› 4v1d

X-ray diffraction
3.1Å resolution

Ternary complex among two human derived single chain antibody fragments and Cn2 toxin from scorpion Centruroides noxius.

Released:
DOI: 10.2210/pdb4v1d/pdb
PDB entry 4v1d coloured by chain, front view.
PDB entry 4v1d coloured by chain, side view.
PDB entry 4v1d coloured by chain, top view.
Source organisms:
Primary publication:
Optimal Neutralization of Centruroides noxius Venom Is Understood through a Structural Complex between Two Antibody Fragments and the Cn2 Toxin.
Riaño-Umbarila L, Ledezma-Candanoza LM, Serrano-Posada H, Fernández-Taboada G, Olamendi-Portugal T, Rojas-Trejo S, Gómez-Ramírez IV, Rudiño-Piñera E, Possani LD, Becerril B
J Biol Chem 291 1619-1630 (2016)
PMID: 26589800

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-208430 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
SINGLE CHAIN ANTIBODY FRAGMENT LR, HEAVY CHAIN Chain: A
Molecule details ›
Chain: A
Length: 117 amino acids
Theoretical weight: 12.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
Structure domains: Immunoglobulins
SINGLE CHAIN ANTIBODY FRAGMENT LR, LIGHT CHAIN Chain: B
Molecule details ›
Chain: B
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 Chain: C
Molecule details ›
Chain: C
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
SINGLE CHAIN ANTIBODY FRAGMENT RU1, HEAVY CHAIN Chain: D
Molecule details ›
Chain: D
Length: 124 amino acids
Theoretical weight: 13.56 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
Structure domains: Immunoglobulins
SINGLE CHAIN ANTIBODY FRAGMENT RU1, LIGHT CHAIN Chain: E
Molecule details ›
Chain: E
Length: 149 amino acids
Theoretical weight: 15.15 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
Structure domains: Immunoglobulins

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X6A
Unit cell:
a: 45.576Å b: 74.643Å c: 140.239Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.187 0.185 0.229
Expression system: Escherichia coli K-12

Quick links

Citations

2 review citations

Biotechnological Trends in Spider and Scorpion Antivenom Development.
Laustsen et al. (2016)
1 more

5 mentions without citation

Structural Basis of Protection against H7N9 Influenza Virus by Human Anti-N9 Neuraminidase Antibodies.
Zhu et al. (2019)
4 more