SMTL ID : 6bfu.1

Glycan shield and fusion activation of a deltacoronavirus spike glycoprotein fine-tuned for enteric infections

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

9 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.75, N.77, T.206, Q.208, Y.210, L.245 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.3: 7 residues within 4Å: Chain A: M.93, N.95, M.123, Y.126, Q.127, T.128, N.244 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.128 NAG-NAG-BMA-MAN-MAN-MAN.12: 11 residues within 4Å: Chain A: Q.560, N.561, T.562, R.563, I.566, E.808, N.917, V.940, P.941, N.942 Chain C: Q.645 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.563, A:I.566 Hydrogen bonds: A:Q.560, A:R.563 NAG-NAG-BMA-MAN-MAN-MAN.14: 6 residues within 4Å: Chain B: L.75, N.77, T.206, Q.208, Y.210, L.245 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.16: 7 residues within 4Å: Chain B: M.93, N.95, M.123, Y.126, Q.127, T.128, N.244 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.128 NAG-NAG-BMA-MAN-MAN-MAN.25: 11 residues within 4Å: Chain A: Q.645 Chain B: Q.560, N.561, T.562, R.563, I.566, E.808, N.917, V.940, P.941, N.942 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:R.563, B:I.566 Hydrogen bonds: B:Q.560, B:R.563 NAG-NAG-BMA-MAN-MAN-MAN.27: 6 residues within 4Å: Chain C: L.75, N.77, T.206, Q.208, Y.210, L.245 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.29: 7 residues within 4Å: Chain C: M.93, N.95, M.123, Y.126, Q.127, T.128, N.244 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.128 NAG-NAG-BMA-MAN-MAN-MAN.38: 11 residues within 4Å: Chain B: Q.645 Chain C: Q.560, N.561, T.562, R.563, I.566, E.808, N.917, V.940, P.941, N.942 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:R.563, C:I.566 Hydrogen bonds: C:Q.560, C:R.563

21 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: 7 residues within 4Å: Chain A: E.154, N.155, Y.156, V.157, Y.166, L.170, N.187 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 7 residues within 4Å: Chain A: Q.312, N.314, T.330, N.332, G.333, E.347, N.349 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.312 NAG-NAG-BMA.7: 1 residues within 4Å: Chain A: N.497 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 6 residues within 4Å: Chain A: V.500, N.513, R.514, F.515, T.516, N.529 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.513 NAG-NAG-BMA.9: 4 residues within 4Å: Chain A: N.655, T.670, T.671, R.672 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 2 residues within 4Å: Chain A: N.664, S.666 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 4 residues within 4Å: Chain A: Q.787, G.790, N.791, L.794 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 7 residues within 4Å: Chain B: E.154, N.155, Y.156, V.157, Y.166, L.170, N.187 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 7 residues within 4Å: Chain B: Q.312, N.314, T.330, N.332, G.333, E.347, N.349 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.312 NAG-NAG-BMA.20: 1 residues within 4Å: Chain B: N.497 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 6 residues within 4Å: Chain B: V.500, N.513, R.514, F.515, T.516, N.529 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:N.513 NAG-NAG-BMA.22: 4 residues within 4Å: Chain B: N.655, T.670, T.671, R.672 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 2 residues within 4Å: Chain B: N.664, S.666 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.24: 4 residues within 4Å: Chain B: Q.787, G.790, N.791, L.794 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.28: 7 residues within 4Å: Chain C: E.154, N.155, Y.156, V.157, Y.166, L.170, N.187 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.31: 7 residues within 4Å: Chain C: Q.312, N.314, T.330, N.332, G.333, E.347, N.349 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.312 NAG-NAG-BMA.33: 1 residues within 4Å: Chain C: N.497 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.34: 6 residues within 4Å: Chain C: V.500, N.513, R.514, F.515, T.516, N.529 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:N.513 NAG-NAG-BMA.35: 4 residues within 4Å: Chain C: N.655, T.670, T.671, R.672 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.36: 2 residues within 4Å: Chain C: N.664, S.666 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.37: 4 residues within 4Å: Chain C: Q.787, G.790, N.791, L.794 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.4: 4 residues within 4Å: Chain A: N.83, T.253, N.254 Chain B: L.455 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain A: V.1002, F.1004, N.1006 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain B: N.83, T.253, N.254 Chain C: L.455 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain B: V.1002, F.1004, N.1006 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 4 residues within 4Å: Chain A: L.455 Chain C: N.83, T.253, N.254 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 3 residues within 4Å: Chain C: V.1002, F.1004, N.1006 No protein-ligand interaction detected (PLIP)

3 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.6: 6 residues within 4Å: Chain A: V.300, S.429, S.430, V.431, N.475, T.478 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.19: 6 residues within 4Å: Chain B: V.300, S.429, S.430, V.431, N.475, T.478 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.32: 6 residues within 4Å: Chain C: V.300, S.429, S.430, V.431, N.475, T.478 No protein-ligand interaction detected (PLIP)

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

NAG.40: 2 residues within 4Å: Chain A: N.102, Y.117 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain A: N.165 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain A: T.168, H.171, N.172 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain A: G.333, N.334 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain A: N.508, E.511 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain A: T.532, N.534, C.535 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain A: N.948 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain A: F.972, N.973 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain B: N.102, Y.117 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain B: N.165 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain B: T.168, H.171, N.172 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain B: G.333, N.334 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain B: N.508, E.511 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain B: T.532, N.534, C.535 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain B: N.948 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain B: F.972, N.973 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain C: N.102, Y.117 Ligand excluded by PLIP NAG.57: 1 residues within 4Å: Chain C: N.165 Ligand excluded by PLIP NAG.58: 3 residues within 4Å: Chain C: T.168, H.171, N.172 Ligand excluded by PLIP NAG.59: 2 residues within 4Å: Chain C: G.333, N.334 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain C: N.508, E.511 Ligand excluded by PLIP NAG.61: 3 residues within 4Å: Chain C: T.532, N.534, C.535 Ligand excluded by PLIP NAG.62: 1 residues within 4Å: Chain C: N.948 Ligand excluded by PLIP NAG.63: 2 residues within 4Å: Chain C: F.972, N.973 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiong, X. et al., Glycan Shield and Fusion Activation of a Deltacoronavirus Spike Glycoprotein Fine-Tuned for Enteric Infections. J. Virol. (2018)

Release Date

2017-11-22

Peptides

Spike protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike protein