3NSU

A Systematic Screen for Protein-Lipid Interactions in Saccharomyces cerevisiae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A systematic screen for protein-lipid interactions in Saccharomyces cerevisiae.

Gallego, O.Betts, M.J.Gvozdenovic-Jeremic, J.Maeda, K.Matetzki, C.Aguilar-Gurrieri, C.Beltran-Alvarez, P.Bonn, S.Fernandez-Tornero, C.Jensen, L.J.Kuhn, M.Trott, J.Rybin, V.Muller, C.W.Bork, P.Kaksonen, M.Russell, R.B.Gavin, A.C.

(2010) Mol Syst Biol 6: 430-430

  • DOI: 10.1038/msb.2010.87
  • Primary Citation of Related Structures:  
    3NSU

  • PubMed Abstract: 
  • Protein-metabolite networks are central to biological systems, but are incompletely understood. Here, we report a screen to catalog protein-lipid interactions in yeast. We used arrays of 56 metabolites to measure lipid-binding fingerprints of 172 proteins, including 91 with predicted lipid-binding domains ...

    Protein-metabolite networks are central to biological systems, but are incompletely understood. Here, we report a screen to catalog protein-lipid interactions in yeast. We used arrays of 56 metabolites to measure lipid-binding fingerprints of 172 proteins, including 91 with predicted lipid-binding domains. We identified 530 protein-lipid associations, the majority of which are novel. To show the data set's biological value, we studied further several novel interactions with sphingolipids, a class of conserved bioactive lipids with an elusive mode of action. Integration of live-cell imaging suggests new cellular targets for these molecules, including several with pleckstrin homology (PH) domains. Validated interactions with Slm1, a regulator of actin polarization, show that PH domains can have unexpected lipid-binding specificities and can act as coincidence sensors for both phosphatidylinositol phosphates and phosphorylated sphingolipids.


    Organizational Affiliation

    Structural and Computational Biology Unit, European Molecular Biology Laboratory, EMBL, Heidelberg, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphatidylinositol 4,5-bisphosphate-binding protein SLM1A, B120Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: LIT2SLM1YIL105C
Membrane Entity: Yes 
UniProt
Find proteins for P40485 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40485 
Go to UniProtKB:  P40485
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.39α = 90
b = 73.05β = 90
c = 37.51γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance