A Systematic Screen for Protein-Lipid Interactions in Saccharomyces cerevisiae

Experimental Data Snapshot

  • 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

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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: https://doi.org/10.1038/msb.2010.87
  • Primary Citation of Related Structures:  

  • 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. 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 4,5-bisphosphate-binding protein SLM1
A, B
120Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: LIT2SLM1YIL105C
Membrane Entity: Yes 
Find proteins for P40485 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40485 
Go to UniProtKB:  P40485
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40485
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • 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
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
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description