SMTL ID : 9n14.1

Cryo-EM structure of HCoV-HKU1 glycoprotein in complex with 9OAc-GD3(mutant T31VPR34 to GGGG)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.08 Å

Oligo State

homo-trimer

Ligands

2 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: 9 residues within 4Å: Chain A: D.4, F.5, I.118, N.119, T.141, D.164 Chain C: N.551, S.553 Ligands: NAG.24 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.551 NAG-NAG-BMA-MAN-MAN.17: 7 residues within 4Å: Chain B: N.551 Chain C: D.4, F.5, I.118, N.119, T.141 Ligands: NAG.48 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.551

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: 7 residues within 4Å: Chain A: H.129, V.132, E.134, K.151, K.173, K.174, N.175 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 11 residues within 4Å: Chain A: D.313, D.317, K.318, N.342, T.345, L.349, N.594, L.597 Chain C: Y.515, D.516, P.517 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: V.651, T.652, N.653 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: H.671, N.673, Y.734, N.735 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain A: D.606, V.607, I.621, Y.688, N.691, N.692 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.606 NAG-NAG.7: 5 residues within 4Å: Chain A: F.701, D.702, N.713, T.715, D.716 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain A: I.484 Chain B: N.6, N.9 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.10 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 7 residues within 4Å: Chain B: H.129, V.132, E.134, K.151, K.173, K.174, N.175 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 12 residues within 4Å: Chain A: Y.515, D.516, P.517, R.518, S.519 Chain B: D.313, C.314, N.340, F.341, N.342, N.594, L.597 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.597 NAG-NAG.13: 4 residues within 4Å: Chain B: S.632, V.651, T.652, N.653 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 7 residues within 4Å: Chain B: D.606, V.607, C.608, I.621, Y.688, N.691, N.692 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain B: F.701, D.702, N.713, T.715, D.716 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 8 residues within 4Å: Chain B: V.1201, N.1202 Chain C: D.869, V.870, D.871, N.872, Q.992, K.993 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.872 NAG-NAG.18: 7 residues within 4Å: Chain C: H.129, V.132, E.134, K.151, K.173, K.174, N.175 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 8 residues within 4Å: Chain B: Y.515, D.516, P.517 Chain C: D.313, N.342, T.345, N.594, L.597 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.515 NAG-NAG.20: 5 residues within 4Å: Chain C: S.632, F.650, V.651, T.652, N.653 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 8 residues within 4Å: Chain C: T.605, D.606, V.607, C.608, I.621, Y.688, N.691, N.692 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 5 residues within 4Å: Chain C: F.701, 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.8: 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:N.872 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.869, A:N.872

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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-MAN.10: 15 residues within 4Å: Chain A: R.433, R.434, S.481, P.483, I.484, S.553, L.555 Chain B: D.4, F.5, I.118, N.119, T.141, D.164 Ligands: NAG-NAG.9, NAG-NAG.9 No protein-ligand interaction detected (PLIP)

35 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.45, N.259 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain A: N.179, S.181, T.182, D.183 Ligand excluded by PLIP NAG.27: 6 residues within 4Å: Chain A: S.233, S.234, N.235, T.236, D.237, N.238 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain A: F.323, I.419, N.420 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain A: N.457, T.459, C.520, S.521, K.523 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain A: S.549, N.551, V.552 Ligand excluded by PLIP NAG.31: 5 residues within 4Å: Chain A: S.720, E.759, P.760, F.761, N.762 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain A: N.767 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain A: N.784, N.991, I.1142, Y.1182 Ligand excluded by PLIP NAG.34: 5 residues within 4Å: Chain A: K.903, G.908, E.911, A.912, N.915 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: N.45, N.259 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain B: N.179, S.181, T.182, D.183 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain B: S.234, N.235, T.236, D.237, N.238 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain B: F.323, I.419, N.420 Ligand excluded by PLIP NAG.40: 5 residues within 4Å: Chain B: N.457, T.459, S.521 Chain C: K.79, D.84 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain B: S.549, N.551, V.552 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain B: H.671, N.673, Y.734 Ligand excluded by PLIP NAG.43: 5 residues within 4Å: Chain B: V.719, S.720, N.762, V.763, S.764 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain B: N.767 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain B: N.784, L.994, I.1142, Y.1182 Ligand excluded by PLIP NAG.46: 6 residues within 4Å: Chain B: K.903, G.908, E.911, A.912, N.915, S.920 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain C: N.6, T.8, N.9 Ligands: NAG-NAG-BMA-MAN-MAN.17 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain C: N.45, N.259 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain C: F.10, S.156, R.157, N.158 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain C: N.179, S.181, T.182, D.183 Ligand excluded by PLIP NAG.52: 5 residues within 4Å: Chain C: S.234, N.235, T.236, D.237, N.238 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain C: F.323, I.419, N.420 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain C: N.441 Ligand excluded by PLIP NAG.55: 4 residues within 4Å: Chain A: D.84 Chain C: N.457, S.521, K.523 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain C: S.549, N.551, V.552 Ligand excluded by PLIP NAG.57: 5 residues within 4Å: Chain C: S.720, E.759, P.760, F.761, N.762 Ligand excluded by PLIP NAG.58: 2 residues within 4Å: Chain C: N.767, K.780 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain C: N.784, I.1142, Y.1182 Ligand excluded by PLIP NAG.60: 5 residues within 4Å: Chain C: K.903, G.908, 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

01.35: 15 residues within 4Å: Chain A: N.13, L.15, T.17, L.66, K.67, G.68, T.69, Y.71, L.72, S.73, W.76, N.230, S.233, N.235, T.236 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:T.17, A:L.66, A:Y.71, A:W.76, A:T.236 Hydrogen bonds: A:N.13, A:T.17, A:K.67, A:K.67, A:T.69, A:T.69, A:T.69, A:S.233, A:N.235, A:N.235 Salt bridges: A:K.67 01.47: 16 residues within 4Å: Chain B: N.13, L.15, T.17, L.66, K.67, G.68, T.69, Y.71, L.72, S.73, W.76, N.230, A.231, S.233, N.235, T.236 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:L.15, B:T.17, B:L.66, B:W.76 Hydrogen bonds: B:N.13, B:T.17, B:T.17, B:K.67, B:K.67, B:T.69, B:T.69, B:T.69, B:S.233, B:N.235, B:N.235 Salt bridges: B:K.67 01.61: 18 residues within 4Å: Chain C: N.13, L.15, T.17, L.66, K.67, G.68, T.69, Y.71, L.72, S.73, W.76, C.229, N.230, A.231, I.232, S.233, N.235, T.236 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:T.17, C:L.66, C:Y.71, C:W.76, C:T.236 Hydrogen bonds: C:N.13, C:T.17, 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
A

B
B

C
C

Spike glycoprotein

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