SMTL ID : 7w6m.1

Cryo-EM map of PEDV (Pintung 52) S protein with all three protomers in the D0-down conformation determined in situ on intact viral particles.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

6 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: 6 residues within 4Å: Chain A: A.43, P.44, A.45, V.46, N.216, T.218 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.218 Hydrogen bonds: A:T.218 NAG-NAG-BMA-FUC.3: 2 residues within 4Å: Chain A: N.300, Q.301 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.300 NAG-NAG-BMA-FUC.16: 6 residues within 4Å: Chain B: A.43, P.44, A.45, V.46, N.216, T.218 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.218 Hydrogen bonds: B:T.218 NAG-NAG-BMA-FUC.18: 2 residues within 4Å: Chain B: N.300, Q.301 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.300 NAG-NAG-BMA-FUC.31: 7 residues within 4Å: Chain C: A.43, P.44, A.45, V.46, N.216, T.218, I.225 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:T.218, C:I.225 Hydrogen bonds: C:T.218 NAG-NAG-BMA-FUC.33: 2 residues within 4Å: Chain C: N.300, Q.301 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.300

21 x NAG- NAG- BMA- MAN- MAN: 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.2: 5 residues within 4Å: Chain A: L.262, N.264, Y.403, D.405, Y.407 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.403 NAG-NAG-BMA-MAN-MAN.7: 3 residues within 4Å: Chain A: F.512, N.514, N.537 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.512 NAG-NAG-BMA-MAN-MAN.9: 7 residues within 4Å: Chain A: D.640, S.642, N.688, T.690, S.691 Chain B: A.366, T.367 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:D.640 NAG-NAG-BMA-MAN-MAN.10: 2 residues within 4Å: Chain A: N.726, N.739 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.726, A:N.739, A:N.739 NAG-NAG-BMA-MAN-MAN.11: 5 residues within 4Å: Chain A: N.781, I.1167 Chain B: F.966, T.967, A.969 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.12: 5 residues within 4Å: Chain A: T.786, N.787, D.1162, F.1163, V.1164 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.14: 4 residues within 4Å: Chain A: V.1228, Y.1230, V.1231, N.1232 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.1228 NAG-NAG-BMA-MAN-MAN.17: 5 residues within 4Å: Chain B: L.262, N.264, Y.403, D.405, Y.407 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.403 NAG-NAG-BMA-MAN-MAN.22: 3 residues within 4Å: Chain B: F.512, N.514, N.537 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.512 NAG-NAG-BMA-MAN-MAN.24: 7 residues within 4Å: Chain B: D.640, S.642, N.688, T.690, S.691 Chain C: A.366, T.367 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:D.640 NAG-NAG-BMA-MAN-MAN.25: 2 residues within 4Å: Chain B: N.726, N.739 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.726, B:N.739, B:N.739 NAG-NAG-BMA-MAN-MAN.26: 5 residues within 4Å: Chain B: N.781, I.1167 Chain C: F.966, T.967, A.969 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.27: 5 residues within 4Å: Chain B: T.786, N.787, D.1162, F.1163, V.1164 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.29: 4 residues within 4Å: Chain B: V.1228, Y.1230, V.1231, N.1232 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.1228 NAG-NAG-BMA-MAN-MAN.32: 5 residues within 4Å: Chain C: L.262, N.264, Y.403, D.405, Y.407 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.403 NAG-NAG-BMA-MAN-MAN.37: 3 residues within 4Å: Chain C: F.512, N.514, N.537 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.512 NAG-NAG-BMA-MAN-MAN.39: 7 residues within 4Å: Chain A: A.366, T.367 Chain C: D.640, S.642, N.688, T.690, S.691 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:D.640 NAG-NAG-BMA-MAN-MAN.40: 2 residues within 4Å: Chain C: N.726, N.739 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.726, C:N.739, C:N.739 NAG-NAG-BMA-MAN-MAN.41: 5 residues within 4Å: Chain A: F.966, T.967, A.969 Chain C: N.781, I.1167 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.42: 5 residues within 4Å: Chain C: T.786, N.787, D.1162, F.1163, V.1164 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.44: 4 residues within 4Å: Chain C: V.1228, Y.1230, V.1231, N.1232 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.1228

9 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: 9 residues within 4Å: Chain A: A.232, N.233, I.287, N.324, D.433, D.434, V.435, S.436, W.439 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.233 NAG-NAG-BMA.5: 4 residues within 4Å: Chain A: H.338, G.342, N.344, Y.380 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 5 residues within 4Å: Chain A: T.137, A.138, N.139, N.873, T.875 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.137, A:N.139 NAG-NAG-BMA.19: 9 residues within 4Å: Chain B: A.232, N.233, I.287, N.324, D.433, D.434, V.435, S.436, W.439 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.233 NAG-NAG-BMA.20: 4 residues within 4Å: Chain B: H.338, G.342, N.344, Y.380 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.28: 5 residues within 4Å: Chain B: T.137, A.138, N.139, N.873, T.875 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.137, B:N.139 NAG-NAG-BMA.34: 9 residues within 4Å: Chain C: A.232, N.233, I.287, N.324, D.433, D.434, V.435, S.436, W.439 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.233 NAG-NAG-BMA.35: 4 residues within 4Å: Chain C: H.338, G.342, N.344, Y.380 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.43: 5 residues within 4Å: Chain C: T.137, A.138, N.139, N.873, T.875 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.137, C:N.139

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

NAG-NAG.6: 3 residues within 4Å: Chain A: Y.380, N.381, Y.561 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain B: Y.380, N.381, Y.561 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 3 residues within 4Å: Chain C: Y.380, N.381, Y.561 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-3)-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-MAN-FUC.8: 4 residues within 4Å: Chain A: S.518, A.531, D.533, N.556 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.531 Hydrogen bonds: A:S.518 NAG-NAG-BMA-MAN-FUC.23: 4 residues within 4Å: Chain B: S.518, A.531, D.533, N.556 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.531 Hydrogen bonds: B:S.518 NAG-NAG-BMA-MAN-FUC.38: 4 residues within 4Å: Chain C: S.518, A.531, D.533, N.556 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.531 Hydrogen bonds: C:S.518

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.15: 5 residues within 4Å: Chain A: R.729, N.743, I.762, G.763, Y.764 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.729, A:R.729 NAG-NAG-FUC.30: 5 residues within 4Å: Chain B: R.729, N.743, I.762, G.763, Y.764 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.729, B:R.729 NAG-NAG-FUC.45: 5 residues within 4Å: Chain C: R.729, N.743, I.762, G.763, Y.764 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.729, C:R.729

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

NAG.46: 4 residues within 4Å: Chain A: A.112, T.113, N.114, N.118 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain A: L.293, G.294, N.425 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain A: L.665, N.667 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain A: N.351, S.353, Y.371 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain A: N.1249, K.1250, D.1253 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain A: S.1005, N.1009 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain B: A.112, T.113, N.114, N.118 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain B: L.293, G.294, N.425 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain B: L.665, N.667 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain B: N.351, S.353, Y.371 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain B: N.1249, K.1250, D.1253 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain B: S.1005, N.1009 Ligand excluded by PLIP NAG.58: 4 residues within 4Å: Chain C: A.112, T.113, N.114, N.118 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain C: L.293, G.294, N.425 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain C: L.665, N.667 Ligand excluded by PLIP NAG.61: 3 residues within 4Å: Chain C: N.351, S.353, Y.371 Ligand excluded by PLIP NAG.62: 3 residues within 4Å: Chain C: N.1249, K.1250, D.1253 Ligand excluded by PLIP NAG.63: 2 residues within 4Å: Chain C: S.1005, N.1009 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

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

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