› 8p89

X-ray diffraction
3.19Å resolution

X-ray structure of cardiotoxic light chain H3 in complex to neutralizing nanobody B5

Released:
DOI: 10.2210/pdb8p89/pdb
PDB entry 8p89 coloured by chain, front view.
PDB entry 8p89 coloured by chain, side view.
PDB entry 8p89 coloured by chain, top view.
Source organisms:
Primary publication:
Nanobodies counteract the toxicity of an amyloidogenic light chain by stabilizing a partially open dimeric conformation.
Broggini L, Barzago MM, Speranzini V, Schulte T, Sonzini F, Giono M, Romeo M, Milani P, Caminito S, Mazzini G, Rognoni P, Merlini G, Pappone C, Anastasia L, Nuvolone M, Palladini G, Diomede L, Ricagno S
J Mol Biol 435 168320 (2023)
PMID: 37865287

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-239457 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Light chain H3 Chains: A, B
Molecule details ›
Chains: A, B
Length: 216 amino acids
Theoretical weight: 22.76 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Nanobody B5 Chains: C, D
Molecule details ›
Chains: C, D
Length: 120 amino acids
Theoretical weight: 13.15 KDa
Source organism: Lama glama
Expression system: Escherichia coli

Ligands and Environments

1 bound ligand:
Ligand CL 15 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID30B
Spacegroup: I4122
Unit cell:
a: 145.215Å b: 145.215Å c: 245.184Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.231 0.229 0.276
Expression system: Escherichia coli

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