SMTL ID : 8y16.1

Cryo-EM structure of SARS-CoV-2 Omicron JN.1 spike protein in complex with human ACE2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

6 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.1: 3 residues within 4Å: Chain A: K.8, N.72 Chain B: T.412 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.412 NAG-NAG-BMA.2: 1 residues within 4Å: Chain A: N.304 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 3 residues within 4Å: Chain C: T.412 Chain E: K.8, N.72 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.412 NAG-NAG-BMA.13: 1 residues within 4Å: Chain E: N.304 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.16: 3 residues within 4Å: Chain D: T.412 Chain F: K.8, N.72 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.412 NAG-NAG-BMA.17: 1 residues within 4Å: Chain F: N.304 No protein-ligand interaction detected (PLIP)

13 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 2 residues within 4Å: Chain A: S.402, N.528 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: N.85, S.88 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: N.797, S.799, Q.800 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.1094, T.1096, H.1097 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: H.336, N.340, F.368 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain C: N.797, S.799, Q.800 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain C: H.336, N.340, F.368 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain D: N.797, S.799, Q.800 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain D: H.336, N.340, F.368 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain E: S.402, N.528 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain E: N.85, S.88 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 2 residues within 4Å: Chain F: S.402, N.528 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 2 residues within 4Å: Chain F: N.85, S.88 No protein-ligand interaction detected (PLIP)

3 x ZN: ZINC ION(Non-covalent)

ZN.20: 4 residues within 4Å: Chain A: H.356, E.357, H.360, E.384 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.356, A:H.360, A:E.384, A:E.384 ZN.54: 4 residues within 4Å: Chain E: H.356, E.357, H.360, E.384 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.356, E:H.360, E:E.384, E:E.384 ZN.57: 4 residues within 4Å: Chain F: H.356, E.357, H.360, E.384 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.356, F:H.360, F:E.384, F:E.384

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

NAG.21: 3 residues within 4Å: Chain A: N.31, N.35, Q.322 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: F.267, N.414, E.415 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: E.278, N.279 Chain C: K.554 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.328, Q.576 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.612, T.614 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.705 Chain D: Y.792 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.713, Q.1067 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.1130 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain B: F.344, N.351, T.353, S.396 Ligand excluded by PLIP NAG.30: 5 residues within 4Å: Chain B: A.709, E.1068, K.1069, N.1070 Chain D: Q.891 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: N.612, T.614 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: Y.792 Chain C: N.705, N.706 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: N.713, Q.1067 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain C: N.1094, T.1096, H.1097, F.1099 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain C: N.1130 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain C: F.344, N.351, T.353, S.396 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: N.328, V.329, Q.576 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain B: Q.891 Chain C: A.702, N.1070 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain C: N.277, E.278, N.279 Chain D: K.554 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain D: Y.29, N.62 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain D: N.162, N.163 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain D: N.612, T.614 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: Y.792 Chain D: N.705 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain D: N.713, Q.1067 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain D: N.1094, G.1095, T.1096 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain B: K.554 Chain D: N.277, E.278, N.279 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain C: Q.891 Chain D: A.702, N.1070 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain D: Y.651, N.653 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain D: F.344, N.351, T.353, S.396 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain D: N.328, V.329, T.330 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain D: I.1128, N.1130 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain D: N.599 Ligand excluded by PLIP NAG.53: 7 residues within 4Å: Chain D: N.120, N.121, A.122, T.123, N.124, F.126, E.152 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain E: N.31, N.35, Q.322 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain E: F.267, N.414, E.415 Ligand excluded by PLIP NAG.58: 3 residues within 4Å: Chain F: N.31, N.35, Q.322 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain F: F.267, N.414, E.415 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, L. et al., Spike structures, receptor binding, and immune escape of recently circulating SARS-CoV-2 Omicron BA.2.86, JN.1, EG.5, EG.5.1, and HV.1 sub-variants. Structure (2024)

Release Date

2024-07-03

Peptides

Angiotensin-converting enzyme 2: AEF
Spike glycoprotein: BCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

F
F

B
B

C
C

D
D

Angiotensin-converting enzyme 2

Spike glycoprotein

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