› 8en0

X-ray diffraction
2.99Å resolution

Structure of GII.17 norovirus in complex with Nanobody 7

Released:
DOI: 10.2210/pdb8en0/pdb
PDB entry 8en0 coloured by chain, front view.
PDB entry 8en0 coloured by chain, side view.
PDB entry 8en0 coloured by chain, top view.
Source organisms:
Primary publication:
Direct Blockade of the Norovirus Histo-Blood Group Antigen Binding Pocket by Nanobodies.
Kher G, Sabin C, Lun JH, Devant JM, Ruoff K, Koromyslova AD, von Itzstein M, Pancera M, Hansman GS
J Virol 97 e0183322 (2023)
PMID: 36971561

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-233077 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Nanobody 7 Chain: D
Molecule details ›
Chain: D
Length: 136 amino acids
Theoretical weight: 14.65 KDa
Source organism: Vicugna pacos
Expression system: Escherichia coli
VP1 Chain: A
Molecule details ›
Chain: A
Length: 308 amino acids
Theoretical weight: 34.32 KDa
Source organism: Norovirus
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A1D8MBE6 (Residues: 225-530; Coverage: 57%)
Sequence domains: Calicivirus coat protein C-terminal

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)
Spacegroup: I222
Unit cell:
a: 74.82Å b: 85.459Å c: 223.853Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.252 0.249 0.306
Expression system: Escherichia coli

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Citations

1 mention without citation

Direct Blockade of the Norovirus Histo-Blood Group Antigen Binding Pocket by Nanobodies.
Kher et al. (2023)