4M59

Crystal structure of the pentatricopeptide repeat protein PPR10 in complex with an 18-nt psaJ RNA element


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.261 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for the modular recognition of single-stranded RNA by PPR proteins.

Yin, P.Li, Q.Yan, C.Liu, Y.Liu, J.Yu, F.Wang, Z.Long, J.He, J.Wang, H.W.Wang, J.Zhu, J.K.Shi, Y.Yan, N.

(2013) Nature 504: 168-171

  • DOI: 10.1038/nature12651
  • Primary Citation of Related Structures:  
    4M57, 4M59

  • PubMed Abstract: 
  • Pentatricopeptide repeat (PPR) proteins represent a large family of sequence-specific RNA-binding proteins that are involved in multiple aspects of RNA metabolism. PPR proteins, which are found in exceptionally large numbers in the mitochondria and c ...

    Pentatricopeptide repeat (PPR) proteins represent a large family of sequence-specific RNA-binding proteins that are involved in multiple aspects of RNA metabolism. PPR proteins, which are found in exceptionally large numbers in the mitochondria and chloroplasts of terrestrial plants, recognize single-stranded RNA (ssRNA) in a modular fashion. The maize chloroplast protein PPR10 binds to two similar RNA sequences from the ATPI-ATPH and PSAJ-RPL33 intergenic regions, referred to as ATPH and PSAJ, respectively. By protecting the target RNA elements from 5' or 3' exonucleases, PPR10 defines the corresponding 5' and 3' messenger RNA termini. Despite rigorous functional characterizations, the structural basis of sequence-specific ssRNA recognition by PPR proteins remains to be elucidated. Here we report the crystal structures of PPR10 in RNA-free and RNA-bound states at resolutions of 2.85 and 2.45 Å, respectively. In the absence of RNA binding, the nineteen repeats of PPR10 are assembled into a right-handed superhelical spiral. PPR10 forms an antiparallel, intertwined homodimer and exhibits considerable conformational changes upon binding to its target ssRNA, an 18-nucleotide PSAJ element. Six nucleotides of PSAJ are specifically recognized by six corresponding PPR10 repeats following the predicted code. The molecular basis for the specific and modular recognition of RNA bases A, G and U is revealed. The structural elucidation of RNA recognition by PPR proteins provides an important framework for potential biotechnological applications of PPR proteins in RNA-related research areas.


    Organizational Affiliation

    1] State Key Laboratory of Bio-membrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, China [2] Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China [3].



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Chloroplast pentatricopeptide repeat protein 10AB718Zea maysMutation(s): 4 
Gene Names: PPR10ZEAMMB73_867042ZEAMMB73_Zm00001d036698
Find proteins for B8Y6I0 (Zea mays)
Explore B8Y6I0 
Go to UniProtKB:  B8Y6I0
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    psaJ RNAC, D18N/A
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    PO4
    Query on PO4

    Download CCD File 
    B
    PHOSPHATE ION
    O4 P
    NBIIXXVUZAFLBC-UHFFFAOYSA-K
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.46 Å
    • R-Value Free: 0.287 
    • R-Value Work: 0.260 
    • R-Value Observed: 0.261 
    • Space Group: P 43
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 83.428α = 90
    b = 83.428β = 90
    c = 226.913γ = 90
    Software Package:
    Software NamePurpose
    ADSCdata collection
    PHASERphasing
    PHENIXrefinement
    HKL-2000data reduction
    HKL-2000data scaling

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2013-10-30
      Type: Initial release
    • Version 1.1: 2013-11-20
      Changes: Database references
    • Version 1.2: 2013-12-18
      Changes: Database references