SMTL ID : 9ct2.1

Cryo-EM structure of SARS-CoV-2 spike protein Ecto-domain with internal tag, All RBD down conformation, State-3

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

10 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.756, L.961, Q.965, Q.1110 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.961 NAG-NAG.2: 3 residues within 4Å: Chain A: N.840, S.842, Q.843 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1137, T.1139, H.1140, F.1142 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain B: N.1173 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.840, S.842, Q.843 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain A: D.835 Chain C: N.748, G.1170 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain C: N.840, S.842, Q.843 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain C: N.1137, T.1139, H.1140, F.1142 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 1 residues within 4Å: Chain C: N.1173 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 1 residues within 4Å: Chain A: N.1173 No protein-ligand interaction detected (PLIP)

4 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.5: 4 residues within 4Å: Chain B: N.1137, T.1139, H.1140, F.1142 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 4 residues within 4Å: Chain B: N.756, L.961, Q.965, Q.1110 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.961 NAG-NAG-BMA.8: 4 residues within 4Å: Chain B: K.597 Chain C: N.319, E.320, N.321 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 4 residues within 4Å: Chain C: N.756, L.961, Q.965, Q.1110 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.961

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

NAG.15: 1 residues within 4Å: Chain A: N.100 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain A: N.161, N.164, V.166, K.168 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: N.319, E.320, N.321 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: P.369, N.370, P.618, Q.619 Ligand excluded by PLIP NAG.19: 5 residues within 4Å: Chain A: F.377, G.378, F.381, N.382, L.407 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.642 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.655, Q.683 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: H.694, N.696 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: N.748, I.1169, G.1170 Chain B: D.835 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain A: A.745, E.1111, K.1112, N.1113 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: E.171, N.204 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: T.147, N.273, T.275 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.100 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain B: N.161, A.162, N.164, V.166, K.168 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: N.319, E.320, N.321 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain B: P.369, N.370, P.618, Q.619 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain B: F.377, G.378, F.381, N.382 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: N.642, T.643 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: N.655, Q.683 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: H.694, N.696 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: N.748, G.1170 Chain C: D.835 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain B: A.745, E.1111, N.1113 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain A: K.501 Chain B: T.147, N.273, T.275 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: Y.67, N.100 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain C: N.161, A.162, N.164, V.166 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain C: P.369, N.370, I.371, Q.619 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain C: F.377, G.378, F.381, N.382 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.642 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.655, Q.683 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: H.694, N.696 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain C: A.745, E.1111, K.1112, N.1113 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain C: E.171, N.204 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain C: T.147, N.273, T.275 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
B

C
C

Spike glycoprotein

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