3NSU | pdb_00003nsu

A Systematic Screen for Protein-Lipid Interactions in Saccharomyces cerevisiae

• PDB DOI: https://doi.org/10.2210/pdb3NSU/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2010-07-02 Released: 2010-12-15 
• Deposition Author(s): Gallego, O., Fernandez-Tornero, C., Aguilar-Gurrieri, C., Muller, C., Gavin, A.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.271 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

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

• PubMed: 21119626 
• DOI: https://doi.org/10.1038/msb.2010.87
• Primary Citation 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. 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.

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Organizational Affiliation: 
• Structural and Computational Biology Unit, European Molecular Biology Laboratory, EMBL, Heidelberg, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 27.94 kDa 
• Atom Count: 1,851 
• Modeled Residue Count: 212 
• Deposited Residue Count: 240 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 4,5-bisphosphate-binding protein SLM1	A, B	120	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: LIT2, SLM1, YIL105C Membrane Entity: Yes
UniProt
Find proteins for P40485 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40485  Go to UniProtKB:  P40485

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.271 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.39	α = 90
b = 73.05	β = 90
c = 37.51	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-15 
Deposition Author(s): Gallego, O., Fernandez-Tornero, C., Aguilar-Gurrieri, C., Muller, C., Gavin, A.C.

Revision History  

• 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