8QBF

Compact state - Pil1 dimer with lipid headgroups fitted in native eisosome lattice bound to plasma membrane microdomain


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.67 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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This is version 1.3 of the entry. See complete history


Literature

Cryo-EM architecture of a near-native stretch-sensitive membrane microdomain.

Kefauver, J.M.Hakala, M.Zou, L.Alba, J.Espadas, J.Tettamanti, M.G.Gajic, J.Gabus, C.Campomanes, P.Estrozi, L.F.Sen, N.E.Vanni, S.Roux, A.Desfosses, A.Loewith, R.

(2024) Nature 632: 664-671

  • DOI: https://doi.org/10.1038/s41586-024-07720-6
  • Primary Citation of Related Structures:  
    8QB7, 8QB8, 8QB9, 8QBB, 8QBD, 8QBE, 8QBF, 8QBG

  • PubMed Abstract: 

    Biological membranes are partitioned into functional zones termed membrane microdomains, which contain specific lipids and proteins 1-3 . The composition and organization of membrane microdomains remain controversial because few techniques are available that allow the visualization of lipids in situ without disrupting their native behaviour 3,4 . The yeast eisosome, composed of the BAR-domain proteins Pil1 and Lsp1 (hereafter, Pil1/Lsp1), scaffolds a membrane compartment that senses and responds to mechanical stress by flattening and releasing sequestered factors 5-9 . Here we isolated near-native eisosomes as helical tubules made up of a lattice of Pil1/Lsp1 bound to plasma membrane lipids, and solved their structures by helical reconstruction. Our structures reveal a striking organization of membrane lipids, and, using in vitro reconstitutions and molecular dynamics simulations, we confirmed the positioning of individual PI(4,5)P 2 , phosphatidylserine and sterol molecules sequestered beneath the Pil1/Lsp1 coat. Three-dimensional variability analysis of the native-source eisosomes revealed a dynamic stretching of the Pil1/Lsp1 lattice that affects the sequestration of these lipids. Collectively, our results support a mechanism in which stretching of the Pil1/Lsp1 lattice liberates lipids that would otherwise be anchored by the Pil1/Lsp1 coat, and thus provide mechanistic insight into how eisosome BAR-domain proteins create a mechanosensitive membrane microdomain.


  • Organizational Affiliation

    Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sphingolipid long chain base-responsive protein PIL1
A, B
271Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P53252 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53252 
Go to UniProtKB:  P53252
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53252
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.67 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.1.2
MODEL REFINEMENTPHENIX1.20-4459

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
H2020 Marie Curie Actions of the European CommissionEuropean Union101026765
European Research Council (ERC)European UnionAdG TENDO
Swiss National Science FoundationSwitzerlandCRSII5_189996
Swiss National Science FoundationSwitzerland310030_207754

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-24
    Type: Initial release
  • Version 1.1: 2024-07-31
    Changes: Database references
  • Version 1.2: 2024-08-07
    Changes: Database references
  • Version 1.3: 2024-08-28
    Changes: Database references