SMTL ID : 8tc5.1

Cryo-EM Structure of Spike Glycoprotein from Civet Coronavirus SZ3 in Closed Conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

7 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: 4 residues within 4Å: Chain A: N.1065, G.1066, T.1067, F.1070 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain B: N.1065, G.1066, T.1067, F.1070 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain C: N.1065, T.1067, F.1070 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain C: N.315, S.343 Ligands: NAG-NAG-BMA-MAN-FUC.34 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain A: N.58 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 1 residues within 4Å: Chain B: N.58 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 2 residues within 4Å: Chain C: N.58 Ligands: NAG.49 No protein-ligand interaction detected (PLIP)

11 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.4: 2 residues within 4Å: Chain A: N.303, K.551 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.5: 6 residues within 4Å: Chain A: Q.862 Chain C: A.673, T.678, E.1039, R.1040, N.1041 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.673 NAG-NAG-FUC.13: 3 residues within 4Å: Chain A: D.252, N.254 Chain C: R.529 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.16: 4 residues within 4Å: Chain A: T.678, E.1039, R.1040, N.1041 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.678 NAG-NAG-FUC.17: 2 residues within 4Å: Chain A: N.315, S.343 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.23: 2 residues within 4Å: Chain B: N.303, K.551 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.25: 3 residues within 4Å: Chain A: R.529 Chain B: D.252, N.254 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.28: 5 residues within 4Å: Chain B: T.678, E.1039, R.1040, N.1041 Chain C: Q.862 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.678 NAG-NAG-FUC.29: 2 residues within 4Å: Chain B: N.315, S.343 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.35: 2 residues within 4Å: Chain C: N.303, K.551 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.37: 3 residues within 4Å: Chain B: R.529 Chain C: D.252, N.254 No protein-ligand interaction detected (PLIP)

9 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.7: 4 residues within 4Å: Chain A: N.93, N.94, E.116, F.142 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.116 NAG-NAG-BMA-FUC.10: 10 residues within 4Å: Chain A: N.104, S.105, T.106, N.107, V.109, R.111, Q.132, T.135, F.138, I.149 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.111 NAG-NAG-BMA-FUC.15: 7 residues within 4Å: Chain A: D.763, N.768, S.770, Q.771, I.898, S.899, Q.902 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.771 NAG-NAG-BMA-FUC.18: 5 residues within 4Å: Chain B: N.93, N.94, K.95, E.116, F.142 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.21: 9 residues within 4Å: Chain B: N.104, S.105, T.106, N.107, V.109, R.111, Q.132, F.138, I.149 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.111 NAG-NAG-BMA-FUC.27: 7 residues within 4Å: Chain B: D.763, N.768, S.770, Q.771, I.898, S.899, Q.902 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Q.771 NAG-NAG-BMA-FUC.30: 4 residues within 4Å: Chain C: N.93, N.94, E.116, F.142 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.33: 10 residues within 4Å: Chain C: N.104, S.105, T.106, N.107, V.109, R.111, Q.132, T.135, F.138, I.149 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.111 NAG-NAG-BMA-FUC.39: 7 residues within 4Å: Chain C: D.763, N.768, S.770, Q.771, I.898, S.899, Q.902 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Q.771

6 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.8: 5 residues within 4Å: Chain A: F.142, N.143 Chain C: Y.323, A.324, I.440 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 7 residues within 4Å: Chain A: N.50, V.51, T.52, K.69, V.239, G.240, Y.241 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.69 NAG-NAG-BMA.19: 5 residues within 4Å: Chain A: Y.323, A.324, I.440 Chain B: F.142, N.143 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.24: 7 residues within 4Å: Chain B: N.50, V.51, T.52, K.69, V.239, G.240, Y.241 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.69 NAG-NAG-BMA.31: 5 residues within 4Å: Chain B: Y.323, A.324, I.440 Chain C: F.142, N.143 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.36: 7 residues within 4Å: Chain C: N.50, V.51, T.52, K.69, V.239, G.240, Y.241 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.69

6 x NAG- NAG- BMA- MAN- FUC: 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-FUC.11: 4 residues within 4Å: Chain A: N.342 Chain C: Y.427, L.428, Y.460 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-FUC.14: 5 residues within 4Å: Chain A: N.587, T.589, D.590, Q.615 Chain B: M.801 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-FUC.22: 4 residues within 4Å: Chain A: Y.427, L.428, Y.460 Chain B: N.342 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-FUC.26: 4 residues within 4Å: Chain B: N.587, T.589, D.590 Chain C: M.801 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-FUC.34: 5 residues within 4Å: Chain B: Y.427, L.428, Y.460 Chain C: N.342 Ligands: NAG-NAG.6 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-FUC.38: 4 residues within 4Å: Chain A: M.801 Chain C: N.587, T.589, D.590 No protein-ligand interaction detected (PLIP)

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

NAG.40: 5 residues within 4Å: Chain A: Q.11, A.12, P.13, N.14, T.60 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.11, A:T.60 NAG.42: 1 residues within 4Å: Chain A: N.574 No protein-ligand interaction detected (PLIP) NAG.43: 3 residues within 4Å: Chain A: N.676, I.1097, G.1098 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.676 NAG.44: 5 residues within 4Å: Chain B: Q.11, A.12, P.13, N.14, T.60 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.60 Hydrogen bonds: B:Q.11, B:A.12 NAG.46: 1 residues within 4Å: Chain B: N.574 No protein-ligand interaction detected (PLIP) NAG.47: 3 residues within 4Å: Chain B: N.676, I.1097, G.1098 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.676 NAG.49: 4 residues within 4Å: Chain C: Q.11, N.14, T.60 Ligands: NAG-NAG.32 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.11, C:N.14 NAG.50: 4 residues within 4Å: Chain C: N.676, N.677, I.1097, G.1098 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.676 NAG.51: 2 residues within 4Å: Chain C: N.574, A.575 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.575 Hydrogen bonds: C:N.574

3 x EIC: LINOLEIC ACID(Non-covalent)

EIC.41: 24 residues within 4Å: Chain A: C.308, P.309, F.310, V.313, F.314, I.330, A.335, Y.337, L.340, Y.341, F.346, F.349, L.359, F.364, V.367, A.369, L.406, L.484, F.486, V.495 Chain C: R.380, Q.381, T.387, G.388 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:V.313, A:Y.337, A:Y.337, A:F.364, A:F.364, A:L.484, A:L.484, A:F.486 Water bridges: C:R.380, C:R.380, C:R.380, C:Q.381 Salt bridges: C:R.380 EIC.45: 24 residues within 4Å: Chain A: R.380, Q.381, T.387, G.388 Chain B: C.308, P.309, F.310, V.313, F.314, I.330, A.335, Y.337, L.340, Y.341, F.346, F.349, L.359, F.364, V.367, A.369, L.406, L.484, F.486, V.495 16 PLIP interactions: 11 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:F.310, B:F.310, B:V.313, B:A.335, B:Y.337, B:Y.337, B:Y.337, B:F.364, B:F.364, B:L.484, B:F.486 Water bridges: A:R.380, A:R.380, A:R.380, A:Q.381 Salt bridges: A:R.380 EIC.48: 24 residues within 4Å: Chain B: R.380, Q.381, T.387, G.388 Chain C: C.308, P.309, F.310, V.313, F.314, I.330, A.335, Y.337, L.340, Y.341, F.346, F.349, L.359, F.364, V.367, A.369, L.406, L.484, F.486, V.495 14 PLIP interactions: 9 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:V.313, C:A.335, C:Y.337, C:Y.337, C:Y.337, C:F.364, C:F.364, C:L.484, C:F.486 Water bridges: B:R.380, B:R.380, B:R.380, B:Q.381 Salt bridges: B:R.380

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hills, F.R. et al., Variation in structural motifs within SARS-related coronavirus spike proteins. Plos Pathog. (2024)

Release Date

2024-05-15

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein