5DDZ

Crystal structure of the RTA-c10-P2 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.148 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structural insights into the interaction of the ribosomal P stalk protein P2 with a type II ribosome-inactivating protein ricin

Fan, X.Zhu, Y.Wang, C.Niu, L.Teng, M.Li, X.

(2016) Sci Rep 6: 37803-37803

  • DOI: https://doi.org/10.1038/srep37803
  • Primary Citation of Related Structures:  
    5DDZ

  • PubMed Abstract: 

    Ricin is a type II ribosome-inactivating protein (RIP) that depurinates A 4324 at the sarcin-ricin loop of 28 S ribosomal RNA (rRNA), thus inactivating the ribosome by preventing elongation factors from binding to the GTPase activation centre. Recent studies have disclosed that the conserved C-terminal domain (CTD) of eukaryotic ribosomal P stalk proteins is involved in the process that RIPs target ribosome. However, the details of the molecular interaction between ricin and P stalk proteins remain unknown. Here, we report the structure of ricin-A chain (RTA) in a complex with the CTD of the human ribosomal protein P2. The structure shows that the Phe 111 , Leu 113 and Phe 114 residues of P2 insert into a hydrophobic pocket formed by the Tyr 183 , Arg 235 , Phe 240 and Ile 251 residues of RTA, while Asp 115 of P2 forms hydrogen bonds with Arg 235 of RTA. The key residues in RTA and P2 for complex formation were mutated, and their importance was determined by pull-down assays. The results from cell-free translation assays further confirmed that the interaction with P stalk proteins is essential for the inhibition of protein synthesis by RTA. Taken together, our results provide a structural basis that will improve our understanding of the process by which ricin targets the ribosome, which will benefit the development of effective small-molecule inhibitors for use as therapeutic agents.


  • Organizational Affiliation

    Hefei National Laboratory for Physical Sciences at Microscale, Innovation Center for Cell Signaling Networks, School of Life Science, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ricin275Ricinus communisMutation(s): 0 
EC: 3.2.2.22
UniProt
Find proteins for P02879 (Ricinus communis)
Explore P02879 
Go to UniProtKB:  P02879
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02879
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
60S acidic ribosomal protein P210Homo 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
GTEx:  ENSG00000177600 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05387
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.148 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.626α = 90
b = 67.626β = 90
c = 140.652γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-07
    Type: Initial release
  • Version 1.1: 2016-12-28
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description