- PDB-2jdl: Structure of C-terminal region of acidic P2 ribosomal protein com... -
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Basic information
Entry
Database: PDB / ID: 2jdl
Title
Structure of C-terminal region of acidic P2 ribosomal protein complexed with trichosanthin
Components
ACIDIC RIBOSOMAL PROTEIN P2
RIBOSOME-INACTIVATING PROTEIN ALPHA-TRICHOSANTHIN
Keywords
HYDROLASE / RIBOSOME INACTIVIATING PROTEIN / RIBOSOMAL PROTEIN / PROTEIN SYNTHESIS INHIBITOR / TOXIN / PLANT DEFENSE / ANTIVIRAL PROTEIN
Function / homology
Function and homology information
cytoplasmic translational elongation / regulation of defense response to virus / rRNA N-glycosylase / rRNA N-glycosylase activity / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane ...cytoplasmic translational elongation / regulation of defense response to virus / rRNA N-glycosylase / rRNA N-glycosylase activity / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / defense response / Regulation of expression of SLITs and ROBOs / toxin activity / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / structural constituent of ribosome / translation / focal adhesion / extracellular exosome / membrane / cytoplasm / cytosol Similarity search - Function
Ribosomal protein P2 / Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / 60s Acidic ribosomal protein / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. ...Ribosomal protein P2 / Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / 60s Acidic ribosomal protein / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 / Ribosome-inactivating protein superfamily / Ribosome inactivating protein / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology
Large ribosomal subunit protein P2 / Ribosome-inactivating protein alpha-trichosanthin Similarity search - Component
Biological species
TRICHOSANTHES KIRILOWII (gua lou) HOMO SAPIENS (human)
Method
X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
A: RIBOSOME-INACTIVATING PROTEIN ALPHA-TRICHOSANTHIN B: RIBOSOME-INACTIVATING PROTEIN ALPHA-TRICHOSANTHIN C: ACIDIC RIBOSOMAL PROTEIN P2 D: ACIDIC RIBOSOMAL PROTEIN P2
Resolution: 2.2→25.47 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.907 / SU B: 5.878 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.285 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.238
1283
5.1 %
RANDOM
Rwork
0.163
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obs
0.167
24055
98 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK