3GVO

Structure and RNA binding of the mouse Pumilio-2 Puf Domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure and RNA binding of the mouse Pumilio-2 Puf domain

Jenkins, H.T.Baker-Wilding, R.Edwards, T.A.

(2009) J Struct Biol 167: 271-276

  • DOI: https://doi.org/10.1016/j.jsb.2009.06.007
  • Primary Citation of Related Structures:  
    3GVO, 3GVT

  • PubMed Abstract: 

    Puf proteins control translation through the interaction of a C-terminal Puf domain with specific sequences present in the 3' untranslated region of messenger RNAs. In Drosophila, binding of the protein Pumilio to mRNA leads to translational repression which is required for anterior/posterior patterning during embryogenesis. The vertebrate Pumilio homologue 2 (Pum2) has been implicated in controlling germ cell development through interactions with the RNA binding proteins deleted in azoospermia (DAZ), DAZ-like (DAZL) and BOULE. We present the 1.6A resolution X-ray crystal structure of the Puf domain from murine Pum2 and demonstrate that this domain is capable of binding with nanomolar affinity to RNA sequences from the hunchback Nanos response element (NRE) and a previously identified Pum2 binding element (PBE).


  • Organizational Affiliation

    Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pumilio homolog 2351Mus musculusMutation(s): 0 
Gene Names: Pum2
UniProt & NIH Common Fund Data Resources
Find proteins for Q80U58 (Mus musculus)
Explore Q80U58 
Go to UniProtKB:  Q80U58
IMPC:  MGI:1931751
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ80U58
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.393α = 90
b = 142.393β = 90
c = 112.233γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
MOSFLMdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description