SMTL ID : 8z7p.1

Cryo-EM structure of SARS-CoV-2 S trimer in the early fusion intermediate conformation (E-FIC)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

21 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: 1 residues within 4Å: Chain A: N.90 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: S.420, D.543, S.545, N.546 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain B: C.15, N.17, N.137 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.137 NAG-NAG.4: 5 residues within 4Å: Chain B: N.122, T.124, V.127, E.154, V.171 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.171 NAG-NAG.5: 5 residues within 4Å: Chain B: H.146, N.149, S.151, W.152, M.153 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: Y.28, N.30, N.61 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.28 NAG-NAG.7: 4 residues within 4Å: Chain B: F.338, G.339, F.342, N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain C: N.90 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain C: S.420, D.543, S.545, N.546 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain D: C.15, N.17, N.137 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.137 NAG-NAG.12: 5 residues within 4Å: Chain D: N.122, T.124, V.127, E.154, V.171 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:V.171 NAG-NAG.13: 5 residues within 4Å: Chain D: H.146, N.149, S.151, W.152, M.153 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain D: Y.28, N.30, N.61 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Y.28 NAG-NAG.15: 4 residues within 4Å: Chain D: F.338, G.339, F.342, N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 1 residues within 4Å: Chain E: N.90 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain E: S.420, D.543, S.545, N.546 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain F: C.15, N.17, N.137 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.137 NAG-NAG.20: 5 residues within 4Å: Chain F: N.122, T.124, V.127, E.154, V.171 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:V.171 NAG-NAG.21: 5 residues within 4Å: Chain F: H.146, N.149, S.151, W.152, M.153 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain F: Y.28, N.30, N.61 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:Y.28 NAG-NAG.23: 4 residues within 4Å: Chain F: F.338, G.339, F.342, N.343 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.8: 2 residues within 4Å: Chain B: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.16: 2 residues within 4Å: Chain D: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.24: 2 residues within 4Å: Chain F: N.331, Q.580 No protein-ligand interaction detected (PLIP)

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

NAG.25: 2 residues within 4Å: Chain A: N.53, Q.340 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain A: Q.81, Q.101, N.103, V.107 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain A: N.322 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain A: N.432, W.594 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.1134 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.1074 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: T.716, N.717 Chain D: G.1124 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.801 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain B: S.708, N.709, N.710, S.711 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain B: N.234 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: Q.115, N.165 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain B: N.282 Chain D: K.558 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.53, Q.340 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain C: Q.81, Q.101, N.103, V.107 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.322 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: N.432, W.594 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain D: N.1134 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain D: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain D: N.1074 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain D: T.716, N.717 Chain F: G.1124 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain D: N.801 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain D: S.708, N.709, N.710, S.711 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain D: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain D: N.234 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain D: Q.115, N.165 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain D: N.282 Chain F: K.558 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain E: N.53, Q.340 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain E: Q.81, Q.101, N.103, V.107 Ligand excluded by PLIP NAG.55: 1 residues within 4Å: Chain E: N.322 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain E: N.432, W.594 Ligand excluded by PLIP NAG.57: 1 residues within 4Å: Chain F: N.1134 Ligand excluded by PLIP NAG.58: 4 residues within 4Å: Chain F: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.59: 1 residues within 4Å: Chain F: N.1074 Ligand excluded by PLIP NAG.60: 3 residues within 4Å: Chain B: G.1124 Chain F: T.716, N.717 Ligand excluded by PLIP NAG.61: 1 residues within 4Å: Chain F: N.801 Ligand excluded by PLIP NAG.62: 4 residues within 4Å: Chain F: S.708, N.709, N.710, S.711 Ligand excluded by PLIP NAG.63: 3 residues within 4Å: Chain F: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.64: 1 residues within 4Å: Chain F: N.234 Ligand excluded by PLIP NAG.65: 2 residues within 4Å: Chain F: Q.115, N.165 Ligand excluded by PLIP NAG.66: 2 residues within 4Å: Chain B: K.558 Chain F: N.282 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xing, L. et al., Early fusion intermediate of ACE2-using coronavirus spike acting as an antiviral target. Cell (2025)

Release Date

2025-02-05

Peptides

Angiotensin-converting enzyme 2: ACE
Spike glycoprotein: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

C
E

E
F

B
A

D
B

F
C

Membrane

We predict this structure to be a membrane protein.
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Angiotensin-converting enzyme 2

Spike glycoprotein

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