 4Å: Chain A: L.33, V.36, I.37, S.41, L.101, L.105, I.109, R.112, N.113, L.117, L.121 Chain B: M.1 Chain E: Y.303 Ligands: CPL.14 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:I.37, A:L.101, A:L.105, A:I.109, A:L.117, A:L.121 Hydrogen bonds: A:N.113, A:N.113 Salt bridges: A:R.112 pi-Cation interactions: E:Y.303 CPL.13: 17 residues within 4Å: Chain A: G.26, I.29, L.33 Chain B: M.1, I.2 Chain C: L.22, A.29, I.30, T.75, A.78, S.81, F.82, G.83, Y.85 Chain E: D.301 Ligands: KZB.12, CPL.14 10 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A, 3 interactions with chain B, 1 interactions with chain E Hydrophobic interactions: C:A.29, C:I.30, C:A.78, C:F.82, A:I.29, A:L.33 Hydrogen bonds: B:M.1, B:M.1, B:I.2 Salt bridges: E:D.301 CPL.14: 11 residues within 4Å: Chain A: I.109 Chain C: T.75, V.84 Chain E: W.241, Q.250, E.252, Y.409, F.410, I.453 Ligands: CPL.6, CPL.13 8 PLIP interactions: 2 interactions with chain C, 6 interactions with chain E Hydrophobic interactions: C:T.75, C:V.84, E:F.410, E:F.410, E:I.453 Hydrogen bonds: E:Y.409 Salt bridges: E:E.252 pi-Cation interactions: E:W.241 CPL.15: 21 residues within 4Å: Chain A: L.67, T.92, F.96, L.199, F.202, Y.203, S.206, Q.252, I.253, P.254 Chain D: F.123, V.124, H.127 Chain F: F.244, F.248, Y.251, T.255, S.256, I.257 Chain G: R.385 Ligands: KZB.9 17 PLIP interactions: 8 interactions with chain A, 4 interactions with chain D, 5 interactions with chain F Hydrophobic interactions: A:L.67, A:T.92, A:F.96, A:L.199, A:F.202, A:Y.203, A:I.253, A:P.254, D:F.123, D:V.124, F:F.244, F:F.248 Salt bridges: D:H.127, D:H.127 Hydrogen bonds: F:Y.251, F:I.257 pi-Cation interactions: F:Y.251

1 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.7: 8 residues within 4Å: Chain A: L.224, R.230, F.378, L.381, I.389 Chain H: S.216, R.217, W.220 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain H Hydrophobic interactions: A:L.224, A:F.378, A:L.381, A:I.389 Hydrogen bonds: A:R.230 Salt bridges: H:R.217

8 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)(Covalent)

KZB.8: 6 residues within 4Å: Chain A: F.258, I.261, R.262 Chain D: N.71, F.72, F.74 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.74 KZB.9: 11 residues within 4Å: Chain A: L.58, V.59, N.61, F.63, T.92, A.95, F.96, W.98, H.99 Chain F: F.258 Ligands: CPL.15 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.92, A:A.95, A:F.96, A:W.98, A:H.99 KZB.10: 4 residues within 4Å: Chain A: F.375, L.379 Chain H: I.218, F.293 3 PLIP interactions: 2 interactions with chain H, 1 interactions with chain A Hydrophobic interactions: H:I.218, H:F.293, A:L.379 KZB.11: 3 residues within 4Å: Chain B: I.12, T.13, V.17 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.12, B:T.13, B:V.17 KZB.12: 2 residues within 4Å: Chain B: Q.6 Ligands: CPL.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.6, B:Q.6 KZB.16: 2 residues within 4Å: Chain F: R.250, L.253 No protein-ligand interaction detected (PLIP) KZB.17: 6 residues within 4Å: Chain F: A.249, Y.252, L.253 Chain G: W.387, I.396 Ligands: KZB.20 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain G Hydrophobic interactions: F:A.249, F:Y.252, G:W.387 KZB.20: 10 residues within 4Å: Chain F: V.200, F.204, I.207 Chain G: W.387, W.393, I.396, S.397, C.400, G.401 Ligands: KZB.17 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain G Hydrophobic interactions: F:V.200, F:F.204, F:I.207, G:W.393, G:I.396

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

NAG.18: 1 residues within 4Å: Chain G: N.332 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.332 NAG.19: 3 residues within 4Å: Chain G: Q.32, S.33, N.60 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:Q.32

1 x 323: 2-[3,6-bis(dimethylamino)xanthen-9-yl]-5-methanoyl-benzoate(Non-covalent)

323.21: 6 residues within 4Å: Chain A: F.361, T.472, A.473, S.476 Chain H: F.262 Ligands: TYR-ALA-ASN-ALA-THR-SER-ALA.1 No protein-ligand interaction detected (PLIP)

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
OST4 isoform 1: 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 2: F
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1: G
OST3 isoform 1: 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

OST4 isoform 1

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1

OST3 isoform 1

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