Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 28.37 kDa 
• Atom Count: 2145 
• Modelled Residue Count: 247 
• Deposited Residue Count: 247 
• Unique protein chains: 1

2JJR

V232K, N236D-trichosanthin

• DOI: 10.2210/pdb2JJR/pdb

• Classification: HYDROLASE
• Organism(s): Trichosanthes kirilowii
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2008-04-21 Released: 2008-12-30 
• Deposition Author(s): Too, P.H., Ma, M.K., Mak, A.N., Tung, C.K., Zhu, G., Au, S.W., Wong, K.B., Shaw, P.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.214 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

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

• PubMed: 19073700 
• 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. 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.

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOME-INACTIVATING PROTEIN ALPHA-TRICHOSANTHIN	A	247	Trichosanthes kirilowii	Mutation(s): 2  EC: 3.2.2.22
Find proteins for P09989 (Trichosanthes kirilowii) Explore P09989  Go to UniProtKB:  P09989

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TAM	A	TRIS(HYDROXYETHYL)AMINOMETHANE C7 H17 N O3 GKODZWOPPOTFGA-UHFFFAOYSA-N
PEG	A	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
TAM	IC50 :  6.28000020980835   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.214 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.64	α = 90
b = 73.64	β = 90
c = 143.443	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
MOSFLM	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-04-21 
• Released Date: 2008-12-30 
Deposition Author(s): Too, P.H., Ma, M.K., Mak, A.N., Tung, C.K., Zhu, G., Au, S.W., Wong, K.B., Shaw, P.C.

Revision History  

• Version 1.0: 2008-12-30
  Type: Initial release
  
• Version 1.1: 2011-05-07
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-06-28
  Changes: Data collection