5I9G

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

Summary for 5I9G

• Entry DOI: 10.2210/pdb5i9g/pdb
• Related: 5I9D 5I9F 5I9H
• Descriptor: pentatricopeptide repeat protein dPPR-U8C2, RNA (5'-R(*GP*GP*G*GP*UP*UP*UP*UP*CP*CP*UP*UP*UP*UP*CP*CP*CP*C)-3') (3 entities in total)
• Functional Keywords: single-stranded rna, designer pentatricopeptide repeat protein, rna binding protein-rna complex, rna binding protein/rna
• Biological source: unidentified; More
• Total number of polymer chains: 2
• Total formula weight: 57078.89

Authors

Shen, C.,Zhang, D.,Guan, Z.,Zou, T.,Yin, P. (deposition date: 2016-02-20, release date: 2016-04-27, Last modification date: 2024-03-20)

Primary citation

Shen, C.,Zhang, D.,Guan, Z.,Liu, Y.,Yang, Z.,Yang, Y.,Wang, X.,Wang, Q.,Zhang, Q.,Fan, S.,Zou, T.,Yin, P.
Structural basis for specific single-stranded RNA recognition by designer pentatricopeptide repeat proteins.
Nat Commun, 7:11285-11285, 2016

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 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.

PubMed: 27088764
DOI: 10.1038/ncomms11285

Experimental method

X-RAY DIFFRACTION (2.288 Å)