SMTL ID : 7xco.1

Cryo-EM structure of SARS-CoV-2 Omicron spike protein (S-6P-RRAR) in complex with S309 fab

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

19 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: 6 residues within 4Å: Chain A: N.107, N.110, V.112, K.114, F.139, Y.142 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.264, E.265, N.266 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.693 Chain B: Y.780 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.701, L.906, Q.910, Q.1055 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.785, S.787, Q.788 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.1082, T.1084, H.1085, F.1087 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain A: N.1118 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: N.693 Chain C: I.778, Y.780 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain B: N.701, L.906, Q.910, Q.1055 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain B: N.785, S.787 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain B: A.690, E.1056, N.1058 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.690 NAG-NAG.12: 4 residues within 4Å: Chain B: N.1082, T.1084, H.1085, F.1087 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 1 residues within 4Å: Chain B: N.1118 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain C: N.701, L.906, Q.910 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain C: N.785, S.787, Q.788 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain C: A.690, E.1056, N.1058 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain C: N.1082, T.1084, H.1085, F.1087 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 1 residues within 4Å: Chain C: N.1118 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 2 residues within 4Å: Chain C: N.315, Q.564 No protein-ligand interaction detected (PLIP)

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

NAG.20: 1 residues within 4Å: Chain A: N.4 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: Y.15, N.48 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: E.117, N.146, N.147 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: T.93, N.218, T.220 Ligand excluded by PLIP NAG.24: 8 residues within 4Å: Chain A: F.322, D.323, F.326, N.327, N.354, L.355 Chain D: Y.100 Chain E: Y.50 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: A.690, E.1056, N.1058 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: N.315, Q.564 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: N.600, T.602 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain B: N.4, L.5, R.8, N.122, D.123 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: Y.15, N.48 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.107, T.109 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain A: R.450 Chain B: Q.100, N.147, T.149 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: N.264, E.265, N.266 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: N.315, Q.564 Ligand excluded by PLIP NAG.34: 7 residues within 4Å: Chain B: F.322, D.323, F.326, N.327, N.354, L.355 Chain F: Y.100 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: N.600, T.602, Q.628 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain A: K.446 Chain B: T.93, N.218, T.220 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: N.4, N.122 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: Y.15, N.17, N.48 Ligand excluded by PLIP NAG.39: 5 residues within 4Å: Chain C: V.105, N.107, T.109, V.112, F.139 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: N.146, N.147 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain B: E.449 Chain C: T.93, N.218 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain B: K.542 Chain C: N.264, E.265, N.266 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain A: I.778, Y.780 Chain C: N.693 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP

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

2022-09-21

Peptides

Spike glycoprotein: ABC
S309 Fab heavy chain: DFH
S309 fab light chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

F
M

H
O

E
L

G
N

I
P

Spike glycoprotein

S309 Fab heavy chain

S309 fab light chain

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