SMTL ID : 9bt0.1

Cryo-EM structure of HCoV-HKU1 Spike glycoprotein (DDD 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: 7 residues within 4Å: Chain A: D.4, F.5, I.118, N.119, T.141 Chain C: N.551 Ligands: NAG.22 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.551 NAG-NAG-BMA-MAN-MAN.8: 6 residues within 4Å: Chain A: N.551 Chain B: D.4, F.5, N.119, T.141 Ligands: NAG.35 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.15: 6 residues within 4Å: Chain B: N.551 Chain C: D.4, F.5, N.119, T.141 Ligands: NAG.48 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.551

15 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: 4 residues within 4Å: Chain A: H.129, V.132, E.134, N.175 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: N.342, T.345, N.594, L.597 Chain C: Y.515, D.516 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:D.516 Hydrogen bonds: C:R.504, C:Y.515 NAG-NAG.4: 2 residues within 4Å: Chain A: V.651, N.653 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 6 residues within 4Å: Chain A: T.605, D.606, V.607, C.608, N.691, N.692 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.605 NAG-NAG.6: 4 residues within 4Å: Chain A: D.702, N.713, T.715, D.716 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain B: H.129, V.132, E.134, N.175 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 6 residues within 4Å: Chain A: Y.515, D.516 Chain B: N.342, T.345, N.594, L.597 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.516 Hydrogen bonds: A:Y.515 NAG-NAG.11: 2 residues within 4Å: Chain B: V.651, N.653 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain B: D.606, V.607, N.691, N.692 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain B: D.702, N.713, T.715, D.716 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain C: H.129, V.132, E.134, N.175 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 9 residues within 4Å: Chain B: Y.515, D.516, P.517, R.518 Chain C: D.313, N.342, N.594, D.595, L.597 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.516 NAG-NAG.18: 2 residues within 4Å: Chain C: V.651, N.653 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 7 residues within 4Å: Chain C: T.605, D.606, V.607, C.608, I.621, N.691, N.692 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.605 NAG-NAG.20: 4 residues within 4Å: Chain C: D.702, N.713, T.715, D.716 No protein-ligand interaction detected (PLIP)

3 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.7: 7 residues within 4Å: Chain A: V.1201, N.1202 Chain B: D.869, V.870, D.871, N.872, Q.992 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.869, B:N.872 NAG-NAG-BMA.14: 7 residues within 4Å: Chain B: V.1201, N.1202 Chain C: D.869, V.870, D.871, N.872, Q.992 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.869, C:N.872 NAG-NAG-BMA.21: 6 residues within 4Å: Chain A: D.869, D.871, N.872, Q.992 Chain C: V.1201, N.1202 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.869, A:N.872

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

NAG.22: 3 residues within 4Å: Chain A: N.6, N.9 Ligands: NAG-NAG-BMA-MAN-MAN.1 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: N.45, N.259 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain A: F.10, S.156, R.157, N.158 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: N.179, S.181, T.182 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain A: S.234, T.236, D.237, N.238 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: F.323, N.420 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain A: N.441 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain A: N.457, T.459 Chain B: D.84 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain A: S.549, N.551 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain A: S.720, N.762 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain A: N.767 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain A: N.784 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain A: N.915 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: N.6, N.9 Ligands: NAG-NAG-BMA-MAN-MAN.8 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: N.45, N.259 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: F.10, N.158 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain B: N.179, S.181, T.182 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain B: S.234, T.236, D.237, N.238 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain B: F.323, N.420 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain B: N.441 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain B: N.457 Chain C: D.84 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain B: S.549, N.551 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain B: S.720, N.762 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain B: N.767 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain B: N.784 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain B: E.911, A.912, N.915 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain C: N.6, N.9 Ligands: NAG-NAG-BMA-MAN-MAN.15 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain C: N.45 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain C: F.10, N.158 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain C: N.179, S.181, T.182 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain C: S.234, T.236, D.237, N.238 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain C: F.323, N.420 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain C: N.441 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain A: D.84 Chain C: N.457 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain C: S.549, N.551 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain C: S.720, N.762 Ligand excluded by PLIP NAG.58: 1 residues within 4Å: Chain C: N.767 Ligand excluded by PLIP NAG.59: 1 residues within 4Å: Chain C: N.784 Ligand excluded by PLIP NAG.60: 3 residues within 4Å: Chain C: E.911, A.912, N.915 Ligand excluded by PLIP

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
C

B
B

C
A

Spike glycoprotein

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