4DZS

Crystal structure of yeast Puf4p RNA binding domain in complex with HO-4BE mutant RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.14 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.260 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Patterns and plasticity in RNA-protein interactions enable recruitment of multiple proteins through a single site.

Valley, C.T.Porter, D.F.Qiu, C.Campbell, Z.T.Hall, T.M.Wickens, M.

(2012) Proc.Natl.Acad.Sci.USA 109: 6054-6059

  • DOI: 10.1073/pnas.1200521109

  • PubMed Abstract: 
  • mRNA control hinges on the specificity and affinity of proteins for their RNA binding sites. Regulatory proteins must bind their own sites and reject even closely related noncognate sites. In the PUF [Pumilio and fem-3 binding factor (FBF)] family of ...

    mRNA control hinges on the specificity and affinity of proteins for their RNA binding sites. Regulatory proteins must bind their own sites and reject even closely related noncognate sites. In the PUF [Pumilio and fem-3 binding factor (FBF)] family of RNA binding proteins, individual proteins discriminate differences in the length and sequence of binding sites, allowing each PUF to bind a distinct battery of mRNAs. Here, we show that despite these differences, the pattern of RNA interactions is conserved among PUF proteins: the two ends of the PUF protein make critical contacts with the two ends of the RNA sites. Despite this conserved "two-handed" pattern of recognition, the RNA sequence is flexible. Among the binding sites of yeast Puf4p, RNA sequence dictates the pattern in which RNA bases are flipped away from the binding surface of the protein. Small differences in RNA sequence allow new modes of control, recruiting Puf5p in addition to Puf4p to a single site. This embedded information adds a new layer of biological meaning to the connections between RNA targets and PUF proteins.


    Organizational Affiliation

    Graduate Program in Cellular and Molecular Biology, University of Wisconsin, Madison, WI 53706, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pumilio homology domain family member 4
A, B
357Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PUF4
Find proteins for P25339 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25339
Entity ID: 2
MoleculeChainsLengthOrganism
5'-R(*UP*GP*UP*AP*UP*CP*AP*UP*A)-3'C,D9N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.14 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.260 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.420α = 90.00
b = 135.750β = 90.00
c = 148.411γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
HKL-2000data reduction
PHENIXrefinement
PHENIXmodel building
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-03-01 
  • Released Date: 2012-04-25 
  • Deposition Author(s): Qiu, C., Hall, T.M.T.

Revision History 

  • Version 1.0: 2012-04-25
    Type: Initial release
  • Version 1.1: 2012-05-16
    Type: Database references
  • Version 1.2: 2018-01-24
    Type: Structure summary