SMTL ID : 7cyd.1

Cryo-EM structures of Alphacoronavirus spike glycoprotein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN.1: 5 residues within 4Å: Chain A: N.62, T.198, H.200, Y.202 Chain C: E.621 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.198 NAG-NAG-BMA-MAN-MAN-MAN-MAN.3: 5 residues within 4Å: Chain A: E.621 Chain B: N.62, T.198, H.200, Y.202 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.198 NAG-NAG-BMA-MAN-MAN-MAN-MAN.5: 5 residues within 4Å: Chain B: E.621 Chain C: N.62, T.198, H.200, Y.202 No protein-ligand interaction detected (PLIP)

3 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.2: 5 residues within 4Å: Chain A: N.243, S.245, A.250, N.251, F.269 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.245, A:S.245 NAG-NAG-BMA.4: 5 residues within 4Å: Chain B: N.243, S.245, A.250, N.251, F.269 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.245, B:S.245 NAG-NAG-BMA.6: 5 residues within 4Å: Chain C: N.243, S.245, A.250, N.251, F.269 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.245, C:S.245

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

NAG.7: 2 residues within 4Å: Chain A: Y.96, N.98 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain A: N.55, N.122, T.227, C.230 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: Y.144, N.171, S.180 Ligand excluded by PLIP NAG.10: 5 residues within 4Å: Chain A: F.90, T.131, L.133, N.218, N.220 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain A: Y.305, D.307, N.326, I.327 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain A: N.518 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: V.288, N.440 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.663, S.665, L.679 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.542 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.568 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.581, D.959 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.587 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.671 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.1015 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: Y.96, N.98 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain B: N.55, N.122, T.227, C.230 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: Y.144, N.171, S.180 Ligand excluded by PLIP NAG.24: 6 residues within 4Å: Chain B: F.90, R.129, T.131, L.133, N.218, N.220 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain B: Y.305, D.307, N.326, I.327 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.518 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: V.288, I.290, N.440 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: N.663, S.665, L.679 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.542 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.568 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.581, D.959 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.587 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.671 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: N.1015, T.1017, F.1018 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: Y.96, N.98 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain C: N.55, N.56, N.122, T.227, C.230 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: Y.144, N.171, S.180 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain C: F.90, T.131, L.133, N.218, N.220 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain C: Y.305, D.307, N.326, I.327 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: N.518 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: V.288, I.290, N.440 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: N.663, S.665, L.679 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.542 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain C: N.568 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: N.581, D.959 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain C: N.587 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.671 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain C: N.1015, F.1018 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Song, X. et al., Cryo-EM analysis of the HCoV-229E spike glycoprotein reveals dynamic prefusion conformational changes. Nat Commun (2021)

Release Date

2020-12-23

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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