SMTL ID : 7e7b.1

Cryo-EM structure of the SARS-CoV-2 furin site mutant S-Trimer from a subunit vaccine candidate

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

39 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: 5 residues within 4Å: Chain A: N.616, Q.644, T.645, R.646 Chain B: I.834 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: T.716, N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 9 residues within 4Å: Chain A: T.108, N.234, T.236 Chain C: R.457, K.458, S.459, N.460, K.462, E.465 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.458 NAG-NAG.7: 5 residues within 4Å: Chain A: N.122, T.124, N.125, V.127, V.171 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain A: H.146, K.147, N.148, N.149, M.153 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: 2 residues within 4Å: Chain A: N.709, G.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain A: N.165 Chain C: Y.351, I.468 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: 3 residues within 4Å: Chain A: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain B: N.616, Q.644, T.645 Chain C: I.834 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain B: T.716, N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain B: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.458 NAG-NAG.20: 5 residues within 4Å: Chain B: N.122, T.124, N.125, V.127, V.171 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.171 NAG-NAG.21: 4 residues within 4Å: Chain B: H.146, K.147, N.149, M.153 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.146 NAG-NAG.22: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 2 residues within 4Å: Chain B: N.709, G.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 3 residues within 4Å: Chain A: Y.351, I.468 Chain B: N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain B: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain B: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 3 residues within 4Å: Chain A: I.834 Chain C: N.616, R.646 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 3 residues within 4Å: Chain C: T.716, N.717, L.922 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 3 residues within 4Å: Chain C: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 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 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.459 NAG-NAG.33: 5 residues within 4Å: Chain C: N.122, T.124, N.125, V.127, V.171 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.171 NAG-NAG.34: 4 residues within 4Å: Chain C: H.146, K.147, N.149, M.153 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 2 residues within 4Å: Chain C: N.709, G.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.37: 3 residues within 4Å: Chain B: Y.351, I.468 Chain C: N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 3 residues within 4Å: Chain C: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 3 residues within 4Å: Chain C: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP)

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

NAG.40: 2 residues within 4Å: Chain A: N.343, S.371 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.343, A:S.371, A:S.371 NAG.41: 2 residues within 4Å: Chain A: N.331, Q.580 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.331 NAG.42: 2 residues within 4Å: Chain A: N.603, T.604 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.604 NAG.43: 2 residues within 4Å: Chain A: H.655, N.657 No protein-ligand interaction detected (PLIP) NAG.44: 2 residues within 4Å: Chain A: Y.28, N.61 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.61 NAG.49: 2 residues within 4Å: Chain B: N.343, S.371 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.371 NAG.50: 2 residues within 4Å: Chain B: N.331, Q.580 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.331 NAG.51: 2 residues within 4Å: Chain B: N.603, T.604 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.604 NAG.52: 1 residues within 4Å: Chain B: N.657 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.657 NAG.53: 2 residues within 4Å: Chain B: Y.28, N.61 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.61 NAG.56: 2 residues within 4Å: Chain C: N.343, S.371 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.371, C:S.371 NAG.57: 3 residues within 4Å: Chain C: N.331, Q.580, L.582 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.331 NAG.58: 2 residues within 4Å: Chain C: N.603, T.604 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.604 NAG.59: 1 residues within 4Å: Chain C: N.657 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.657 NAG.60: 2 residues within 4Å: Chain C: Y.28, N.61 No protein-ligand interaction detected (PLIP)

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

ELA.45: 18 residues within 4Å: Chain A: F.338, F.342, I.358, A.363, Y.365, Y.369, F.374, F.377, L.387, F.392, V.395, L.513, F.515, V.524 Chain C: R.408, Q.409, T.415, G.416 23 PLIP interactions: 21 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:F.338, A:F.338, A:F.342, A:I.358, A:A.363, A:Y.365, A:Y.365, A:Y.369, A:F.374, A:F.374, A:F.377, A:F.377, A:L.387, A:L.387, A:F.392, A:F.392, A:V.395, A:L.513, A:L.513, A:F.515, A:V.524 Hydrogen bonds: C:Q.409 Salt bridges: C:R.408 ELA.46: 17 residues within 4Å: Chain A: R.408, Q.409, T.415, G.416 Chain B: P.337, F.338, A.363, Y.365, Y.369, F.374, F.377, L.387, F.392, V.395, I.434, L.513, F.515 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.338, B:F.338, B:A.363, 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:L.387, B:F.392, B:I.434, B:L.513, B:F.515 Hydrogen bonds: A:Q.409 Salt bridges: A:R.408 ELA.54: 14 residues within 4Å: Chain B: R.408, T.415, G.416 Chain C: P.337, F.338, A.363, Y.365, F.374, F.377, L.387, F.392, V.395, I.434, L.513 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:F.338, C:A.363, C:Y.365, C:Y.365, 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

3 x VCG: 2-hydroxyethyl 2-deoxy-3,5-bis-O-(2-hydroxyethyl)-6-O-(2-{[(9E)-octadec-9-enoyl]oxy}ethyl)-alpha-L-xylo-hexofuranoside(Non-covalent)

VCG.47: 14 residues within 4Å: Chain A: N.121, V.126, F.168, Y.170, F.175, R.190, F.192, I.203, L.226, V.227, P.230 Chain C: R.355, R.357, Y.396 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:F.168, A:F.168, A:Y.170, A:Y.170, A:V.227, C:R.357 Hydrogen bonds: A:Y.170 VCG.48: 15 residues within 4Å: Chain A: R.355, R.357, Y.396 Chain B: N.121, V.126, F.168, Y.170, F.175, R.190, F.192, I.203, L.226, V.227, L.229, P.230 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.126, B:F.168, B:F.168, B:Y.170, B:Y.170, B:V.227, B:L.229, A:R.357 Hydrogen bonds: B:N.121, B:Y.170 VCG.55: 13 residues within 4Å: Chain B: R.355, R.357, Y.396 Chain C: N.121, V.126, F.168, Y.170, R.190, F.192, I.203, L.226, V.227, P.230 12 PLIP interactions: 10 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:V.126, C:F.168, C:F.168, C:F.168, C:Y.170, C:Y.170, C:V.227, C:V.227, B:R.357, B:Y.396 Hydrogen bonds: C:N.121, C:Y.170

Links

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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