6ZBK

Crystal structure of the human complex between RPAP3 and TRBP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The interaction between RPAP3 and TRBP reveals a possible involvement of the HSP90/R2TP chaperone complex in the regulation of miRNA activity.

Abel, Y.Charron, C.Virciglio, C.Bourguignon-Igel, V.Quinternet, M.Chagot, M.E.Robert, M.C.Verheggen, C.Branlant, C.Bertrand, E.Manival, X.Charpentier, B.Rederstorff, M.

(2022) Nucleic Acids Res 50: 2172-2189

  • DOI: https://doi.org/10.1093/nar/gkac086
  • Primary Citation of Related Structures:  
    6ZBK

  • PubMed Abstract: 

    MicroRNAs silence mRNAs by guiding the RISC complex. RISC assembly occurs following cleavage of pre-miRNAs by Dicer, assisted by TRBP or PACT, and the transfer of miRNAs to AGO proteins. The R2TP complex is an HSP90 co-chaperone involved in the assembly of ribonucleoprotein particles. Here, we show that the R2TP component RPAP3 binds TRBP but not PACT. The RPAP3-TPR1 domain interacts with the TRBP-dsRBD3, and the 1.5 Å resolution crystal structure of this complex identifies key residues involved in the interaction. Remarkably, binding of TRBP to RPAP3 or Dicer is mutually exclusive. Additionally, we found that AGO(1/2), TRBP and Dicer are all sensitive to HSP90 inhibition, and that TRBP sensitivity is increased in the absence of RPAP3. Finally, RPAP3 seems to impede miRNA activity, raising the possibility that the R2TP chaperone might sequester TRBP to regulate the miRNA pathway.


  • Organizational Affiliation

    Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II-associated protein 3123Homo sapiensMutation(s): 0 
Gene Names: RPAP3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H6T3 (Homo sapiens)
Explore Q9H6T3 
Go to UniProtKB:  Q9H6T3
PHAROS:  Q9H6T3
GTEx:  ENSG00000005175 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H6T3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RISC-loading complex subunit TARBP2109Homo sapiensMutation(s): 0 
Gene Names: TARBP2TRBP
UniProt & NIH Common Fund Data Resources
Find proteins for Q15633 (Homo sapiens)
Explore Q15633 
Go to UniProtKB:  Q15633
PHAROS:  Q15633
GTEx:  ENSG00000139546 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15633
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.77α = 90
b = 158.13β = 90
c = 32.7γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-30
    Type: Initial release
  • Version 1.1: 2022-03-09
    Changes: Database references, Structure summary
  • Version 1.2: 2024-01-24
    Changes: Data collection, Refinement description