SMTL ID : 9bsx.1

Cryo-EM structure of HCoV-HKU1 glycoprotein in complex with 9O-acetyl GD3 sialoglycan (DAA state)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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.1: 5 residues within 4Å: Chain A: D.4, F.5, N.119, T.141 Ligands: NAG.24 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.7: 7 residues within 4Å: Chain B: D.4, F.5, I.118, N.119, T.141, D.164 Ligands: NAG.41 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.16: 7 residues within 4Å: Chain B: N.551 Chain C: D.4, F.5, I.118, N.119, T.141, D.164 No protein-ligand interaction detected (PLIP)

18 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: 5 residues within 4Å: Chain A: H.129, V.132, E.134, K.173, N.175 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 8 residues within 4Å: Chain A: D.313, N.340, F.341, N.342, L.597 Chain C: D.516, P.517, R.518 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.516 NAG-NAG.4: 3 residues within 4Å: Chain A: D.702, N.713, T.715 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 7 residues within 4Å: Chain A: V.1201, N.1202 Chain B: D.869, V.870, D.871, N.872, Q.992 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.869, B:N.872 NAG-NAG.6: 2 residues within 4Å: Chain B: N.16, V.19 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: H.129, V.132, N.175 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 9 residues within 4Å: Chain A: Y.515, D.516, P.517, R.518 Chain B: D.313, N.340, N.342, N.594, L.597 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain B: V.651, N.653 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain B: D.606, Y.688, N.691, N.692 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain B: F.701, D.702, N.713, T.715, D.716 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 7 residues within 4Å: Chain B: V.1201, N.1202 Chain C: D.869, V.870, D.871, N.872, Q.992 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.869, C:N.872 NAG-NAG.14: 2 residues within 4Å: Chain C: N.6, N.9 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain C: N.45, N.259 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain C: N.179, S.181, T.182 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 2 residues within 4Å: Chain C: V.651, N.653 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain C: H.671, N.673, Y.734, N.735 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 5 residues within 4Å: Chain C: T.605, D.606, Y.688, N.691, N.692 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.605 NAG-NAG.22: 4 residues within 4Å: Chain C: D.702, N.713, T.715, D.716 No protein-ligand interaction detected (PLIP)

2 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.17: 5 residues within 4Å: Chain C: H.129, V.132, E.134, K.173, N.175 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 7 residues within 4Å: Chain A: D.869, V.870, D.871, N.872, Q.992 Chain C: V.1201, N.1202 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.872, A:N.872

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

NAG.24: 3 residues within 4Å: Chain A: N.6, N.9 Ligands: NAG-NAG-BMA-MAN-MAN.1 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: N.16, V.19 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: N.45, N.259 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: F.10, S.156, N.158 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain A: N.179, S.181, T.182 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain A: S.234, T.236, D.237, N.238 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain A: F.323, I.419, N.420 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain A: N.457, T.459, K.523 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain A: S.549, N.551 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain A: V.651, N.653 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain A: H.671, N.673, Y.734 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain A: D.606, N.691, N.692 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain A: S.720, P.760, N.762 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain A: N.767 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain A: N.784, I.1142 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain A: E.911, N.915, S.920 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain B: N.6, N.9 Ligands: NAG-NAG-BMA-MAN-MAN.7 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain B: N.45 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain B: F.10, N.158 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain B: N.179, S.181, T.182 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain B: S.234, T.236, N.238 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain B: F.323, N.420 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain B: N.457, T.459, S.521 Chain C: D.84 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain B: N.551 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain B: H.671, N.673, Y.734, N.735 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain B: S.720, P.760, N.762 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain B: N.767 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain B: N.784 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain B: E.911, N.914, N.915 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain C: N.16, V.19 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain C: F.10, N.158 Ligand excluded by PLIP NAG.57: 4 residues within 4Å: Chain C: S.234, T.236, D.237, N.238 Ligand excluded by PLIP NAG.58: 7 residues within 4Å: Chain B: A.514, Y.515 Chain C: D.313, N.340, F.341, N.342, L.597 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain C: F.323, I.419, N.420 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain C: N.457, S.521 Ligand excluded by PLIP NAG.61: 2 residues within 4Å: Chain C: S.720, N.762 Ligand excluded by PLIP NAG.62: 1 residues within 4Å: Chain C: N.767 Ligand excluded by PLIP NAG.63: 1 residues within 4Å: Chain C: N.784 Ligand excluded by PLIP NAG.64: 3 residues within 4Å: Chain C: E.911, A.912, N.915 Ligand excluded by PLIP

3 x 01: 5-acetamido-8-O-(5-acetamido-9-O-acetyl-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid

01.40: 17 residues within 4Å: Chain A: N.13, L.15, T.17, T.18, L.66, K.67, G.68, T.69, T.70, Y.71, L.72, S.73, W.76, N.230, A.231, S.233, N.235 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:T.18, A:L.66 Hydrogen bonds: A:N.13, A:T.17, A:T.17, A:K.67, A:K.67, A:K.67, A:T.69, A:T.69, A:T.69, A:T.70, A:S.233, A:N.235 Salt bridges: A:K.67 01.54: 18 residues within 4Å: Chain B: N.13, L.15, T.17, T.18, L.66, K.67, G.68, T.69, Y.71, L.72, S.73, W.76, C.229, N.230, A.231, S.233, N.235, T.236 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:L.15, B:T.17, B:T.18, B:L.66, B:W.76, B:T.236 Hydrogen bonds: B:N.13, B:T.17, B:T.17, B:K.67, B:K.67, B:K.67, B:T.69, B:T.69, B:T.69, B:S.233, B:N.235 Salt bridges: B:K.67 01.65: 14 residues within 4Å: Chain C: N.13, L.15, T.17, L.66, K.67, G.68, T.69, Y.71, S.73, W.76, N.230, A.231, S.233, N.235 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:T.17, C:L.66, C:Y.71, C:W.76 Hydrogen bonds: C:N.13, C:T.17, C:K.67, C:T.69, C:T.69, C:T.69, C:S.233, C:N.235 Salt bridges: C:K.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jin, M. et al., Human coronavirus HKU1 spike structures reveal the basis for sialoglycan specificity and carbohydrate-promoted conformational changes. Nat Commun (2025)

Release Date

2025-05-14

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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