SMTL ID : 9n19.1

Cryo-EM structure of HCoV-HKU1spike glycoprotein D1 Domain in complex with 9OAc-GD3 tetrasacchride (Deletion 33Pro34Arg)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.02 Å

Oligo State

monomer

Ligands

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.1: 6 residues within 4Å: Chain A: D.4, F.5, I.116, N.117, T.139 Ligands: NAG.3 No protein-ligand interaction detected (PLIP)

1 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: 6 residues within 4Å: Chain A: H.127, V.130, E.132, K.149, K.171, N.173 No protein-ligand interaction detected (PLIP)

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

NAG.3: 4 residues within 4Å: Chain A: N.6, N.9, E.142 Ligands: NAG-NAG-BMA-MAN-MAN.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.6 NAG.4: 2 residues within 4Å: Chain A: N.43, N.257 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.43 NAG.5: 4 residues within 4Å: Chain A: F.10, S.154, R.155, N.156 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.10 Hydrogen bonds: A:N.156 NAG.6: 3 residues within 4Å: Chain A: N.177, S.179, T.180 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.177 NAG.7: 5 residues within 4Å: Chain A: S.232, N.233, T.234, D.235, N.236 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.232, A:N.236 NAG.8: 4 residues within 4Å: Chain A: N.16, T.18, V.19, L.73 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.16

1 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

01.9: 17 residues within 4Å: Chain A: N.13, L.15, T.17, T.18, L.64, K.65, G.66, T.67, Y.69, L.70, S.71, W.74, N.228, A.229, S.231, N.233, T.234 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:T.17, A:T.18, A:L.64, A:Y.69, A:W.74, A:T.234 Hydrogen bonds: A:N.13, A:T.17, A:K.65, A:K.65, A:T.67, A:T.67, A:T.67, A:S.231, A:N.233 Salt bridges: A:K.65

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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