SMTL ID : 9ecz.1

Cryo-EM structure of SARS-CoV-2 spike protein in complex with human neutralizing antibody WRAIR-2008 (focused refinement of NTD and WRAIR-2008)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

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.1: 7 residues within 4Å: Chain A: Y.28, T.29, N.30, F.59, S.60, N.61, V.62 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 6 residues within 4Å: Chain A: N.122, A.123, T.124, N.125, V.127, V.171 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 4 residues within 4Å: Chain A: Q.115, E.132, N.164, N.165 No protein-ligand interaction detected (PLIP)

1 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: 3 residues within 4Å: Chain A: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP)

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

NAG.5: 2 residues within 4Å: Chain A: N.17, N.137 No protein-ligand interaction detected (PLIP) NAG.6: 4 residues within 4Å: Chain A: H.146, N.148, N.149, M.153 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dussupt, V. et al., First-generation N-terminal domain supersite public antibodies retain activity against Omicron-derived lineages and protect mice against Omicron BA.5 challenge. Mbio (2025)

Release Date

2025-08-20

Peptides

Spike glycoprotein: A
WRAIR-2008 antibody Fab heavy chain: B
WRAIR-2008 antibody Fab light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

Spike glycoprotein

WRAIR-2008 antibody Fab heavy chain

WRAIR-2008 antibody Fab light chain

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