SMTL ID : 8u28.1

Gaussian mixture model based single particle refinement - SARS (SARS-CoV-2 Spike Proteins on intact virions from EMPIAR-10492)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

15 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: T.108, T.109, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: N.717, F.718, L.922, N.925, Q.926 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.922 NAG-NAG.3: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: N.1098, G.1099, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: I.1132, V.1133, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: T.108, T.109, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain B: N.717, F.718, L.922, N.925, Q.926 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.922 NAG-NAG.8: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain B: N.1098, G.1099, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain B: I.1132, V.1133, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain C: T.108, T.109, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 6 residues within 4Å: Chain C: N.717, F.718, L.922, N.925, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.922 NAG-NAG.13: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain C: N.1098, G.1099, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain C: I.1132, V.1133, N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.16: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: N.122, A.123, N.125, V.127 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: N.280, E.281, N.282 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: N.331, T.333, Q.580, T.581 Ligand excluded by PLIP NAG.20: 7 residues within 4Å: Chain A: G.339, F.342, N.343, L.368, S.371, S.373, F.374 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.603, T.604 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: N.616, T.618, E.619 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: N.657, N.658 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain A: N.709, I.1130, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: A.706, N.1074 Chain C: Q.895 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: E.132, N.165 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: Y.28, T.29, N.61 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: N.122, A.123, N.125, V.127 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain B: N.331, T.333, Q.580, T.581 Ligand excluded by PLIP NAG.31: 6 residues within 4Å: Chain B: G.339, F.342, N.343, S.371, S.373, F.374 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: N.603, T.604 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain B: N.616, T.618, E.619 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: N.657, N.658 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain A: D.796 Chain B: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain A: Q.895 Chain B: A.706, N.1074 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: E.132, N.165 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: N.122, A.123, N.125 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain C: N.331, T.333, Q.580, T.581 Ligand excluded by PLIP NAG.42: 6 residues within 4Å: Chain C: G.339, F.342, N.343, S.371, S.373, F.374 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.603, T.604 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: N.616, T.618, E.619 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain B: D.796 Chain C: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain B: Q.895 Chain C: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain C: N.165 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, M. et al., Improving resolution and resolvability of single-particle cryoEM structures using Gaussian mixture models. Nat.Methods (2024)

Release Date

2023-11-15

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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