SMTL ID : 9vg7.1

Cryo-EM Structure of Rc-o319 Ectodomain trimer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

9 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: Y.12, N.45 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.12 NAG-NAG.3: 3 residues within 4Å: Chain A: N.291, P.530, K.531 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: D.744, N.749, S.751, Q.752 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain B: Y.12, N.45 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.12 NAG-NAG.7: 3 residues within 4Å: Chain B: N.291, P.530, K.531 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: D.744, N.749, S.751, Q.752 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain C: Y.12, N.45 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.12 NAG-NAG.11: 3 residues within 4Å: Chain C: N.291, P.530, K.531 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain C: D.744, N.749, S.751, Q.752 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: 8 residues within 4Å: Chain A: T.85, N.204, T.206, Q.480 Chain C: R.417, S.418, E.419, K.420 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:E.419, A:Q.480 NAG-NAG-BMA.6: 8 residues within 4Å: Chain A: R.417, S.418, E.419, K.420 Chain B: T.85, N.204, T.206, Q.480 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.419, B:Q.480 NAG-NAG-BMA.10: 8 residues within 4Å: Chain B: R.417, S.418, E.419, K.420 Chain C: T.85, N.204, T.206, Q.480 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:E.419, C:Q.480

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

NAG.13: 8 residues within 4Å: Chain A: R.104, E.106, C.108, F.110, Y.126, A.129, C.132, N.135 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.110, A:A.129 Hydrogen bonds: A:R.104, A:E.106, A:N.135 NAG.14: 3 residues within 4Å: Chain A: N.330, S.331 Chain C: V.435 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.330 NAG.15: 4 residues within 4Å: Chain A: N.665, L.870, Q.874, Q.1019 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.665, A:Q.1019 NAG.16: 8 residues within 4Å: Chain B: R.104, E.106, C.108, F.110, Y.126, A.129, C.132, N.135 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.110, B:A.129 Hydrogen bonds: B:R.104, B:E.106, B:N.135 NAG.17: 3 residues within 4Å: Chain A: V.435 Chain B: N.330, S.331 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.330 NAG.18: 4 residues within 4Å: Chain B: N.665, L.870, Q.874, Q.1019 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.665, B:Q.1019 NAG.19: 8 residues within 4Å: Chain C: R.104, E.106, C.108, F.110, Y.126, A.129, C.132, N.135 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.110, C:A.129 Hydrogen bonds: C:R.104, C:E.106, C:N.135 NAG.20: 3 residues within 4Å: Chain B: V.435 Chain C: N.330, S.331 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.330 NAG.21: 4 residues within 4Å: Chain C: N.665, L.870, Q.874, Q.1019 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.665, C:Q.1019

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kosugi, Y. et al., Molecular basis of sarbecovirus evolution and receptor tropism in natural hosts, potential intermediate hosts, and humans. Cell Rep (2025)

Release Date

2025-08-27

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein