› 2yc1

X-ray diffraction
1.9Å resolution

Crystal structure of the human derived single chain antibody fragment (scFv) 9004G in complex with Cn2 toxin from the scorpion Centruroides noxius Hoffmann

Released:
DOI: 10.2210/pdb2yc1/pdb
PDB entry 2yc1 coloured by chain, front view.
PDB entry 2yc1 coloured by chain, side view.
PDB entry 2yc1 coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of neutralization of the major toxic component from the scorpion Centruroides noxius Hoffmann by a human-derived single-chain antibody fragment.
Canul-Tec JC, Riaño-Umbarila L, Rudiño-Piñera E, Becerril B, Possani LD, Torres-Larios A
J Biol Chem 286 20892-900 (2011)
PMID: 21489992

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-208429 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
SINGLE CHAIN ANTIBODY FRAGMENT 9004G Chains: A, D
Molecule details ›
Chains: A, D
Length: 117 amino acids
Theoretical weight: 12.53 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
Structure domains: Immunoglobulins
SINGLE CHAIN ANTIBODY FRAGMENT 9004G Chains: B, E
Molecule details ›
Chains: B, E
Length: 146 amino acids
Theoretical weight: 15.42 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
Structure domains: Immunoglobulins
Beta-mammal toxin Cn2 Chains: C, F
Molecule details ›
Chains: C, F
Length: 66 amino acids
Theoretical weight: 7.61 KDa
Source organism: Centruroides noxius
UniProt:
  • Canonical: P01495 (Residues: 17-82; Coverage: 97%)
Sequence domains: Scorpion toxin-like domain
Structure domains: Knottin, scorpion toxin-like

Ligands and Environments

1 bound ligand:
Ligand GOL 9 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: F23
Unit cell:
a: 219.709Å b: 219.709Å c: 219.709Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.187 0.186 0.212
Expression system: Escherichia coli K-12

Quick links

Citations

2 review citations

Computational methods of studying the binding of toxins from venomous animals to biological ion channels: theory and applications.
Gordon et al. (2013)
1 more

8 mentions without citation

Human IgE against the major allergen Bet v 1--defining an epitope with limited cross-reactivity between different PR-10 family proteins.
Levin et al. (2014)
7 more