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
  • Primary Citation of Related Structures:  
    2JDL, 2JJR, 2VS6

  • 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 centre of the ribosome ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOME-INACTIVATING PROTEIN ALPHA-TRICHOSANTHINA, B247Trichosanthes kirilowiiMutation(s): 0 
EC: 3.2.2.22
UniProt
Find proteins for P09989 (Trichosanthes kirilowii)
Explore P09989 
Go to UniProtKB:  P09989
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ACIDIC RIBOSOMAL PROTEIN P2C, D11Homo sapiensMutation(s): 0 
Gene Names: RPLP2D11S2243ERPP2
UniProt & NIH Common Fund Data Resources
Find proteins for P05387 (Homo sapiens)
Explore P05387 
Go to UniProtKB:  P05387
PHAROS:  P05387
Protein Feature View
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  • Reference Sequence
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

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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