5BZ5

Crystal structure of the RNA-binding domain of yeast Puf5p bound to AMN1 RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

RNA regulatory networks diversified through curvature of the PUF protein scaffold.

Wilinski, D.Qiu, C.Lapointe, C.P.Nevil, M.Campbell, Z.T.Tanaka Hall, T.M.Wickens, M.

(2015) Nat Commun 6: 8213-8213

  • DOI: 10.1038/ncomms9213
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Proteins bind and control mRNAs, directing their localization, translation and stability. Members of the PUF family of RNA-binding proteins control multiple mRNAs in a single cell, and play key roles in development, stem cell maintenance and memory f ...

    Proteins bind and control mRNAs, directing their localization, translation and stability. Members of the PUF family of RNA-binding proteins control multiple mRNAs in a single cell, and play key roles in development, stem cell maintenance and memory formation. Here we identified the mRNA targets of a S. cerevisiae PUF protein, Puf5p, by ultraviolet-crosslinking-affinity purification and high-throughput sequencing (HITS-CLIP). The binding sites recognized by Puf5p are diverse, with variable spacer lengths between two specific sequences. Each length of site correlates with a distinct biological function. Crystal structures of Puf5p-RNA complexes reveal that the protein scaffold presents an exceptionally flat and extended interaction surface relative to other PUF proteins. In complexes with RNAs of different lengths, the protein is unchanged. A single PUF protein repeat is sufficient to induce broadening of specificity. Changes in protein architecture, such as alterations in curvature, may lead to evolution of mRNA regulatory networks.


    Organizational Affiliation

    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Suppressor protein MPT5
A
400Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MPT5 (HTR1, PUF5)
Find proteins for P39016 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P39016
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*UP*GP*UP*AP*AP*CP*UP*UP*UP*A)-3')B12synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.201 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 105.852α = 90.00
b = 105.852β = 90.00
c = 168.404γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-06-11 
  • Released Date: 2015-09-23 
  • Deposition Author(s): Qiu, C., Hall, T.M.T.

Revision History 

  • Version 1.0: 2015-09-23
    Type: Initial release
  • Version 1.1: 2015-09-30
    Type: Database references