SMTL ID : 7xog.1

Cryo-EM structure of S glycoprotein encoded by the Covid-19 mRNA vaccine candidate RQ3013 (Postfusion state)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

6 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG.1: 1 residues within 4Å: Chain A: N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain A: N.1191 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1191 NAG-NAG.6: 1 residues within 4Å: Chain B: N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain B: N.1191, L.1194 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 1 residues within 4Å: Chain C: N.1071 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.1071 NAG-NAG.15: 3 residues within 4Å: Chain B: Q.932 Chain C: A.1187, N.1191 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-MAN-MAN.2: 5 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 Ligands: MAN.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.1095, A:H.1098 NAG-NAG-MAN-MAN.3: 3 residues within 4Å: Chain A: N.1131, T.1133 Chain C: I.723 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.1133, A:N.1131 NAG-NAG-MAN-MAN.7: 5 residues within 4Å: Chain B: N.1095, G.1096, T.1097, H.1098 Ligands: MAN.22 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.1095, B:H.1098 NAG-NAG-MAN-MAN.8: 1 residues within 4Å: Chain B: N.1131 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.1131 NAG-NAG-MAN-MAN.12: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098 Ligands: MAN.26 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.1095, C:H.1098 NAG-NAG-MAN-MAN.13: 5 residues within 4Å: Chain B: P.1054, H.1055 Chain C: I.1129, V.1130, N.1131 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.1131

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

NAG-NAG-MAN.4: 4 residues within 4Å: Chain A: K.1146, D.1150, F.1153, N.1155 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.9: 3 residues within 4Å: Chain B: D.1150, F.1153, N.1155 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.14: 1 residues within 4Å: Chain C: N.1155 No protein-ligand interaction detected (PLIP)

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

NAG.16: 4 residues within 4Å: Chain A: Y.704, N.706, T.1073, S.1094 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.1094 NAG.17: 2 residues within 4Å: Chain A: N.714, Q.1068 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.714 NAG.19: 1 residues within 4Å: Chain A: N.1170 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1170 NAG.20: 3 residues within 4Å: Chain B: N.706, T.1073, S.1094 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.1094 NAG.21: 1 residues within 4Å: Chain B: N.714 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.714 NAG.23: 1 residues within 4Å: Chain B: N.1170 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.1170 NAG.24: 4 residues within 4Å: Chain C: Y.704, N.706, T.1073, S.1094 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.1094 NAG.25: 1 residues within 4Å: Chain C: N.714 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.714 NAG.27: 1 residues within 4Å: Chain C: N.1170 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.1170

3 x MAN: alpha-D-mannopyranose(Non-functional Binders)

MAN.18: 1 residues within 4Å: Ligands: NAG-NAG-MAN-MAN.2 No protein-ligand interaction detected (PLIP) MAN.22: 1 residues within 4Å: Ligands: NAG-NAG-MAN-MAN.7 No protein-ligand interaction detected (PLIP) MAN.26: 1 residues within 4Å: Ligands: NAG-NAG-MAN-MAN.12 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tan, S. et al., Preclinical evaluation of RQ3013, a broad-spectrum mRNA vaccine against SARS-CoV-2 variants. Sci Bull (Beijing) (2023)

Release Date

2024-03-20

Peptides

Spike glycoprotein,peptide: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

Spike glycoprotein,peptide