SMTL ID : 7w73.1

Cryo-EM map of PEDV S protein with one protomer in the D0-up conformation while the other two in the D0-down conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

25 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.1: 6 residues within 4Å: Chain A: S.263, N.264, Y.403, Y.407, H.415, F.446 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.403 NAG-NAG-BMA-MAN-MAN.3: 5 residues within 4Å: Chain A: S.518, A.519, A.531, N.556, T.558 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.4: 6 residues within 4Å: Chain A: P.505, D.640, N.688, V.689, T.690, S.691 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.640 NAG-NAG-BMA-MAN-MAN.5: 3 residues within 4Å: Chain A: T.724, N.726, N.739 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.739 Hydrogen bonds: A:N.726 NAG-NAG-BMA-MAN-MAN.7: 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.11: 4 residues within 4Å: Chain A: H.338, G.342, N.344, Y.380 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.380 NAG-NAG-BMA-MAN-MAN.13: 4 residues within 4Å: Chain A: Q.42, N.324, T.394, R.396 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.42 NAG-NAG-BMA-MAN-MAN.15: 5 residues within 4Å: Chain A: N.781 Chain B: F.966, T.967, A.968, A.969 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.17: 4 residues within 4Å: Chain B: N.264, Y.403, Y.407, F.446 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.18: 5 residues within 4Å: Chain B: N.233, N.324, D.434, V.435, W.439 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.20: 4 residues within 4Å: Chain B: S.518, A.519, N.556, T.558 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.21: 6 residues within 4Å: Chain B: D.640, M.644, N.688, T.690, S.691, Y.695 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.22: 2 residues within 4Å: Chain B: N.726, N.739 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.24: 5 residues within 4Å: Chain B: N.781, D.1165, V.1166, I.1167 Chain C: A.969 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.25: 3 residues within 4Å: Chain B: T.786, N.787, D.1162 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.27: 8 residues within 4Å: Chain B: F.296, H.338, G.342, T.343, N.344, D.378, T.379, Y.380 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.30: 4 residues within 4Å: Chain C: V.46, N.216, T.218, I.225 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.31: 7 residues within 4Å: Chain A: R.818 Chain C: L.262, S.263, N.264, Y.403, Y.407, F.446 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.818 NAG-NAG-BMA-MAN-MAN.33: 7 residues within 4Å: Chain C: A.232, N.233, N.324, D.434, V.435, S.436, W.439 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.233 NAG-NAG-BMA-MAN-MAN.34: 5 residues within 4Å: Chain C: H.338, G.342, N.344, T.379, Y.380 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.36: 6 residues within 4Å: Chain C: S.518, A.519, S.520, N.556, V.557, T.558 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.37: 2 residues within 4Å: Chain C: N.726, N.739 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.739 NAG-NAG-BMA-MAN-MAN.38: 6 residues within 4Å: Chain A: A.969 Chain C: G.780, N.781, V.1166, I.1167, L.1194 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.1194 NAG-NAG-BMA-MAN-MAN.39: 2 residues within 4Å: Chain C: N.787, D.1162 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.44: 10 residues within 4Å: Chain C: P.505, G.637, V.638, T.639, D.640, N.688, T.690, S.691, A.693, Y.695 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.639

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.2: 3 residues within 4Å: Chain A: F.512, N.514, S.552 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.512 NAG-NAG-BMA.8: 3 residues within 4Å: Chain A: G.871, N.873, T.875 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 6 residues within 4Å: Chain A: Y.184, K.186, A.331, E.332, S.334, N.425 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.186 NAG-NAG-BMA.19: 4 residues within 4Å: Chain B: F.512, N.514, N.537, S.552 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.512 NAG-NAG-BMA.26: 3 residues within 4Å: Chain B: N.139, N.873, T.875 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.139, B:N.139, B:T.875 NAG-NAG-BMA.29: 4 residues within 4Å: Chain B: V.1228, Y.1230, V.1231, N.1232 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.35: 4 residues within 4Å: Chain C: F.512, N.514, N.537, S.552 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.512 NAG-NAG-BMA.40: 7 residues within 4Å: Chain C: I.131, P.136, T.137, A.138, N.873, T.875, N.876 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.41: 2 residues within 4Å: Chain C: D.1176, N.1232 No protein-ligand interaction detected (PLIP)

4 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.6: 3 residues within 4Å: Chain A: N.743, T.745 Chain B: R.887 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.887 NAG-NAG-BMA-FUC.10: 3 residues within 4Å: Chain A: F.299, N.300, A.315 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.23: 3 residues within 4Å: Chain B: G.741, S.742, N.743 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.43: 6 residues within 4Å: Chain A: A.886, R.887 Chain C: R.729, S.742, N.743, I.762 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.886, A:R.887

1 x NAG- NAG- BMA- MAN: 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.9: 5 residues within 4Å: Chain A: D.1176, V.1227, V.1228, Y.1230, N.1232 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.1228

4 x NAG- NAG- BMA- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-FUC.12: 7 residues within 4Å: Chain A: A.45, V.46, N.216, T.218, S.219, I.225, N.233 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.225 NAG-NAG-BMA-MAN-MAN-FUC.16: 4 residues within 4Å: Chain B: V.46, N.216, T.218, I.225 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.225 NAG-NAG-BMA-MAN-MAN-FUC.28: 2 residues within 4Å: Chain B: N.300, Q.301 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-FUC.32: 2 residues within 4Å: Chain C: N.300, Q.301 No protein-ligand interaction detected (PLIP)

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

NAG-FUC.42: 4 residues within 4Å: Chain A: R.924 Chain C: T.666, N.667, S.668 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.924, C:N.667, A:R.924

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

NAG.45: 4 residues within 4Å: Chain A: N.351, S.352, S.353, Y.371 Ligand excluded by PLIP NAG.46: 5 residues within 4Å: Chain A: T.666, N.667, S.668 Chain B: R.924, S.925 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain A: S.1005, G.1008, N.1009, S.1012 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain A: N.1249, K.1250, D.1253 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain A: N.381, Y.561 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain A: G.115, N.116, T.117, N.118 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain B: T.113, N.114, N.118 Ligand excluded by PLIP NAG.52: 5 residues within 4Å: Chain B: T.666, N.667, S.668 Chain C: R.924, S.925 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain B: S.1005, G.1008, N.1009, S.1012 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain B: N.1249 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain B: N.381, Y.561 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain B: L.293, G.294, N.425 Ligand excluded by PLIP NAG.57: 4 residues within 4Å: Chain B: N.351, S.352, Q.368, Y.371 Ligand excluded by PLIP NAG.58: 4 residues within 4Å: Chain C: E.332, S.334, N.425, F.426 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain C: S.1005, G.1008, N.1009 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain C: N.1249, D.1253 Ligand excluded by PLIP NAG.61: 3 residues within 4Å: Chain C: A.112, N.114, N.118 Ligand excluded by PLIP NAG.62: 3 residues within 4Å: Chain C: Y.380, N.381, Y.561 Ligand excluded by PLIP NAG.63: 6 residues within 4Å: Chain C: S.327, L.330, A.331, N.351, Q.368, Y.371 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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