3GVO

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1016/j.jsb.2009.06.007
  • Primary Citation of Related Structures:  

  • 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 repressi ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pumilio homolog 2
A
351Mus musculusMutation(s): 0 
Gene Names: Pum2 (Kiaa0235)
Find proteins for Q80U58 (Mus musculus)
Go to UniProtKB:  Q80U58
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DTD
Query on DTD

Download SDF File 
Download CCD File 
A
DITHIANE DIOL
C4 H8 O2 S2
YPGMOWHXEQDBBV-IMJSIDKUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.167 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 142.393α = 90.00
b = 142.393β = 90.00
c = 112.233γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALAdata scaling
MOSFLMdata reduction
PHASERphasing
MAR345data collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description