title: Structural basis for specific single-stranded RNA recognition by designer pentatricopeptide repeat proteins.
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.
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Cuicui
authors.initials: C
authors.lastname: Shen
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Delin
authors.initials: D
authors.lastname: Zhang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Zeyuan
authors.initials: Z
authors.lastname: Guan
authors.affiliation: Center for Structural Biology, School of Life Science, Tsinghua University, Beijing 100084, China.
authors.forename: Yexing
authors.initials: Y
authors.lastname: Liu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Zhao
authors.initials: Z
authors.lastname: Yang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Yang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Xiang
authors.initials: X
authors.lastname: Wang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Wang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: QunXia
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Center for Structural Biology, School of Life Science, Tsinghua University, Beijing 100084, China.
authors.forename: Shilong
authors.initials: S
authors.lastname: Fan
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Tingting
authors.initials: T
authors.lastname: Zou
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Ping
authors.initials: P
authors.lastname: Yin
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001665:Binding Sites / Q000235:genetics; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D008969:Molecular Sequence Data; D015394:Molecular Structure; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012313:RNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D020449:Repetitive Sequences, Amino Acid; D017386:Sequence Homology, Amino Acid
chemical_list: D010940:Plant Proteins; D016601:RNA-Binding Proteins; D012313:RNA