SMTL ID : 9jmh.1

Cryo-EM structure of HKU25-BatCoV S-trimer stabilized with 2P and x1 disulfide bond

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.00 Å

Oligo State

homo-trimer

Ligands

10 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: 6 residues within 4Å: Chain A: I.35, N.111, N.114, R.168, S.210, S.211 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.168 NAG-NAG.3: 4 residues within 4Å: Chain A: D.20, L.21, P.23, N.230 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.20, A:D.20 NAG-NAG.5: 4 residues within 4Å: Chain A: N.418, K.421, M.586 Chain C: Q.509 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.509 NAG-NAG.6: 6 residues within 4Å: Chain B: P.37, Q.38, Q.41, N.111, N.114, E.115 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.41 NAG-NAG.7: 8 residues within 4Å: Chain B: I.35, N.111, T.113, N.114, R.168, A.208, S.210, S.211 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.168, B:A.208 NAG-NAG.10: 4 residues within 4Å: Chain B: D.20, G.22, N.230, F.248 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.248 Hydrogen bonds: B:D.20, B:D.20 NAG-NAG.11: 4 residues within 4Å: Chain A: Q.509 Chain B: N.418, K.421, M.586 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.509 NAG-NAG.12: 6 residues within 4Å: Chain C: I.35, N.111, N.114, R.168, S.210, S.211 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.168 NAG-NAG.15: 5 residues within 4Å: Chain C: D.20, L.21, P.23, N.230, L.233 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.20 NAG-NAG.16: 4 residues within 4Å: Chain B: Q.509 Chain C: N.418, K.421, M.586 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.509

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.2: 5 residues within 4Å: Chain A: Y.160, N.174 Chain C: G.533, V.536, Q.537 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.536, C:Q.537 NAG-NAG-BMA.4: 6 residues within 4Å: Chain A: G.128, N.132, E.257, H.258, A.259, Y.282 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 7 residues within 4Å: Chain B: G.128, A.131, N.132, E.257, H.258, A.259, Y.282 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 6 residues within 4Å: Chain A: L.532, G.533, V.536, Q.537 Chain B: Y.160, N.174 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 5 residues within 4Å: Chain C: G.128, N.132, E.257, H.258, Y.282 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 4 residues within 4Å: Chain B: G.533, V.536, Q.537 Chain C: N.174 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.537

3 x EIC: LINOLEIC ACID(Non-covalent)

EIC.17: 18 residues within 4Å: Chain A: F.393, M.396, Y.417, L.419, F.426, V.428, F.431, P.438, L.441, I.488, A.490, F.570, I.572 Chain C: S.462, Y.463, S.468, T.469, G.470 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:F.393, A:L.419, A:F.426, A:F.426, A:V.428, A:F.431, A:P.438, A:L.441, A:I.488, A:I.488, A:A.490, A:F.570, A:F.570, A:I.572, C:T.469 Hydrogen bonds: C:G.470 EIC.31: 16 residues within 4Å: Chain A: S.462, Y.463, S.468, G.470 Chain B: F.393, Y.417, L.419, L.423, F.426, V.428, F.431, P.438, L.441, I.488, F.570, I.572 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.393, B:L.419, B:F.426, B:F.426, B:V.428, B:F.431, B:P.438, B:L.441, B:I.488, B:I.488, B:F.570, B:F.570, B:I.572 EIC.44: 16 residues within 4Å: Chain B: Y.463, S.468, T.469 Chain C: F.393, Y.417, L.419, L.422, L.423, F.426, V.428, F.431, P.438, L.441, I.488, F.570, I.572 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:F.393, C:L.419, C:L.422, C:F.426, C:F.426, C:V.428, C:F.431, C:P.438, C:L.441, C:I.488, C:I.488, C:F.570, C:F.570, C:I.572, B:T.469

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

NAG.18: 2 residues within 4Å: Chain A: N.66, V.337 Ligand excluded by PLIP NAG.19: 5 residues within 4Å: Chain A: P.37, Q.41, N.111, N.114, E.115 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: G.162, N.163 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: T.165, N.166, N.167 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: D.24, P.197, N.241 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain A: N.252 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: N.591 Chain C: A.515, F.516 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: N.618, N.646 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain A: Q.706, N.717, S.719, L.751 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: N.755, R.758 Chain B: Y.878 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain A: N.777, Y.1185 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain A: N.862, T.864 Ligand excluded by PLIP NAG.30: 5 residues within 4Å: Chain A: S.768, Q.1201, T.1203, F.1205, N.1207 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: N.66, V.337 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain B: I.161, G.162, N.163, N.167 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: T.165, N.167 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain B: D.24, I.196, P.197, N.241 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain B: N.252 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain A: F.516 Chain B: N.591 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain B: N.618, N.646 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain B: Q.706, N.717, L.751 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain B: V.753, N.755, R.758 Chain C: Y.878 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain B: N.777, Y.1185 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain B: N.862, T.864, N.998 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain B: S.768, T.1203, F.1205, N.1207 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: N.66, V.337 Ligand excluded by PLIP NAG.46: 5 residues within 4Å: Chain C: P.37, Q.41, N.111, N.114, E.115 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain C: G.162, N.163, N.167 Ligands: NAG.48 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain C: T.165, N.167 Ligands: NAG.47 Ligand excluded by PLIP NAG.49: 5 residues within 4Å: Chain C: D.24, I.196, P.197, R.198, N.241 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain C: N.252 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain C: N.591 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain C: N.618, N.646 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain C: Q.706, N.717, S.719, L.751 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain A: Y.878 Chain C: V.753, N.755, R.758 Ligand excluded by PLIP NAG.55: 1 residues within 4Å: Chain C: N.777 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain C: N.862, T.864 Ligand excluded by PLIP NAG.57: 5 residues within 4Å: Chain C: S.768, T.1203, F.1205, E.1206, N.1207 Ligand excluded by PLIP

Links

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Citation

Yuan, H. et al., Structures and receptor binding activities of merbecovirus spike proteins reveal key signatures for human DPP4 adaptation. Sci Adv (2025)

Release Date

2025-06-18

Peptides

Spike glycoprotein,Fibritin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein,Fibritin