SMTL ID : 7yad.1

Cryo-EM structure of S309-RBD-RBD-S309 in the S309-bound Omicron spike protein (local refinement)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-mer

Ligands

2 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.1: 7 residues within 4Å: Chain A: Y.100, D.115 Chain B: Y.50 Chain C: F.9, D.10, F.13, N.14 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.100 Hydrogen bonds: A:D.115 NAG-NAG-FUC.2: 9 residues within 4Å: Chain D: R.98, Y.100, D.115 Chain E: Y.50 Chain F: F.9, D.10, F.13, N.14, L.42 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:Y.100 Hydrogen bonds: D:R.98, D:D.115, D:D.115

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, Z. et al., Omicron SARS-CoV-2 mutations stabilize spike up-RBD conformation and lead to a non-RBM-binding monoclonal antibody escape. Nat Commun (2022)

Release Date

2022-08-31

Peptides

S309 neutralizing antibody heavy chain: AD
S309 neutralizing antibody light chain: BE
Spike protein S1: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
C

B
B

E
D

C
M

F
E

S309 neutralizing antibody heavy chain

S309 neutralizing antibody light chain

Spike protein S1

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