8QBD | pdb_00008qbd

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)

PDB DOI: https://doi.org/10.2210/pdb8QBD/pdb
EM Map EMD-18310: EMDB EMDataResource

Classification: LIPID BINDING PROTEIN
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2023-08-24 Released: 2024-07-24
Deposition Author(s): Kefauver, J.M., Zou, L., Desfosses, A., Loewith, R.J.
Funding Organization(s): H2020 Marie Curie Actions of the European Commission, European Research Council (ERC), Swiss National Science Foundation

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

PubMed: 39048819 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41586-024-07720-6
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 554.47 kDa
Atom Count: 30,814
Modeled Residue Count: 3,794
Deposited Residue Count: 4,746
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sphingolipid long chain base-responsive protein PIL1	A B C D [auth I] E [auth D] A, B, C, D [auth I], E [auth D], F [auth J], G [auth E], H [auth K], I [auth F], J [auth L], K [auth G], L [auth M], M [auth H], N	339	Saccharomyces cerevisiae	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53252
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P5S (Subject of Investigation/LOI) Query on P5S Download:Ideal Coordinates CCD File SDF format, chain DA [auth K] SDF format, chain FA [auth F] SDF format, chain LA [auth M] SDF format, chain P [auth A] SDF format, chain X [auth D] SDF format, chain Z [auth J] SDF format, chain V [auth I] SDF format, chain T [auth C] SDF format, chain R [auth B] SDF format, chain PA [auth N] SDF format, chain NA [auth H] SDF format, chain JA [auth G] SDF format, chain HA [auth L] SDF format, chain BA [auth E] MOL2 format, chain DA [auth K] MOL2 format, chain FA [auth F] MOL2 format, chain LA [auth M] MOL2 format, chain P [auth A] MOL2 format, chain X [auth D] MOL2 format, chain Z [auth J] MOL2 format, chain V [auth I] MOL2 format, chain T [auth C] MOL2 format, chain R [auth B] MOL2 format, chain PA [auth N] MOL2 format, chain NA [auth H] MOL2 format, chain JA [auth G] MOL2 format, chain HA [auth L] MOL2 format, chain BA [auth E] mmCIF format, chain DA [auth K] mmCIF format, chain FA [auth F] mmCIF format, chain LA [auth M] mmCIF format, chain P [auth A] mmCIF format, chain X [auth D] mmCIF format, chain Z [auth J] mmCIF format, chain V [auth I] mmCIF format, chain T [auth C] mmCIF format, chain R [auth B] mmCIF format, chain PA [auth N] mmCIF format, chain NA [auth H] mmCIF format, chain JA [auth G] mmCIF format, chain HA [auth L] mmCIF format, chain BA [auth E]	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		Interactions Focus chain BA [auth E] Focus chain DA [auth K] Focus chain FA [auth F] Focus chain HA [auth L] Focus chain JA [auth G] Focus chain LA [auth M] Focus chain NA [auth H] Focus chain P [auth A] Focus chain PA [auth N] Focus chain R [auth B] Focus chain T [auth C] Focus chain V [auth I] Focus chain X [auth D] Focus chain Z [auth J] Interactions & Density Focus chain BA [auth E] Focus chain DA [auth K] Focus chain FA [auth F] Focus chain HA [auth L] Focus chain JA [auth G] Focus chain LA [auth M] Focus chain NA [auth H] Focus chain P [auth A] Focus chain PA [auth N] Focus chain R [auth B] Focus chain T [auth C] Focus chain V [auth I] Focus chain X [auth D] Focus chain Z [auth J]
I3P (Subject of Investigation/LOI) Query on I3P Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain Y [auth J] SDF format, chain U [auth I] SDF format, chain S [auth C] SDF format, chain Q [auth B] SDF format, chain OA [auth N] SDF format, chain O [auth A] SDF format, chain MA [auth H] SDF format, chain KA [auth M] SDF format, chain IA [auth G] SDF format, chain GA [auth L] SDF format, chain EA [auth F] SDF format, chain CA [auth K] SDF format, chain AA [auth E] MOL2 format, chain W [auth D] MOL2 format, chain Y [auth J] MOL2 format, chain U [auth I] MOL2 format, chain S [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain OA [auth N] MOL2 format, chain O [auth A] MOL2 format, chain MA [auth H] MOL2 format, chain KA [auth M] MOL2 format, chain IA [auth G] MOL2 format, chain GA [auth L] MOL2 format, chain EA [auth F] MOL2 format, chain CA [auth K] MOL2 format, chain AA [auth E] mmCIF format, chain W [auth D] mmCIF format, chain Y [auth J] mmCIF format, chain U [auth I] mmCIF format, chain S [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain OA [auth N] mmCIF format, chain O [auth A] mmCIF format, chain MA [auth H] mmCIF format, chain KA [auth M] mmCIF format, chain IA [auth G] mmCIF format, chain GA [auth L] mmCIF format, chain EA [auth F] mmCIF format, chain CA [auth K] mmCIF format, chain AA [auth E]	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		Interactions Focus chain AA [auth E] Focus chain CA [auth K] Focus chain EA [auth F] Focus chain GA [auth L] Focus chain IA [auth G] Focus chain KA [auth M] Focus chain MA [auth H] Focus chain O [auth A] Focus chain OA [auth N] Focus chain Q [auth B] Focus chain S [auth C] Focus chain U [auth I] Focus chain W [auth D] Focus chain Y [auth J] Interactions & Density Focus chain AA [auth E] Focus chain CA [auth K] Focus chain EA [auth F] Focus chain GA [auth L] Focus chain IA [auth G] Focus chain KA [auth M] Focus chain MA [auth H] Focus chain O [auth A] Focus chain OA [auth N] Focus chain Q [auth B] Focus chain S [auth C] Focus chain U [auth I] Focus chain W [auth D] Focus chain Y [auth J]

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-07-24

Deposition Author(s):

Funding Organization	Location	Grant Number
H2020 Marie Curie Actions of the European Commission	European Union	101026765
European Research Council (ERC)	European Union	AdG TENDO
Swiss National Science Foundation	Switzerland	CRSII5_189996
Swiss National Science Foundation	Switzerland	310030_207754