› 6obo

X-ray diffraction
1.9Å resolution

Ricin A chain bound to VHH antibody V6A6

Released:
DOI: 10.2210/pdb6obo/pdb
PDB entry 6obo coloured by chain, front view.
PDB entry 6obo coloured by chain, side view.
PDB entry 6obo coloured by chain, top view.
Source organisms:
Primary publication:
Intracellular Neutralization of Ricin Toxin by Single-domain Antibodies Targeting the Active Site.
Rudolph MJ, Czajka TF, Davis SA, Thi Nguyen CM, Li XP, Tumer NE, Vance DJ, Mantis NJ
J Mol Biol 432 1109-1125 (2020)
PMID: 31931008

Function and Biology Details

Reaction catalysed: 
Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-208817 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ricin A chain Chains: A, B
Molecule details ›
Chains: A, B
Length: 257 amino acids
Theoretical weight: 28.81 KDa
Source organism: Ricinus communis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02879 (Residues: 40-296; Coverage: 48%)
Sequence domains: Ribosome inactivating protein
VHH antibody V6A6 Chains: C, D
Molecule details ›
Chains: C, D
Length: 121 amino acids
Theoretical weight: 12.99 KDa
Source organism: Vicugna pacos
Expression system: Escherichia coli

Ligands and Environments

3 bound ligands:
Ligand EDO 3 x EDO
Ligand ACY 6 x ACY
Ligand CA 2 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: C2
Unit cell:
a: 123.242Å b: 112.929Å c: 93.081Å
α: 90° β: 127.49° γ: 90°
R-values:
R R work R free
0.209 0.207 0.244
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Current and future advances in fluorescence-based visualization of plant cell wall components and cell wall biosynthetic machineries.
DeVree et al. (2021)
1 more

1 mention without citation

Intracellular Neutralization of Ricin Toxin by Single-domain Antibodies Targeting the Active Site.
Rudolph et al. (2020)