Crystal structure of mouse PARN in complex with m7GpppG

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.299 
  • R-Value Observed: 0.300 

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Structural basis of m(7)GpppG binding to poly(A)-specific ribonuclease.

Wu, M.Nilsson, P.Henriksson, N.Niedzwiecka, A.Lim, M.K.Cheng, Z.Kokkoris, K.Virtanen, A.Song, H.

(2009) Structure 17: 276-286

  • DOI: https://doi.org/10.1016/j.str.2008.11.012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Poly(A)-specific ribonuclease (PARN) is a homodimeric, processive, and cap-interacting 3' exoribonuclease that efficiently degrades eukaryotic mRNA poly(A) tails. The crystal structure of a C-terminally truncated PARN in complex with m(7)GpppG reveals that, in one subunit, m(7)GpppG binds to a cavity formed by the RRM domain and the nuclease domain, whereas in the other subunit, it binds almost exclusively to the RRM domain. Importantly, our structural and competition data show that the cap-binding site overlaps with the active site in the nuclease domain. Mutational analysis demonstrates that residues involved in m(7)G recognition are crucial for cap-stimulated deadenylation activity, and those involved in both cap and poly(A) binding are important for catalysis. A modeled PARN, which shows that the RRM domain from one subunit and the R3H domain from the other subunit enclose the active site, provides a structural foundation for further studies to elucidate the mechanism of PARN-mediated deadenylation.

  • Organizational Affiliation

    Institute of Molecular and Cell Biology, Proteos, Singapore; Department of Biological Sciences, National University of Singapore, Singapore.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Poly(A)-specific ribonuclease PARN
A, B
507Mus musculusMutation(s): 0 
Gene Names: Parn
Find proteins for Q8VDG3 (Mus musculus)
Explore Q8VDG3 
Go to UniProtKB:  Q8VDG3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8VDG3
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
7MG PDBBind:  3D45 Kd: 2100 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.299 
  • R-Value Observed: 0.300 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.013α = 90
b = 128.35β = 90
c = 176.844γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Structure summary
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description