4BEH

Solution structure of human ribosomal protein P1.P2 heterodimer


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: LEAST RESTRAINT VIOLATION AND LOWEST ENERGY 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Solution Structure of Human P1P2 Heterodimer Provides Insights Into the Role of Eukaryotic Stalk in Recruiting the Ribosome-Inactivating Protein Trichosanthin to the Ribosome.

Lee, K.M.Yusa, K.Chu, L.O.Wing-Heng Yu, C.Oono, M.Miyoshi, T.Ito, K.Shaw, P.C.Wong, K.B.Uchiumi, T.

(2013) Nucleic Acids Res 41: 8776

  • DOI: https://doi.org/10.1093/nar/gkt636
  • Primary Citation of Related Structures:  
    4BEH

  • PubMed Abstract: 

    Lateral ribosomal stalk is responsible for binding and recruiting translation factors during protein synthesis. The eukaryotic stalk consists of one P0 protein with two copies of P1•P2 heterodimers to form a P0(P1•P2)₂ pentameric P-complex. Here, we have solved the structure of full-length P1•P2 by nuclear magnetic resonance spectroscopy. P1 and P2 dimerize via their helical N-terminal domains, whereas the C-terminal tails of P1•P2 are unstructured and can extend up to ∼125 Å away from the dimerization domains. (15)N relaxation study reveals that the C-terminal tails are flexible, having a much faster internal mobility than the N-terminal domains. Replacement of prokaryotic L10(L7/L12)₄/L11 by eukaryotic P0(P1•P2)₂/eL12 rendered Escherichia coli ribosome, which is insensitive to trichosanthin (TCS), susceptible to depurination by TCS and the C-terminal tail was found to be responsible for this depurination. Truncation and insertion studies showed that depurination of hybrid ribosome is dependent on the length of the proline-alanine rich hinge region within the C-terminal tail. All together, we propose a model that recruitment of TCS to the sarcin-ricin loop required the flexible C-terminal tail, and the proline-alanine rich hinge region lengthens this C-terminal tail, allowing the tail to sweep around the ribosome to recruit TCS.


  • Organizational Affiliation

    School of Life Sciences, Centre for Protein Science and Crystallography, The Chinese University of Hong Kong, Shatin, Hong Kong, China and Department of Biology, Faculty of Science, Niigata University, Ikarashi 2-8050, Nishi-ku, Niigata 950-2181, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
60S ACIDIC RIBOSOMAL PROTEIN P1114Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P05386 (Homo sapiens)
Explore P05386 
Go to UniProtKB:  P05386
GTEx:  ENSG00000137818 
Entity Groups  
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UniProt GroupP05386
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
60S ACIDIC RIBOSOMAL PROTEIN P2116Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P05387 (Homo sapiens)
Explore P05387 
Go to UniProtKB:  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: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: LEAST RESTRAINT VIOLATION AND LOWEST ENERGY 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-14
    Type: Initial release
  • Version 1.1: 2013-10-30
    Changes: Database references
  • Version 2.0: 2023-06-14
    Changes: Advisory, Atomic model, Data collection, Database references, Other