5I9G

Crystal structure of designed pentatricopeptide repeat protein dPPR-U8C2 in complex with its target RNA U8C2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for specific single-stranded RNA recognition by designer pentatricopeptide repeat proteins.

Shen, C.Zhang, D.Guan, Z.Liu, Y.Yang, Z.Yang, Y.Wang, X.Wang, Q.Zhang, Q.Fan, S.Zou, T.Yin, P.

(2016) Nat Commun 7: 11285-11285

  • DOI: 10.1038/ncomms11285
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • As a large family of RNA-binding proteins, pentatricopeptide repeat (PPR) proteins mediate multiple aspects of RNA metabolism in eukaryotes. Binding to their target single-stranded RNAs (ssRNAs) in a modular and base-specific fashion, PPR proteins ca ...

    As a large family of RNA-binding proteins, pentatricopeptide repeat (PPR) proteins mediate multiple aspects of RNA metabolism in eukaryotes. Binding to their target single-stranded RNAs (ssRNAs) in a modular and base-specific fashion, PPR proteins can serve as designable modules for gene manipulation. However, the structural basis for nucleotide-specific recognition by designer PPR (dPPR) proteins remains to be elucidated. Here, we report four crystal structures of dPPR proteins in complex with their respective ssRNA targets. The dPPR repeats are assembled into a right-handed superhelical spiral shell that embraces the ssRNA. Interactions between different PPR codes and RNA bases are observed at the atomic level, revealing the molecular basis for the modular and specific recognition patterns of the RNA bases U, C, A and G. These structures not only provide insights into the functional study of PPR proteins but also open a path towards the potential design of synthetic sequence-specific RNA-binding proteins.


    Organizational Affiliation

    National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
pentatricopeptide repeat protein dPPR-U8C2
C
460unidentifiedMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*GP*G*GP*UP*UP*UP*UP*CP*CP*UP*UP*UP*UP*CP*CP*CP*C)-3')A18synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.226 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.433α = 90
b = 84.782β = 90
c = 94.358γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
HKL-3000data collection
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-04-27
    Type: Initial release
  • Version 1.1: 2017-10-04
    Changes: Data collection, Derived calculations
  • Version 1.2: 2019-12-25
    Changes: Database references