› 2jdl

X-ray diffraction
2.2Å resolution

Structure of C-terminal region of acidic P2 ribosomal protein complexed with trichosanthin

Released:
DOI: 10.2210/pdb2jdl/pdb
PDB entry 2jdl coloured by chain, front view.
PDB entry 2jdl coloured by chain, side view.
PDB entry 2jdl coloured by chain, top view.
Source organisms:
Primary publication:
The C-terminal fragment of the ribosomal P protein complexed to trichosanthin reveals the interaction between the ribosome-inactivating protein and the ribosome.
Too PH, Ma MK, Mak AN, Wong YT, Tung CK, Zhu G, Au SW, Wong KB, Shaw PC
Nucleic Acids Res 37 602-10 (2009)
PMID: 19073700

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 domain:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-138648 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ribosome-inactivating protein alpha-trichosanthin Chains: A, B
Molecule details ›
Chains: A, B
Length: 247 amino acids
Theoretical weight: 27.18 KDa
Source organism: Trichosanthes kirilowii
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P09989 (Residues: 25-270; Coverage: 93%)
Sequence domains: Ribosome inactivating protein
Structure domains:
Large ribosomal subunit protein P2 Chains: C, D
Molecule details ›
Chains: C, D
Length: 11 amino acids
Theoretical weight: 1.22 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P05387 (Residues: 105-115; Coverage: 10%)
Gene names: D11S2243E, RPLP2, RPP2

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: P21
Unit cell:
a: 62.589Å b: 43.964Å c: 92.235Å
α: 90° β: 92.87° γ: 90°
R-values:
R R work R free
0.167 0.163 0.238
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

9 review citations

Interaction of ricin and Shiga toxins with ribosomes.
Tumer et al. (2012)
8 more

10 mentions without citation

Structures and Ribosomal Interaction of Ribosome-Inactivating Proteins.
Shi et al. (2016)
9 more