SMTL ID : 7y6s.1

Cryo-EM map of IPEC-J2 cell-derived PEDV PT52 S protein with three D0-up

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.1: 2 residues within 4Å: Chain A: N.198, S.208 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.13: 2 residues within 4Å: Chain B: N.198, T.200 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.200 NAG-NAG-BMA-FUC.25: 2 residues within 4Å: Chain C: N.198, T.200 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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: 9 residues within 4Å: Chain A: L.244, S.245, N.246, N.258, Y.385, D.387, Y.389, H.397, F.428 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.258 NAG-NAG-BMA-MAN-MAN-MAN-MAN.14: 7 residues within 4Å: Chain B: L.244, N.246, N.258, Y.385, Y.389, H.397, F.428 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.385 NAG-NAG-BMA-MAN-MAN-MAN-MAN.26: 8 residues within 4Å: Chain C: L.244, S.245, N.246, N.258, Y.385, Y.389, H.397, F.428 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.385, C:N.258

3 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.3: 1 residues within 4Å: Chain A: N.282 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.282 NAG-FUC.15: 1 residues within 4Å: Chain B: N.282 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.282 NAG-FUC.27: 2 residues within 4Å: Chain C: N.282, Q.283 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.282

12 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.4: 6 residues within 4Å: Chain A: Q.24, N.306, R.378, D.414, D.415, S.418 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.414, A:D.415 NAG-NAG-BMA.6: 3 residues within 4Å: Chain A: Y.166, G.315, N.407 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.166 NAG-NAG-BMA.8: 6 residues within 4Å: Chain A: D.622, S.624, M.626, N.670, T.672, S.673 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 1 residues within 4Å: Chain A: N.763 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.16: 7 residues within 4Å: Chain B: Q.24, N.306, D.307, R.378, D.414, D.415, S.418 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.415, B:D.415 NAG-NAG-BMA.18: 3 residues within 4Å: Chain B: R.154, Y.166, N.407 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.166 NAG-NAG-BMA.20: 6 residues within 4Å: Chain B: D.622, S.624, F.625, N.670, T.672, S.673 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 1 residues within 4Å: Chain B: N.763 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.28: 5 residues within 4Å: Chain C: Q.24, N.306, R.378, D.414, D.415 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.30: 2 residues within 4Å: Chain C: Y.166, N.407 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.166 NAG-NAG-BMA.32: 5 residues within 4Å: Chain C: S.624, M.626, N.670, T.672, S.673 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.34: 2 residues within 4Å: Chain C: N.763, D.1147 No protein-ligand interaction detected (PLIP)

12 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.5: 3 residues within 4Å: Chain A: H.320, G.324, N.326 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: N.708, N.721, D.722 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:D.722 NAG-NAG.9: 4 residues within 4Å: Chain A: R.711, N.725 Chain C: R.869, R.871 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.869, C:R.869, C:R.871 NAG-NAG.11: 3 residues within 4Å: Chain A: N.855, T.857, N.858 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain B: H.320, G.324, N.326 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 2 residues within 4Å: Chain B: N.708, N.721 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 2 residues within 4Å: Chain A: R.871 Chain B: N.725 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.871, A:R.871 NAG-NAG.23: 3 residues within 4Å: Chain B: N.855, T.857, N.858 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 4 residues within 4Å: Chain C: H.320, G.324, N.326, D.360 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 2 residues within 4Å: Chain C: N.708, N.721 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 6 residues within 4Å: Chain B: R.869, R.871 Chain C: R.711, G.723, S.724, N.725 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.869, B:R.869, B:R.871 NAG-NAG.35: 3 residues within 4Å: Chain C: N.855, T.857, N.858 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.12: 4 residues within 4Å: Chain A: D.1158, V.1210, Y.1212, N.1214 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.24: 3 residues within 4Å: Chain B: V.1210, Y.1212, N.1214 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.36: 4 residues within 4Å: Chain C: D.1158, V.1210, Y.1212, N.1214 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.1210

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

NAG.37: 2 residues within 4Å: Chain A: N.649 Chain C: R.906 No protein-ligand interaction detected (PLIP) NAG.38: 4 residues within 4Å: Chain A: T.768, N.769, D.1144, V.1146 No protein-ligand interaction detected (PLIP) NAG.39: 2 residues within 4Å: Chain A: S.987, N.991 No protein-ligand interaction detected (PLIP) NAG.40: 2 residues within 4Å: Chain A: R.1217, N.1231 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1231 NAG.41: 1 residues within 4Å: Chain B: N.649 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.649 NAG.42: 3 residues within 4Å: Chain B: T.768, N.769, D.1144 No protein-ligand interaction detected (PLIP) NAG.43: 2 residues within 4Å: Chain B: S.987, N.991 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.991 NAG.44: 1 residues within 4Å: Chain B: N.1231 No protein-ligand interaction detected (PLIP) NAG.45: 2 residues within 4Å: Chain B: R.906 Chain C: N.649 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:R.906 NAG.46: 5 residues within 4Å: Chain C: T.768, N.769, R.976, L.980, V.1146 No protein-ligand interaction detected (PLIP) NAG.47: 2 residues within 4Å: Chain C: S.987, N.991 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.991 NAG.48: 2 residues within 4Å: Chain C: R.1217, N.1231 No protein-ligand interaction detected (PLIP)

Links

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Citation

Huang, C.Y. et al., In situ structure and dynamics of an alphacoronavirus spike protein by cryo-ET and cryo-EM. Nat Commun (2022)

Release Date

2022-08-03

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein