SMTL ID : 7e7d.1

Cryo-EM structure of the SARS-CoV-2 wild-type S-Trimer from a subunit vaccine candidate

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.20 Å

Oligo State

homo-trimer

Ligands

32 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: 7 residues within 4Å: Chain B: N.717, F.718, T.719, L.922, Q.926, A.1070, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.616, Q.644, T.645 Chain B: I.834 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.717, F.718, L.922, Q.926 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.922 NAG-NAG.4: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain A: N.280, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 8 residues within 4Å: Chain A: T.108, N.234, T.236 Chain C: R.457, K.458, S.459, N.460, K.462 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain A: N.122, T.124, N.125, V.127, E.154 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain A: N.709 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain A: N.165 Chain C: Y.351 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain B: N.616, Q.644, T.645 Chain C: I.834 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 2 residues within 4Å: Chain B: N.280, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 9 residues within 4Å: Chain A: R.457, K.458, S.459, N.460, K.462, E.465 Chain B: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 5 residues within 4Å: Chain B: N.122, T.124, N.125, V.127, E.154 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 1 residues within 4Å: Chain B: N.709 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 2 residues within 4Å: Chain A: Y.351 Chain B: N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain B: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain C: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Q.926 NAG-NAG.24: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 2 residues within 4Å: Chain C: N.280, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 9 residues within 4Å: Chain B: R.457, K.458, S.459, N.460, K.462, E.465 Chain C: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 5 residues within 4Å: Chain C: N.122, T.124, N.125, V.127, E.154 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 1 residues within 4Å: Chain C: N.709 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 2 residues within 4Å: Chain B: Y.351 Chain C: N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 3 residues within 4Å: Chain C: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP)

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

NAG.33: 2 residues within 4Å: Chain A: N.343, S.371 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain A: N.603, T.604 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain A: C.15, V.16, N.17, N.137 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain A: N.61, P.631 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain B: N.343, S.371 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain B: N.603, T.604 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain B: C.15, N.17, N.137 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain B: N.30, F.59, S.60, N.61 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain C: N.343, S.371 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain C: N.603, T.604 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain C: C.15, V.16, N.17, N.137 Ligand excluded by PLIP NAG.53: 5 residues within 4Å: Chain C: N.30, F.59, S.60, N.61, P.631 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain A: Q.836 Chain C: N.616, E.619, Q.644 Ligand excluded by PLIP

3 x ELA: 9-OCTADECENOIC ACID(Non-covalent)

ELA.38: 17 residues within 4Å: Chain A: C.336, P.337, F.338, V.341, F.342, A.363, Y.365, F.374, F.377, L.387, F.392, V.395, I.434, L.513 Chain C: R.408, T.415, G.416 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:F.338, A:V.341, A:F.342, A:A.363, A:Y.365, A:Y.365, A:F.374, A:F.374, A:F.377, A:F.377, A:F.377, A:L.387, A:F.392, A:V.395, A:I.434, A:L.513 Hydrogen bonds: C:Q.409 Salt bridges: C:R.408 ELA.39: 18 residues within 4Å: Chain A: R.408, Q.409, T.415, G.416 Chain B: C.336, P.337, F.338, V.341, A.363, Y.365, Y.369, F.374, F.377, L.387, F.392, V.395, I.434, L.513 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.338, B:F.338, B:V.341, B:Y.365, B:Y.365, B:Y.369, B:F.374, B:F.374, B:F.377, B:F.377, B:L.387, B:F.392, B:V.395, B:I.434 Hydrogen bonds: A:Q.409 Salt bridges: A:R.408 ELA.41: 17 residues within 4Å: Chain B: R.408, Q.409, T.415, G.416 Chain C: P.337, F.338, V.341, A.363, Y.365, L.368, F.374, F.377, L.387, F.392, V.395, I.434, L.513 16 PLIP interactions: 15 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:F.338, C:F.338, C:V.341, C:Y.365, C:Y.365, C:Y.365, C:L.368, C:F.374, C:F.377, C:F.377, C:L.387, C:F.392, C:V.395, C:I.434, C:L.513 Salt bridges: B:R.408

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ma, J. et al., Cryo-EM structure of S-Trimer, a subunit vaccine candidate for COVID-19. J.Virol. (2021)

Release Date

2021-03-24

Peptides

Spike glycoprotein,Collagen alpha-1(I) chain: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein,Collagen alpha-1(I) chain