SMTL ID : 9n18.1

Cryo-EM structure of HCoV-HKU1 spike glycoprotein in complex with 9OAc-GD3 tetrasacchride (Deletion 33Pro34Arg)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.02 Å

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: 9 residues within 4Å: Chain A: D.4, F.5, I.116, N.117, T.139, S.164 Chain C: N.549, S.551 Ligands: NAG.22 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.549 NAG-NAG-BMA-MAN-MAN.8: 10 residues within 4Å: Chain A: N.549, S.551 Chain B: D.4, F.5, I.116, N.117, T.139, S.164 Ligands: NAG.30, NAG.36 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.549 NAG-NAG-BMA-MAN-MAN.15: 10 residues within 4Å: Chain B: N.549, S.551 Chain C: D.4, F.5, I.116, N.117, T.139, S.164 Ligands: NAG.44, NAG.50 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.549

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: 6 residues within 4Å: Chain A: H.127, V.130, E.132, K.149, K.171, N.173 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 10 residues within 4Å: Chain A: D.311, N.340, T.343, N.592, D.593, L.595 Chain C: R.502, Y.513, D.514, P.515 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:D.514 Hydrogen bonds: C:R.502, C:Y.513 NAG-NAG.4: 4 residues within 4Å: Chain A: S.630, V.649, T.650, N.651 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 8 residues within 4Å: Chain A: T.603, D.604, V.605, C.606, I.619, Y.686, N.689, N.690 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.603 NAG-NAG.6: 5 residues within 4Å: Chain A: F.699, D.700, N.711, T.713, D.714 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 6 residues within 4Å: Chain B: H.127, V.130, E.132, K.149, K.171, N.173 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 10 residues within 4Å: Chain A: Y.513, D.514, P.515, R.516 Chain B: D.311, N.340, T.343, N.592, D.593, L.595 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.514 Hydrogen bonds: A:Y.513 NAG-NAG.11: 5 residues within 4Å: Chain B: S.630, K.646, V.649, T.650, N.651 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 8 residues within 4Å: Chain B: T.603, D.604, V.605, C.606, I.619, Y.686, N.689, N.690 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain B: F.699, D.700, N.711, T.713, D.714 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 7 residues within 4Å: Chain C: H.127, V.130, E.132, K.149, K.171, K.172, N.173 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 10 residues within 4Å: Chain B: Y.513, D.514, P.515, R.516 Chain C: D.311, N.340, T.343, N.592, D.593, L.595 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.514, B:D.514 NAG-NAG.18: 3 residues within 4Å: Chain C: V.649, T.650, N.651 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 8 residues within 4Å: Chain C: T.603, D.604, V.605, C.606, I.619, Y.686, N.689, N.690 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.603 NAG-NAG.20: 5 residues within 4Å: Chain C: F.699, D.700, N.711, T.713, D.714 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.1199, N.1200 Chain B: D.867, V.868, D.869, N.870, Q.990 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.867, B:D.867, B:D.867, B:N.870 NAG-NAG-BMA.14: 7 residues within 4Å: Chain B: V.1199, N.1200 Chain C: D.867, V.868, D.869, N.870, Q.990 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.867, C:D.867, C:D.867, C:N.870 NAG-NAG-BMA.21: 7 residues within 4Å: Chain A: D.867, V.868, D.869, N.870, Q.990 Chain C: V.1199, N.1200 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.867, A:D.867, A:N.870

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

NAG.22: 5 residues within 4Å: Chain A: N.6, N.9, E.142 Chain C: I.482 Ligands: NAG-NAG-BMA-MAN-MAN.1 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: N.43, N.257 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain A: F.10, S.154, R.155, N.156 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: N.177, S.179, T.180 Ligand excluded by PLIP NAG.26: 5 residues within 4Å: Chain A: S.232, N.233, T.234, D.235, N.236 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain A: F.321, P.415, I.417, N.418 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain A: N.439 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain A: N.455, T.457, S.519 Chain B: K.77, D.82 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain A: S.547, N.549, V.550 Ligands: NAG-NAG-BMA-MAN-MAN.8 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain A: S.718, P.758, N.760 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain A: N.765, K.778 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain A: N.782, I.1140 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain A: K.901, E.909, A.910, N.913 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain A: I.482 Chain B: N.6, N.9, E.142 Ligands: NAG-NAG-BMA-MAN-MAN.8 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: N.43, N.257 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain B: F.10, S.154, R.155, N.156 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain B: N.177, S.179, T.180 Ligand excluded by PLIP NAG.40: 5 residues within 4Å: Chain B: S.232, N.233, T.234, D.235, N.236 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain B: F.321, P.415, I.417, N.418 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain B: N.439 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain B: N.455, T.457, S.519 Chain C: D.82 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain B: S.547, N.549, V.550 Ligands: NAG-NAG-BMA-MAN-MAN.15 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain B: S.718, P.758, N.760 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain B: N.765 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain B: N.782, I.1140 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain B: K.901, E.909, A.910, N.913 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain C: N.6, N.9 Ligands: NAG-NAG-BMA-MAN-MAN.15 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain C: N.43, N.257 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain C: F.10, S.154, R.155, N.156 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain C: N.177, S.179, T.180 Ligand excluded by PLIP NAG.54: 6 residues within 4Å: Chain C: S.231, S.232, N.233, T.234, D.235, N.236 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain C: F.321, I.417, N.418 Ligand excluded by PLIP NAG.56: 1 residues within 4Å: Chain C: N.439 Ligand excluded by PLIP NAG.57: 4 residues within 4Å: Chain A: D.82 Chain C: N.455, T.457, S.519 Ligand excluded by PLIP NAG.58: 3 residues within 4Å: Chain C: S.547, N.549, V.550 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain C: S.718, P.758, N.760 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain C: N.765, K.778 Ligand excluded by PLIP NAG.61: 2 residues within 4Å: Chain C: N.782, I.1140 Ligand excluded by PLIP NAG.62: 4 residues within 4Å: Chain C: K.901, E.909, A.910, N.913 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: 18 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, C.227, N.228, A.229, S.231, N.233, T.234 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:T.17, A:L.64, A:Y.69, A:W.74, A:T.234 Hydrogen bonds: A:N.13, A:T.17, A:T.17, A:K.65, A:K.65, A:T.67, A:T.67, A:T.67, A:N.233 Salt bridges: A:K.65 01.49: 18 residues within 4Å: Chain B: N.13, L.15, T.17, T.18, L.64, K.65, G.66, T.67, Y.69, L.70, S.71, W.74, C.227, N.228, A.229, S.231, N.233, T.234 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:T.17, B:L.64, B:Y.69, B:W.74 Hydrogen bonds: B:N.13, B:T.17, B:T.17, B:K.65, B:K.65, B:T.67, B:T.67, B:T.67, B:T.67, B:S.231, B:N.233 Salt bridges: B:K.65 01.63: 17 residues within 4Å: Chain C: 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 C Hydrophobic interactions: C:T.17, C:L.64, C:Y.69, C:W.74, C:T.234 Hydrogen bonds: C:N.13, C:T.17, C:T.17, C:K.65, C:K.65, C:T.67, C:T.67, C:T.67, C:T.67, C:N.233 Salt bridges: C: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: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
B

C
A

Spike glycoprotein

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