SMTL ID : 7kip.1

A 3.4 Angstrom cryo-EM structure of the human coronavirus spike trimer computationally derived from vitrified NL63 virus particles

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG-NAG-BMA-MAN-MAN-MAN.1: 6 residues within 4Å: Chain A: L.238, N.240, T.381, Q.383, Y.385, F.420 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.22: 6 residues within 4Å: Chain B: L.238, N.240, T.381, Q.383, Y.385, F.420 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.43: 6 residues within 4Å: Chain C: L.238, N.240, T.381, Q.383, Y.385, F.420 No protein-ligand interaction detected (PLIP)

33 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 3 residues within 4Å: Chain A: Y.274, N.276, T.278 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.330, D.337, Q.347 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain A: I.357, N.358, S.533, G.534, S.535 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.535 NAG-NAG.7: 3 residues within 4Å: Chain A: N.401, N.403, T.405 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 6 residues within 4Å: Chain A: T.490, A.491, S.492, Q.504, N.506, K.532 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 1 residues within 4Å: Chain A: N.723 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain A: R.746, P.747, N.749 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.746, A:R.746 NAG-NAG.15: 2 residues within 4Å: Chain A: N.762, K.1142 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain A: N.768, I.974, D.1137 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain A: N.844, P.858, R.860, N.861 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.861 NAG-NAG.20: 3 residues within 4Å: Chain A: S.1145, N.1196, T.1198 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 3 residues within 4Å: Chain B: Y.274, N.276, T.278 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain B: N.330, D.337, Q.347 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 5 residues within 4Å: Chain B: I.357, N.358, S.533, G.534, S.535 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.535 NAG-NAG.28: 3 residues within 4Å: Chain B: N.401, N.403, T.405 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 6 residues within 4Å: Chain B: T.490, A.491, S.492, Q.504, N.506, K.532 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 1 residues within 4Å: Chain B: N.723 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 3 residues within 4Å: Chain B: R.746, P.747, N.749 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.746, B:R.746 NAG-NAG.36: 2 residues within 4Å: Chain B: N.762, K.1142 No protein-ligand interaction detected (PLIP) NAG-NAG.37: 3 residues within 4Å: Chain B: N.768, I.974, D.1137 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 4 residues within 4Å: Chain B: N.844, P.858, R.860, N.861 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.861 NAG-NAG.41: 3 residues within 4Å: Chain B: S.1145, N.1196, T.1198 No protein-ligand interaction detected (PLIP) NAG-NAG.44: 3 residues within 4Å: Chain C: Y.274, N.276, T.278 No protein-ligand interaction detected (PLIP) NAG-NAG.46: 3 residues within 4Å: Chain C: N.330, D.337, Q.347 No protein-ligand interaction detected (PLIP) NAG-NAG.48: 5 residues within 4Å: Chain C: I.357, N.358, S.533, G.534, S.535 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.535 NAG-NAG.49: 3 residues within 4Å: Chain C: N.401, N.403, T.405 No protein-ligand interaction detected (PLIP) NAG-NAG.52: 6 residues within 4Å: Chain C: T.490, A.491, S.492, Q.504, N.506, K.532 No protein-ligand interaction detected (PLIP) NAG-NAG.55: 1 residues within 4Å: Chain C: N.723 No protein-ligand interaction detected (PLIP) NAG-NAG.56: 3 residues within 4Å: Chain C: R.746, P.747, N.749 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.746, C:R.746 NAG-NAG.57: 2 residues within 4Å: Chain C: N.762, K.1142 No protein-ligand interaction detected (PLIP) NAG-NAG.58: 3 residues within 4Å: Chain C: N.768, I.974, D.1137 No protein-ligand interaction detected (PLIP) NAG-NAG.59: 4 residues within 4Å: Chain C: N.844, P.858, R.860, N.861 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.861 NAG-NAG.62: 3 residues within 4Å: Chain C: S.1145, N.1196, T.1198 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-MAN.3: 3 residues within 4Å: Chain A: N.301, T.410, W.413 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.18: 3 residues within 4Å: Chain A: N.852, S.854, N.984 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.24: 3 residues within 4Å: Chain B: N.301, T.410, W.413 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.39: 3 residues within 4Å: Chain B: N.852, S.854, N.984 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.45: 3 residues within 4Å: Chain C: N.301, T.410, W.413 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.60: 3 residues within 4Å: Chain C: N.852, S.854, N.984 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-MAN.5: 4 residues within 4Å: Chain A: Y.327, V.335, N.354, S.363 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.26: 4 residues within 4Å: Chain B: Y.327, V.335, N.354, S.363 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.47: 4 residues within 4Å: Chain C: Y.327, V.335, N.354, S.363 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.8: 10 residues within 4Å: Chain A: E.147, Y.166, K.167, N.426, S.428, N.434, F.452 Chain C: S.647, L.648, A.649 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.29: 10 residues within 4Å: Chain A: S.647, L.648, A.649 Chain B: E.147, Y.166, K.167, N.426, S.428, N.434, F.452 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.50: 10 residues within 4Å: Chain B: S.647, L.648, A.649 Chain C: E.147, Y.166, K.167, N.426, S.428, N.434, F.452 No protein-ligand interaction detected (PLIP)

3 x NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)

NAG-BMA.9: 1 residues within 4Å: Ligands: NAG.67 No protein-ligand interaction detected (PLIP) NAG-BMA.30: 1 residues within 4Å: Ligands: NAG.75 No protein-ligand interaction detected (PLIP) NAG-BMA.51: 1 residues within 4Å: Ligands: NAG.83 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-MAN-MAN.11: 4 residues within 4Å: Chain A: V.474, L.622, N.666, S.668 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.19: 3 residues within 4Å: Chain A: S.751, N.1111, L.1134 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.751, A:S.751 NAG-NAG-BMA-MAN-MAN.32: 4 residues within 4Å: Chain B: V.474, L.622, N.666, S.668 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.40: 3 residues within 4Å: Chain B: S.751, N.1111, L.1134 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.751, B:S.751 NAG-NAG-BMA-MAN-MAN.53: 4 residues within 4Å: Chain C: V.474, L.622, N.666, S.668 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.61: 3 residues within 4Å: Chain C: S.751, N.1111, L.1134 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.751, C:S.751

6 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.12: 2 residues within 4Å: Chain A: N.699, Y.715 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 3 residues within 4Å: Chain A: V.1197, F.1199, N.1201 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.33: 2 residues within 4Å: Chain B: N.699, Y.715 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.42: 3 residues within 4Å: Chain B: V.1197, F.1199, N.1201 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.54: 2 residues within 4Å: Chain C: N.699, Y.715 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.63: 3 residues within 4Å: Chain C: V.1197, F.1199, N.1201 No protein-ligand interaction detected (PLIP)

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

NAG.64: 2 residues within 4Å: Chain A: L.28, N.155 Ligand excluded by PLIP NAG.65: 3 residues within 4Å: Chain A: T.46, H.47, N.187 Ligand excluded by PLIP NAG.66: 2 residues within 4Å: Chain A: S.37, N.193 Ligand excluded by PLIP NAG.67: 4 residues within 4Å: Chain A: N.486, N.510, I.527 Ligands: NAG-BMA.9 Ligand excluded by PLIP NAG.68: 2 residues within 4Å: Chain A: N.510, N.512 Ligand excluded by PLIP NAG.69: 1 residues within 4Å: Chain A: N.626 Ligand excluded by PLIP NAG.70: 1 residues within 4Å: Chain A: N.645 Ligand excluded by PLIP NAG.71: 3 residues within 4Å: Chain A: N.1218, L.1221, Q.1222 Ligand excluded by PLIP NAG.72: 2 residues within 4Å: Chain B: L.28, N.155 Ligand excluded by PLIP NAG.73: 3 residues within 4Å: Chain B: T.46, H.47, N.187 Ligand excluded by PLIP NAG.74: 2 residues within 4Å: Chain B: S.37, N.193 Ligand excluded by PLIP NAG.75: 4 residues within 4Å: Chain B: N.486, N.510, I.527 Ligands: NAG-BMA.30 Ligand excluded by PLIP NAG.76: 2 residues within 4Å: Chain B: N.510, N.512 Ligand excluded by PLIP NAG.77: 1 residues within 4Å: Chain B: N.626 Ligand excluded by PLIP NAG.78: 1 residues within 4Å: Chain B: N.645 Ligand excluded by PLIP NAG.79: 3 residues within 4Å: Chain B: N.1218, L.1221, Q.1222 Ligand excluded by PLIP NAG.80: 2 residues within 4Å: Chain C: L.28, N.155 Ligand excluded by PLIP NAG.81: 3 residues within 4Å: Chain C: T.46, H.47, N.187 Ligand excluded by PLIP NAG.82: 2 residues within 4Å: Chain C: S.37, N.193 Ligand excluded by PLIP NAG.83: 4 residues within 4Å: Chain C: N.486, N.510, I.527 Ligands: NAG-BMA.51 Ligand excluded by PLIP NAG.84: 2 residues within 4Å: Chain C: N.510, N.512 Ligand excluded by PLIP NAG.85: 1 residues within 4Å: Chain C: N.626 Ligand excluded by PLIP NAG.86: 1 residues within 4Å: Chain C: N.645 Ligand excluded by PLIP NAG.87: 3 residues within 4Å: Chain C: N.1218, L.1221, Q.1222 Ligand excluded by PLIP

Links

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Citation

Zhang, K. et al., A 3.4- angstrom cryo-EM structure of the human coronavirus spike trimer computationally derived from vitrified NL63 virus particles. Biorxiv (2020)

Release Date

2020-11-11

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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