SMTL ID : 9css.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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.1: 5 residues within 4Å: Chain A: F.377, G.378, F.381, N.382, L.407 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 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-BMA.7: 2 residues within 4Å: Chain A: N.840, S.842 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 2 residues within 4Å: Chain B: N.756, L.961 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.961 NAG-NAG-BMA.17: 2 residues within 4Å: Chain C: N.370, Q.619 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 4 residues within 4Å: Chain C: N.756, L.961, N.964, Q.965 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:N.964

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

NAG-NAG.3: 6 residues within 4Å: Chain C: F.377, G.378, F.381, N.382, V.406, S.412 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.412 NAG-NAG.4: 3 residues within 4Å: Chain C: N.655, T.657, Q.683 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.319, E.320, N.321 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.655, Q.683 Chain B: I.873, Q.875 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain B: E.320, N.321 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain B: N.840, S.842 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 1 residues within 4Å: Chain B: N.1173 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain C: N.840, S.842, Q.843 No protein-ligand interaction detected (PLIP)

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.8: 4 residues within 4Å: Chain A: A.745, E.1111, K.1112, N.1113 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.14: 3 residues within 4Å: Chain B: A.745, E.1111, N.1113 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.20: 3 residues within 4Å: Chain C: A.745, E.1111, N.1113 No protein-ligand interaction detected (PLIP)

5 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN.9: 4 residues within 4Å: Chain A: N.1137, T.1139, H.1140, F.1142 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.10: 1 residues within 4Å: Chain A: N.1173 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.15: 4 residues within 4Å: Chain B: N.1137, T.1139, H.1140, F.1142 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.21: 4 residues within 4Å: Chain C: N.1137, T.1139, H.1140, F.1142 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.22: 1 residues within 4Å: Chain C: N.1173 No protein-ligand interaction detected (PLIP)

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

NAG.23: 2 residues within 4Å: Chain A: Y.67, N.100 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: G.271, I.272, N.273 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain A: N.370 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain A: N.642 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: H.694, N.696 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain A: N.748, I.1169, G.1170 Chain B: D.835 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain A: N.204 Chain C: Y.435 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain A: N.161, T.163, N.164, E.193 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: T.68, N.69, N.100 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: N.370, P.618, Q.619 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain B: F.381, N.382, F.413 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain B: N.642 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: H.694, N.696 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain B: N.748, G.1170 Chain C: D.835 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain A: E.504 Chain B: T.147, N.273, T.275 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain B: N.655 Chain C: I.873, Q.875 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: Y.67, N.100 Ligand excluded by PLIP NAG.40: 5 residues within 4Å: Chain C: N.161, T.163, V.166, F.196, Y.199 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: N.203, N.204 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: T.147, N.273, T.275 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain C: N.319, E.320, N.321 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain C: N.642 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.696 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain A: D.835 Chain C: N.748, 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
B

B
C

C
A

Spike glycoprotein

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