2N3H

Solution structure of DRB4 dsRBD2 (viz. DRB4(81-151))

Summary for 2N3H

• Entry DOI: 10.2210/pdb2n3h/pdb
• Related: 2N3F 2N3G
• Descriptor: Double-stranded RNA-binding protein 4 (1 entity in total)
• Functional Keywords: rnai, rna binding protein
• Biological source: Arabidopsis thaliana (mouse-ear cress,thale-cress)
• Cellular location: Nucleus : Q8H1D4
• Total number of polymer chains: 1
• Total formula weight: 16618.72

Authors

Deshmukh, M.,Chiliveri, S. (deposition date: 2015-05-29, release date: 2016-09-07, Last modification date: 2024-05-15)

Primary citation

Chiliveri, S.C.,Aute, R.,Rai, U.,Deshmukh, M.V.
DRB4 dsRBD1 drives dsRNA recognition in Arabidopsis thaliana tasi/siRNA pathway.
Nucleic Acids Res., 45:8551-8563, 2017

PubMed Abstract: In Arabidopsis thaliana, endogenous trans-acting and exogenous siRNA pathways are initiated by the interaction of DRB4 with trigger dsRNA. Further, DCL4:DRB4 complex cleaves the dsRNA into 21 bp siRNA. Understanding molecular determinants and mechanistic details of dsRNA recognition by DRB4 is vital for inducing long-term RNAi-mediated gene regulation in plants. Here, we present solution structures of individual and concatenated DRB4 dsRBDs and demonstrate modes of dsRNA binding by employing NMR, ITC and site-specific mutagenesis. While both dsRBDs adopt the canonical α-β-β-β-α fold, key structural differences and ms-μs dynamics located at the RNA binding region were observed for dsRBD1. These features favor dsRBD1 to orient itself and make stronger tripartite contact with dsRNA, a feature missing in dsRBD2. Additionally, the inter-domain orientation induced by the linker restricts the mobility of dsRBD2, resulting in the steric hindrance of α1 helix in dsRBD2, and leads in further reduction of its dsRNA binding activity. Our study deciphers functional roles of DRB4 domains by showing that dsRBD1 drives the tasiRNA/siRNA pathway. Furthermore, we identify a potential role of the C-terminal region of DRB4 in protein:protein interaction as it possesses six PxxP motifs, binds to Zn2+ and contains a small structural domain.

PubMed: 28575480
DOI: 10.1093/nar/gkx481

Experimental method

SOLUTION NMR