› 8k46

Electron Microscopy
3.37Å resolution

A potent and broad-spectrum neutralizing nanobody for SARS-CoV-2 viruses including all major Omicron strains

Released:
DOI: 10.2210/pdb8k46/pdb
PDB entry 8k46 coloured by chain, front view.
PDB entry 8k46 coloured by chain, side view.
PDB entry 8k46 coloured by chain, top view.
Source organisms:
Primary publication:
A potent and broad-spectrum neutralizing nanobody for SARS-CoV-2 viruses, including all major Omicron strains.
Yao H, Wang H, Zhang Z, Lu Y, Zhang Z, Zhang Y, Xiong X, Wang Y, Wang Z, Yang H, Zhao J, Xu W
OpenAccess logo MedComm (2020) 4 e397 (2023)
PMID: 37901798
Related structures: EMD-36878

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-535592 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
nanobody Nb4 Chains: E, G, I
Molecule details ›
Chains: E, G, I
Length: 124 amino acids
Theoretical weight: 13.91 KDa
Source organism: Vicugna pacos
Expression system: Escherichia coli
Spike glycoprotein Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 1288 amino acids
Theoretical weight: 142.59 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DTC2 (Residues: 1-1208; Coverage: 95%)
Gene names: 2, S
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
1 bound ligand:
Ligand NAG 25 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.37Å
Relevant EMDB volumes: EMD-36878
Expression systems:
  • Escherichia coli
  • Homo sapiens

Quick links

Citations

2 citation in other articles

A potent and broad-spectrum neutralizing nanobody for SARS-CoV-2 viruses, including all major Omicron strains.
Yao et al. (2023)
1 more