2N3F

Solution structure of both dsRBDs of DRB4 along with linker (viz. DRB4(1-153))


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

DRB4 dsRBD1 drives dsRNA recognition in Arabidopsis thaliana tasi/siRNA pathway.

Chiliveri, S.C.Aute, R.Rai, U.Deshmukh, M.V.

(2017) Nucleic Acids Res. 45: 8551-8563

  • DOI: 10.1093/nar/gkx481
  • Primary Citation of Related Structures:  2N3G, 2N3H

  • 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 mechani ...

    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.


    Organizational Affiliation

    CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Double-stranded RNA-binding protein 4
A
153Arabidopsis thalianaGene Names: DBR4
Find proteins for Q8H1D4 (Arabidopsis thaliana)
Go to UniProtKB:  Q8H1D4
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-09-07
    Type: Initial release
  • Version 1.1: 2017-06-07
    Type: Database references
  • Version 1.2: 2018-02-14
    Type: Database references