3K49

Puf3 RNA binding domain bound to Cox17 RNA 3' UTR recognition sequence site B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A 5' cytosine binding pocket in Puf3p specifies regulation of mitochondrial mRNAs.

Zhu, D.Stumpf, C.R.Krahn, J.M.Wickens, M.Hall, T.M.

(2009) Proc Natl Acad Sci U S A 106: 20192-20197

  • DOI: 10.1073/pnas.0812079106
  • Primary Citation of Related Structures:  
    3K49, 3K4E

  • PubMed Abstract: 
  • A single regulatory protein can control the fate of many mRNAs with related functions. The Puf3 protein of Saccharomyces cerevisiae is exemplary, as it binds and regulates more than 100 mRNAs that encode proteins with mitochondrial function. Here we elucidate the structural basis of that specificity ...

    A single regulatory protein can control the fate of many mRNAs with related functions. The Puf3 protein of Saccharomyces cerevisiae is exemplary, as it binds and regulates more than 100 mRNAs that encode proteins with mitochondrial function. Here we elucidate the structural basis of that specificity. To do so, we explore the crystal structures of Puf3p complexes with 2 cognate RNAs. The key determinant of Puf3p specificity is an unusual interaction between a distinctive pocket of the protein with an RNA base outside the "core" PUF-binding site. That interaction dramatically affects binding affinity in vitro and is required for regulation in vivo. The Puf3p structures, combined with those of Puf4p in the same organism, illuminate the structural basis of natural PUF-RNA networks. Yeast Puf3p binds its own RNAs because they possess a -2C and is excluded from those of Puf4p which contain an additional nucleotide in the core-binding site.


    Organizational Affiliation

    Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
mRNA-binding protein PUF3A, C, E369Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: L1325PUF3YLL013C
UniProt
Find proteins for Q07807 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q07807 
Go to UniProtKB:  Q07807
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (5'-R(*CP*CP*UP*GP*UP*AP*AP*AP*UP*A)-3')B, D, F10N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download Ideal Coordinates CCD File 
G [auth A], H [auth C], I [auth E]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.126α = 90
b = 87.071β = 116.48
c = 125.176γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance