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 1.3 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: https://doi.org/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

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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Chloroplast pentatricopeptide repeat protein 10
A, B
718Zea maysMutation(s): 3 
Gene Names: PPR10, ZEAMMB73_867042, ZEAMMB73_Zm00001d036698
UniProt
Find proteins for B8Y6I0 (Zea mays)
Explore B8Y6I0 
Go to UniProtKB:  B8Y6I0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8Y6I0
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
psaJ RNAC [auth D],
D [auth C]		18N/A
Protein Feature View
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  • Reference Sequence
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

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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
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Refinement description