› 8tfh

X-ray diffraction
3.29Å resolution

Ricin in complex with Fab JB4

Released:
DOI: 10.2210/pdb8tfh/pdb
PDB entry 8tfh coloured by chain, front view.
PDB entry 8tfh coloured by chain, side view.
PDB entry 8tfh coloured by chain, top view.
Source organisms:
Primary publication:
Structural Basis of Antibody-Mediated Inhibition of Ricin Toxin Attachment to Host Cells.
Vance DJ, Rudolph MJ, Davis SA, Mantis NJ
Biochemistry 62 3181-3187 (2023)
PMID: 37903428

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-243121 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (6 distinct):
Ricin A chain Chain: A
Molecule details ›
Chain: A
Length: 260 amino acids
Theoretical weight: 29.13 KDa
Source organism: Ricinus communis
UniProt:
  • Canonical: P02879 (Residues: 39-298; Coverage: 48%)
Sequence domains: Ribosome inactivating protein
Ricin B chain Chain: B
Molecule details ›
Chain: B
Length: 262 amino acids
Theoretical weight: 28.99 KDa
Source organism: Ricinus communis
UniProt:
  • Canonical: P02879 (Residues: 315-576; Coverage: 48%)
Sequence domains: Ricin-type beta-trefoil lectin domain
JB4 monoclonal antibody heavy chain Chain: H
Molecule details ›
Chain: H
Length: 223 amino acids
Theoretical weight: 24.16 KDa
Source organism: Mus musculus
Expression system: Cricetulus griseus
JB4 monoclonal antibody light chain Chain: L
Molecule details ›
Chain: L
Length: 210 amino acids
Theoretical weight: 23.28 KDa
Source organism: Mus musculus
Expression system: Cricetulus griseus

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
3 bound ligands:
Ligand EDO 3 x EDO
Ligand CL 3 x CL
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: I4122
Unit cell:
a: 139.358Å b: 139.358Å c: 444.613Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.277 0.274 0.334
Expression system: Cricetulus griseus

Quick links

Citations

2 citation in other articles

Identification and Biological Evaluation of a Novel Small-Molecule Inhibitor of Ricin Toxin.
Yang et al. (2024)
1 more