SMTL ID : 9bt9.1

Cryo-EM Structure of HKU1 spike D1 Domain (Active state, locally refined)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

2 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: N.6, N.9 Ligands: NAG-NAG-BMA-MAN-MAN.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.9 NAG-NAG.3: 4 residues within 4Å: Chain A: H.129, V.132, E.134, N.175 No protein-ligand interaction detected (PLIP)

1 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.2: 6 residues within 4Å: Chain A: D.4, F.5, N.119, T.141, D.164 Ligands: NAG-NAG.1 No protein-ligand interaction detected (PLIP)

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

NAG.4: 1 residues within 4Å: Chain A: N.16 No protein-ligand interaction detected (PLIP) NAG.5: 1 residues within 4Å: Chain A: N.45 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.45 NAG.6: 3 residues within 4Å: Chain A: N.179, S.181, T.182 No protein-ligand interaction detected (PLIP) NAG.7: 3 residues within 4Å: Chain A: S.234, T.236, N.238 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.234, A:N.238

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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Spike glycoprotein

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