SMTL ID : 8vqa.1

Prefusion stabilized structure of the SARS-CoV-2 fusion machinery

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

12 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: 2 residues within 4Å: Chain A: N.64, L.269 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.148, Q.151 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.445, T.447, H.448, F.450 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.481 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain B: N.64, L.269 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain B: N.148, Q.151 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: N.445, T.447, H.448, F.450 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain B: N.481 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain C: N.64, L.269 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain C: N.148, Q.151 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain C: N.445, T.447, H.448, F.450 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain C: N.481 No protein-ligand interaction detected (PLIP)

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

NAG.13: 3 residues within 4Å: Chain A: C.54, S.55, N.56 No protein-ligand interaction detected (PLIP) NAG.14: 5 residues within 4Å: Chain A: A.60, E.419, K.420, N.421 Chain B: S.231 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.60, A:E.419 Hydrogen bonds: A:N.421, B:S.231 NAG.15: 3 residues within 4Å: Chain B: C.54, S.55, N.56 No protein-ligand interaction detected (PLIP) NAG.16: 5 residues within 4Å: Chain B: A.60, E.419, K.420, N.421 Chain C: S.231 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:A.60, B:E.419 Hydrogen bonds: B:N.421, C:S.231 NAG.17: 3 residues within 4Å: Chain C: C.54, S.55, N.56 No protein-ligand interaction detected (PLIP) NAG.18: 5 residues within 4Å: Chain A: S.231 Chain C: A.60, E.419, K.420, N.421 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:A.60, C:E.419 Hydrogen bonds: C:N.421, A:S.231

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, J. et al., A broadly generalizable stabilization strategy for sarbecovirus fusion machinery vaccines. Nat Commun (2024)

Release Date

2024-07-24

Peptides

Spike protein S2: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike protein S2