8QBD

Helical reconstruction of yeast eisosome protein Pil1 bound to membrane composed of lipid mixture +PIP2/+sterol (DOPC, DOPE, DOPS, cholesterol, PI(4,5)P2 35:20:20:15:10)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.61 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


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 PIL1339Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PIL1
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P5S (Subject of Investigation/LOI)
Query on P5S

Download Ideal Coordinates CCD File 
BA [auth E]
DA [auth K]
FA [auth F]
HA [auth L]
JA [auth G]
BA [auth E],
DA [auth K],
FA [auth F],
HA [auth L],
JA [auth G],
LA [auth M],
NA [auth H],
P [auth A],
PA [auth N],
R [auth B],
T [auth C],
V [auth I],
X [auth D],
Z [auth J]
O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
C42 H82 N O10 P
TZCPCKNHXULUIY-RGULYWFUSA-N
I3P (Subject of Investigation/LOI)
Query on I3P

Download Ideal Coordinates CCD File 
AA [auth E]
CA [auth K]
EA [auth F]
GA [auth L]
IA [auth G]
AA [auth E],
CA [auth K],
EA [auth F],
GA [auth L],
IA [auth G],
KA [auth M],
MA [auth H],
O [auth A],
OA [auth N],
Q [auth B],
S [auth C],
U [auth I],
W [auth D],
Y [auth J]
D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE
C6 H15 O15 P3
MMWCIQZXVOZEGG-XJTPDSDZSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.61 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207

Structure Validation

View Full Validation Report



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: Data collection, Database references
  • Version 1.2: 2024-08-07
    Changes: Data collection, Database references
  • Version 1.3: 2024-08-28
    Changes: Data collection, Database references