2JDL

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The C-Terminal Fragment of the Ribosomal P Protein Complexed to Trichosanthin Reveals the Interaction between the Ribosome-Inactivating Protein and the Ribosome.

Too, P.H.Ma, M.K.Mak, A.N.Wong, Y.T.Tung, C.K.Zhu, G.Au, S.W.Wong, K.B.Shaw, P.C.

(2009) Nucleic Acids Res 37: 602

  • DOI: 10.1093/nar/gkn922
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Ribosome-inactivating proteins (RIPs) inhibit protein synthesis by enzymatically depurinating a specific adenine residue at the sarcin-ricin loop of the 28S rRNA, which thereby prevents the binding of elongation factors to the GTPase activation centr ...

    Ribosome-inactivating proteins (RIPs) inhibit protein synthesis by enzymatically depurinating a specific adenine residue at the sarcin-ricin loop of the 28S rRNA, which thereby prevents the binding of elongation factors to the GTPase activation centre of the ribosome. Here, we present the 2.2 A crystal structure of trichosanthin (TCS) complexed to the peptide SDDDMGFGLFD, which corresponds to the conserved C-terminal elongation factor binding domain of the ribosomal P protein. The N-terminal region of this peptide interacts with Lys173, Arg174 and Lys177 in TCS, while the C-terminal region is inserted into a hydrophobic pocket. The interaction with the P protein contributes to the ribosome-inactivating activity of TCS. This 11-mer C-terminal P peptide can be docked with selected important plant and bacterial RIPs, indicating that a similar interaction may also occur with other RIPs.


    Organizational Affiliation

    Department of Biochemistry, Centre for Protein Science and Crystallography and Molecular Biotechnology Programme, The Chinese University of Hong Kong, Shatin, NT, Hong Kong, China.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RIBOSOME-INACTIVATING PROTEIN ALPHA-TRICHOSANTHIN
A, B
247Trichosanthes kirilowiiMutation(s): 0 
EC: 3.2.2.22
Find proteins for P09989 (Trichosanthes kirilowii)
Go to UniProtKB:  P09989
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ACIDIC RIBOSOMAL PROTEIN P2
C, D
11Homo sapiensMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.167 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.589α = 90
b = 43.964β = 92.87
c = 92.235γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-02-05
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance