SMTL ID : 9cvh.1

Cryo-EM structure of SARS-CoV-2 spike protein Ecto-domain with internal tag, 1RBD UP, State-2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

10 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.1: 7 residues within 4Å: Chain A: T.755, N.756, F.757, L.961, N.964, Q.965, Q.1110 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.961 NAG-NAG-BMA.3: 5 residues within 4Å: Chain A: N.1137, G.1138, T.1139, H.1140, F.1142 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 4 residues within 4Å: Chain A: N.370, T.372, Q.619, T.620 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 4 residues within 4Å: Chain B: N.319, E.320, N.321 Chain C: K.597 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.321 NAG-NAG-BMA.11: 5 residues within 4Å: Chain B: N.1137, G.1138, T.1139, H.1140, F.1142 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 2 residues within 4Å: Chain B: I.1171, N.1173 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 7 residues within 4Å: Chain C: N.756, F.757, T.758, L.961, N.964, Q.965, Q.1110 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.961 NAG-NAG-BMA.15: 3 residues within 4Å: Chain C: N.840, S.842, Q.843 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 4 residues within 4Å: Chain C: N.1137, T.1139, H.1140, F.1142 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.1140 NAG-NAG-BMA.18: 5 residues within 4Å: Chain A: K.596, K.597 Chain C: F.82, E.320, N.321 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.597

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

NAG-NAG.2: 3 residues within 4Å: Chain A: N.840, S.842, Q.974 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: V.1172, N.1173 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 6 residues within 4Å: Chain B: T.755, N.756, L.961, N.964, Q.965, Q.1110 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.961 NAG-NAG.9: 3 residues within 4Å: Chain B: N.840, S.842, Q.843 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 6 residues within 4Å: Chain A: Q.934 Chain B: S.743, A.745, E.1111, K.1112, N.1113 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.745 NAG-NAG.13: 4 residues within 4Å: Chain C: F.377, G.378, F.381, N.382 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 2 residues within 4Å: Chain C: V.1172, N.1173 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(5-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG.6: 4 residues within 4Å: Chain A: N.319, E.320, N.321 Chain B: K.597 No protein-ligand interaction detected (PLIP)

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

NAG.19: 2 residues within 4Å: Chain A: N.655, T.657 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: N.748, N.749, I.1169, G.1170 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.203, N.204 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: T.147, T.153, N.273, T.275 Ligand excluded by PLIP NAG.23: 6 residues within 4Å: Chain A: N.382, S.412, W.475, N.479, L.480, R.548 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain B: F.377, G.378, F.381, N.382 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: N.655, T.657, Q.683 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain B: N.748, N.749, I.1169, G.1170 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: Y.67, N.69, N.100 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: N.370, P.618, Q.619, T.620 Ligand excluded by PLIP NAG.29: 8 residues within 4Å: Chain B: T.147, T.153, Q.154, N.273, T.275 Chain C: K.501, E.504, D.506 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: N.370, Q.619, T.620 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: N.655, T.657, Q.683 Ligand excluded by PLIP NAG.32: 6 residues within 4Å: Chain B: Q.934 Chain C: A.745, A.752, E.1111, K.1112, N.1113 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain C: N.748, I.1169, G.1170 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, S. et al., Production and cryo-electron microscopy structure of an internally tagged SARS-CoV-2 spike ecto-domain construct. J Struct Biol X (2025)

Release Date

2025-03-05

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
B

Spike glycoprotein

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