SMTL ID : 9bt1.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

9 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.16, T.17, V.19 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: D.4, F.5, N.119, T.141 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: D.702, N.713, T.715, D.716 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: N.16, T.17, V.19 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: D.4, F.5, N.119, T.141 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: D.702, N.713, T.715, D.716 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain C: N.16, T.17, V.19 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain C: D.4, F.5, N.119, T.141 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 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.4: 6 residues within 4Å: Chain A: V.1201, N.1202 Chain B: D.869, D.871, N.872, Q.992 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.872, B:D.869 NAG-NAG-BMA.8: 6 residues within 4Å: Chain B: V.1201, N.1202 Chain C: D.869, D.871, N.872, Q.992 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.872, C:D.869 NAG-NAG-BMA.12: 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:N.872, A:D.869

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

NAG.13: 2 residues within 4Å: Chain A: N.6, N.9 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.45, N.259 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: H.129, V.132, N.175 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: N.179, S.181, T.182 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: S.234, N.235, T.236, N.238 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: V.651, N.653 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: H.671, N.673 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.767 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.784 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: E.911, A.912, N.915, S.920 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.6, N.9 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.45, N.259 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: H.129, V.132, N.175 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: N.179, S.181, T.182 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: S.234, N.235, T.236, N.238 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: V.651, N.653 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: H.671, N.673, Y.734 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.767 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.784 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain B: E.911, A.912, N.915, S.920 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: N.6, N.9 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.45, N.259 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: H.129, V.132, N.175 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: N.179, S.181, T.182 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain C: S.234, N.235, T.236, N.238 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: V.651, N.653 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: H.671, N.673 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.767 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.784 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain C: E.911, A.912, N.915, S.920 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

01.23: 13 residues within 4Å: Chain A: N.13, L.15, T.17, L.66, K.67, G.68, T.69, W.76, N.230, A.231, I.232, S.233, N.235 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.15, A:L.66, A:W.76 Hydrogen bonds: A:K.67, A:K.67, A:T.69, A:T.69, A:S.233, A:N.235 Salt bridges: A:K.67 01.34: 11 residues within 4Å: Chain B: N.13, L.15, T.17, L.66, K.67, T.69, W.76, A.231, I.232, S.233, N.235 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.15, B:L.66, B:W.76, B:N.235 Hydrogen bonds: B:K.67, B:K.67, B:T.69, B:T.69, B:S.233, B:N.235, B:N.235 Salt bridges: B:K.67 01.45: 11 residues within 4Å: Chain C: L.15, T.17, L.66, K.67, T.69, W.76, N.230, A.231, I.232, S.233, N.235 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:L.15, C:L.66, C:W.76 Hydrogen bonds: C:K.67, 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
B

B
C

C
A

Spike glycoprotein

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