SMTL ID : 6jx7.1

Cryo-EM structure of spike protein of feline infectious peritonitis virus strain UU4

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

21 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: 3 residues within 4Å: Chain A: V.91, E.93, N.146 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.93 NAG-NAG.3: 4 residues within 4Å: Chain A: Y.71, N.239, T.241, Q.250 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain A: Q.294, N.476 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain A: N.759, Q.760 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain A: Y.786, N.799 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain A: N.853, E.1062, N.1063, I.1066 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain A: V.1289, F.1291, N.1293 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain B: V.91, E.93, N.146 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.93 NAG-NAG.21: 4 residues within 4Å: Chain B: Y.71, N.239, T.241, Q.250 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 2 residues within 4Å: Chain B: Q.294, N.476 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 2 residues within 4Å: Chain B: N.759, Q.760 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 2 residues within 4Å: Chain B: Y.786, N.799 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 4 residues within 4Å: Chain B: N.853, E.1062, N.1063, I.1066 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 3 residues within 4Å: Chain B: V.1289, F.1291, N.1293 No protein-ligand interaction detected (PLIP) NAG-NAG.37: 3 residues within 4Å: Chain C: V.91, E.93, N.146 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.93 NAG-NAG.39: 4 residues within 4Å: Chain C: Y.71, N.239, T.241, Q.250 No protein-ligand interaction detected (PLIP) NAG-NAG.44: 2 residues within 4Å: Chain C: Q.294, N.476 No protein-ligand interaction detected (PLIP) NAG-NAG.46: 2 residues within 4Å: Chain C: N.759, Q.760 No protein-ligand interaction detected (PLIP) NAG-NAG.47: 2 residues within 4Å: Chain C: Y.786, N.799 No protein-ligand interaction detected (PLIP) NAG-NAG.50: 4 residues within 4Å: Chain C: N.853, E.1062, N.1063, I.1066 No protein-ligand interaction detected (PLIP) NAG-NAG.54: 3 residues within 4Å: Chain C: V.1289, F.1291, N.1293 No protein-ligand interaction detected (PLIP)

9 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: 4 residues within 4Å: Chain A: E.93, H.94, N.95, N.231 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 2 residues within 4Å: Chain A: D.187, N.316 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 2 residues within 4Å: Chain A: P.330, N.331 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 4 residues within 4Å: Chain B: E.93, H.94, N.95, N.231 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 2 residues within 4Å: Chain B: D.187, N.316 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 2 residues within 4Å: Chain B: P.330, N.331 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.38: 4 residues within 4Å: Chain C: E.93, H.94, N.95, N.231 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.40: 2 residues within 4Å: Chain C: D.187, N.316 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.41: 2 residues within 4Å: Chain C: P.330, N.331 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-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.6: 8 residues within 4Å: Chain A: A.69, K.70, Y.71, N.265, S.281, N.282, N.342, E.456 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.24: 8 residues within 4Å: Chain B: A.69, K.70, Y.71, N.265, S.281, N.282, N.342, E.456 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.42: 8 residues within 4Å: Chain C: A.69, K.70, Y.71, N.265, S.281, N.282, N.342, E.456 No protein-ligand interaction detected (PLIP)

12 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.7: 6 residues within 4Å: Chain A: Q.306, T.333, D.335, R.428, N.467 Ligands: MAN.58 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.9: 3 residues within 4Å: Chain A: W.530, N.532, K.591 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.12: 6 residues within 4Å: Chain A: N.826, H.829 Chain C: D.922, V.959, M.1020 Ligands: MAN.77 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.13: 1 residues within 4Å: Chain A: N.847 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.25: 6 residues within 4Å: Chain B: Q.306, T.333, D.335, R.428, N.467 Ligands: MAN.69 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.27: 3 residues within 4Å: Chain B: W.530, N.532, K.591 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.30: 6 residues within 4Å: Chain A: D.922, V.959, M.1020 Chain B: N.826, H.829 Ligands: MAN.65 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.31: 1 residues within 4Å: Chain B: N.847 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.43: 6 residues within 4Å: Chain C: Q.306, T.333, D.335, R.428, N.467 Ligands: MAN.81 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.45: 3 residues within 4Å: Chain C: W.530, N.532, K.591 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.48: 6 residues within 4Å: Chain B: D.922, V.959, M.1020 Chain C: N.826, H.829 Ligands: MAN.76 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.49: 1 residues within 4Å: Chain C: N.847 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-FUC.15: 1 residues within 4Å: Chain A: N.934 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.33: 1 residues within 4Å: Chain B: N.934 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.51: 1 residues within 4Å: Chain C: N.934 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.16: 5 residues within 4Å: Chain A: N.1073, G.1076, N.1077, A.1088, T.1091 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.34: 5 residues within 4Å: Chain B: N.1073, G.1076, N.1077, A.1088, T.1091 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.52: 5 residues within 4Å: Chain C: N.1073, G.1076, N.1077, A.1088, T.1091 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: 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.17: 6 residues within 4Å: Chain A: H.829, E.831, D.835, N.1203, L.1226 Chain C: D.916 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.831 NAG-NAG-BMA-MAN-MAN-MAN-MAN.35: 6 residues within 4Å: Chain A: D.916 Chain B: H.829, E.831, D.835, N.1203, L.1226 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.831 NAG-NAG-BMA-MAN-MAN-MAN-MAN.53: 6 residues within 4Å: Chain B: D.916 Chain C: H.829, E.831, D.835, N.1203, L.1226 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.831

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

NAG.55: 2 residues within 4Å: Chain A: G.242, N.245 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain A: D.364, N.365 Ligand excluded by PLIP NAG.57: 4 residues within 4Å: Chain A: V.320, D.356, H.359, N.449 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain A: N.570, G.571, S.572 Ligand excluded by PLIP NAG.60: 3 residues within 4Å: Chain A: N.575, V.576, T.577 Ligand excluded by PLIP NAG.61: 1 residues within 4Å: Chain A: N.804 Ligand excluded by PLIP NAG.62: 2 residues within 4Å: Chain A: N.1242, T.1295 Ligand excluded by PLIP NAG.63: 1 residues within 4Å: Chain A: N.1260 Ligand excluded by PLIP NAG.64: 2 residues within 4Å: Chain A: D.1308, N.1310 Ligand excluded by PLIP NAG.66: 2 residues within 4Å: Chain B: G.242, N.245 Ligand excluded by PLIP NAG.67: 2 residues within 4Å: Chain B: D.364, N.365 Ligand excluded by PLIP NAG.68: 4 residues within 4Å: Chain B: V.320, D.356, H.359, N.449 Ligand excluded by PLIP NAG.70: 3 residues within 4Å: Chain B: N.570, G.571, S.572 Ligand excluded by PLIP NAG.71: 3 residues within 4Å: Chain B: N.575, V.576, T.577 Ligand excluded by PLIP NAG.72: 1 residues within 4Å: Chain B: N.804 Ligand excluded by PLIP NAG.73: 2 residues within 4Å: Chain B: N.1242, T.1295 Ligand excluded by PLIP NAG.74: 1 residues within 4Å: Chain B: N.1260 Ligand excluded by PLIP NAG.75: 2 residues within 4Å: Chain B: D.1308, N.1310 Ligand excluded by PLIP NAG.78: 2 residues within 4Å: Chain C: G.242, N.245 Ligand excluded by PLIP NAG.79: 2 residues within 4Å: Chain C: D.364, N.365 Ligand excluded by PLIP NAG.80: 4 residues within 4Å: Chain C: V.320, D.356, H.359, N.449 Ligand excluded by PLIP NAG.82: 3 residues within 4Å: Chain C: N.570, G.571, S.572 Ligand excluded by PLIP NAG.83: 3 residues within 4Å: Chain C: N.575, V.576, T.577 Ligand excluded by PLIP NAG.84: 1 residues within 4Å: Chain C: N.804 Ligand excluded by PLIP NAG.85: 2 residues within 4Å: Chain C: N.1242, T.1295 Ligand excluded by PLIP NAG.86: 1 residues within 4Å: Chain C: N.1260 Ligand excluded by PLIP NAG.87: 2 residues within 4Å: Chain C: D.1308, N.1310 Ligand excluded by PLIP

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

MAN.58: 2 residues within 4Å: Ligands: NAG-NAG-BMA-MAN.7, NAG-NAG-BMA-MAN.7 No protein-ligand interaction detected (PLIP) MAN.65: 2 residues within 4Å: Ligands: NAG-NAG-BMA-MAN.30, NAG-NAG-BMA-MAN.30 No protein-ligand interaction detected (PLIP) MAN.69: 2 residues within 4Å: Ligands: NAG-NAG-BMA-MAN.25, NAG-NAG-BMA-MAN.25 No protein-ligand interaction detected (PLIP) MAN.76: 2 residues within 4Å: Ligands: NAG-NAG-BMA-MAN.48, NAG-NAG-BMA-MAN.48 No protein-ligand interaction detected (PLIP) MAN.77: 2 residues within 4Å: Ligands: NAG-NAG-BMA-MAN.12, NAG-NAG-BMA-MAN.12 No protein-ligand interaction detected (PLIP) MAN.81: 2 residues within 4Å: Ligands: NAG-NAG-BMA-MAN.43, NAG-NAG-BMA-MAN.43 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, T.J. et al., Cryo-EM analysis of a feline coronavirus spike protein reveals a unique structure and camouflaging glycans. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-01-15

Peptides

Feline Infectious Peritonitis Virus Spike Protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Feline Infectious Peritonitis Virus Spike Protein