5N8L

Structure of TRBP dsRBD 1 and 2 in complex with a 19 bp siRNA (Complex B)


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 30 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis of siRNA recognition by TRBP double-stranded RNA binding domains.

Masliah, G.Maris, C.Konig, S.L.Yulikov, M.Aeschimann, F.Malinowska, A.L.Mabille, J.Weiler, J.Holla, A.Hunziker, J.Meisner-Kober, N.Schuler, B.Jeschke, G.Allain, F.H.

(2018) EMBO J. 37: --

  • DOI: 10.15252/embj.201797089
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The accurate cleavage of pre-micro(mi)RNAs by Dicer and mi/siRNA guide strand selection are important steps in forming the RNA-induced silencing complex (RISC). The role of Dicer binding partner TRBP in these processes remains poorly understood. Here ...

    The accurate cleavage of pre-micro(mi)RNAs by Dicer and mi/siRNA guide strand selection are important steps in forming the RNA-induced silencing complex (RISC). The role of Dicer binding partner TRBP in these processes remains poorly understood. Here, we solved the solution structure of the two N-terminal dsRNA binding domains (dsRBDs) of TRBP in complex with a functionally asymmetric siRNA using NMR, EPR, and single-molecule spectroscopy. We find that siRNA recognition by the dsRBDs is not sequence-specific but rather depends on the RNA shape. The two dsRBDs can swap their binding sites, giving rise to two equally populated, pseudo-symmetrical complexes, showing that TRBP is not a primary sensor of siRNA asymmetry. Using our structure to model a Dicer-TRBP-siRNA ternary complex, we show that TRBP's dsRBDs and Dicer's RNase III domains bind a canonical 19 base pair siRNA on opposite sides, supporting a mechanism whereby TRBP influences Dicer-mediated cleavage accuracy by binding the dsRNA region of the pre-miRNA during Dicer cleavage.


    Organizational Affiliation

    Department of Biochemistry, University of Zürich, Zürich, Switzerland.,Novartis Institutes for Biomedical Research, Basel, Switzerland.,Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland.,Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland.,Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland.,Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland allain@mol.biol.ethz.ch.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RISC-loading complex subunit TARBP2
A
215Homo sapiensMutation(s): 0 
Gene Names: TARBP2 (TRBP)
Find proteins for Q15633 (Homo sapiens)
Go to Gene View: TARBP2
Go to UniProtKB:  Q15633
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*UP*UP*AP*AP*UP*UP*AP*UP*CP*UP*AP*UP*UP*CP*CP*GP*UP*AP*CP*UP*U)-3')B21synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*UP*AP*CP*GP*GP*AP*AP*UP*AP*GP*AP*UP*AP*AP*UP*UP*AP*AP*UP*U)-3')C21synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 30 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
CTISwitzerland11329.1 PFLS-LS
SinergiaSwitzerlandCRSII5_170976
NCCR RNA and DiseaseSwitzerland--

Revision History 

  • Version 1.0: 2018-02-21
    Type: Initial release
  • Version 1.1: 2018-02-28
    Type: Database references
  • Version 1.2: 2018-03-28
    Type: Database references
  • Version 1.3: 2019-05-08
    Type: Data collection