4OE1

Crystal structure of the pentatricopeptide repeat protein PPR10 (C256S/C430S/C449S) in complex with an 18-nt PSAJ rna element


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.264 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Examination of the dimerization states of the single-stranded RNA recognition protein pentatricopeptide repeat 10 (PPR10).

Li, Q.Yan, C.Xu, H.Wang, Z.Long, J.Li, W.Wu, J.Yin, P.Yan, N.

(2014) J Biol Chem 289: 31503-31512

  • DOI: 10.1074/jbc.M114.575472
  • Primary Citation of Related Structures:  
    4OE1

  • PubMed Abstract: 
  • Pentatricopeptide repeat (PPR) proteins, particularly abundant in plastids and mitochrondria of angiosperms, include a large number of sequence-specific RNA binding proteins that are involved in diverse aspects of organelle RNA metabolisms. PPR proteins contain multiple tandom repeats, and each repeat can specifically recognize a RNA base through residues 2, 5, and 35 in a modular fashion ...

    Pentatricopeptide repeat (PPR) proteins, particularly abundant in plastids and mitochrondria of angiosperms, include a large number of sequence-specific RNA binding proteins that are involved in diverse aspects of organelle RNA metabolisms. PPR proteins contain multiple tandom repeats, and each repeat can specifically recognize a RNA base through residues 2, 5, and 35 in a modular fashion. The crystal structure of PPR10 from maize chloroplast exhibits dimeric existence both in the absence and presence of the 18-nucleotide psaJ RNA element. However, previous biochemical analysis suggested a monomeric shift of PPR10 upon RNA binding. In this report, we show that the amino-terminal segments of PPR10 determine the dimerization state of PPR10. A single amino acid alteration of cysteine to serine within repeat 10 of PPR10 further drives dimerization of PPR10. The biochemical elucidation of the determinants for PPR10 dimerization may provide an important foundation to understand the working mechanisms of PPR proteins underlying their diverse physiological functions.


    Organizational Affiliation

    From the State Key Laboratory of Bio-membrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua-Peking Center for Life Sciences, and nyan@tsinghua.edu.cn.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Chloroplast pentatricopeptide repeat protein 10A, B718Zea maysMutation(s): 3 
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 [auth D], D [auth C]18N/A
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    PO4
    Query on PO4

    Download Ideal Coordinates CCD File 
    E [auth B]PHOSPHATE ION
    O4 P
    NBIIXXVUZAFLBC-UHFFFAOYSA-K
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.80 Å
    • R-Value Free: 0.278 
    • R-Value Work: 0.263 
    • R-Value Observed: 0.264 
    • Space Group: P 43
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 83.318α = 90
    b = 83.318β = 90
    c = 225.5γ = 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  (Full details and data files)

    • Version 1.0: 2014-09-24
      Type: Initial release
    • Version 1.1: 2014-10-01
      Changes: Database references
    • Version 1.2: 2015-02-18
      Changes: Database references