SMTL ID : 7rq6.1

Cryo-EM structure of SARS-CoV-2 spike in complex with non-neutralizing NTD-directed CV3-13 Fab isolated from convalescent individual

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

3 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: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.1101 NAG-NAG.2: 4 residues within 4Å: Chain D: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain G: N.1098, T.1100, H.1101, F.1103 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:H.1101

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

NAG.4: 2 residues within 4Å: Chain A: F.59, N.61 Ligand excluded by PLIP NAG.5: 2 residues within 4Å: Chain A: N.164, N.165 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain A: N.234, T.236 Chain G: E.465 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain A: N.280, N.282 Chain G: K.558 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.331 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: N.616, T.618, E.619 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain A: S.708, N.709, I.1130 Chain D: D.796 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.717, Q.926, Q.1071 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: N.801, S.803, Q.804, N.928 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: A.706, N.1074 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain D: F.59, N.61 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain D: N.164, N.165 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: E.465 Chain D: N.234, T.236 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: K.558 Chain D: N.280, N.282 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain D: N.331 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain D: N.616, T.618, E.619 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain D: H.655, N.657 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain D: S.708, N.709, I.1130 Chain G: D.796 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain D: N.717, Q.926, Q.1071 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain D: N.801, S.803, Q.804, N.928 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain D: A.706, N.1074 Chain G: Q.895 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain D: N.1134 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain G: F.59, N.61 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain G: N.164, N.165 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain D: E.465 Chain G: N.234, T.236 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain D: K.558 Chain G: N.280, N.282 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain G: N.331 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain G: N.616, T.618, E.619 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain G: H.655, N.657 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain A: D.796 Chain G: S.708, N.709, I.1130 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain G: N.717, Q.926, Q.1071 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain G: N.801, S.803, N.928 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain G: A.706, N.1074 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain G: N.1134 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Beaudoin-Bussieres, G. et al., A Fc-enhanced NTD-binding non-neutralizing antibody delays virus spread and synergizes with a nAb to protect mice from lethal SARS-CoV-2 infection. Cell Rep (2022)

Release Date

2022-04-20

Peptides

Spike glycoprotein: ADG
CV3-13 Fab heavy chain: BEH
CV3-13 Fab light chain: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

G
C

B
H

E
D

H
J

C
L

F
E

I
K

Spike glycoprotein

CV3-13 Fab heavy chain

CV3-13 Fab light chain