[English] 日本語
Yorodumi
- PDB-8qbb: Helical reconstruction of yeast eisosome protein Pil1 bound to me... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qbb
TitleHelical reconstruction of yeast eisosome protein Pil1 bound to membrane composed of lipid mixture +PIP2/-sterol (DOPC, DOPE, DOPS, PI(4,5)P2 50:20:20:10)
ComponentsSphingolipid long chain base-responsive protein PIL1
KeywordsLIPID BINDING PROTEIN / BAR domain / lipid reconstitution / membrane microdomain
Function / homology
Function and homology information


protein localization to eisosome filament / eisosome filament / eisosome assembly / eisosome / lipid droplet / cell periphery / endocytosis / protein localization / mitochondrial outer membrane / lipid binding ...protein localization to eisosome filament / eisosome filament / eisosome assembly / eisosome / lipid droplet / cell periphery / endocytosis / protein localization / mitochondrial outer membrane / lipid binding / mitochondrion / plasma membrane / cytoplasm
Similarity search - Function
Eisosome component PIL1/LSP1 / Eisosome component PIL1 / AH/BAR domain superfamily
Similarity search - Domain/homology
D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Sphingolipid long chain base-responsive protein PIL1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.86 Å
AuthorsKefauver, J.M. / Zou, L. / Desfosses, A. / Loewith, R.J.
Funding supportEuropean Union, Switzerland, 4items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission101026765European Union
European Research Council (ERC)AdG TENDOEuropean Union
Swiss National Science FoundationCRSII5_189996 Switzerland
Swiss National Science Foundation310030_207754 Switzerland
CitationJournal: Nature / Year: 2024
Title: Cryo-EM architecture of a near-native stretch-sensitive membrane microdomain.
Authors: Jennifer M Kefauver / Markku Hakala / Luoming Zou / Josephine Alba / Javier Espadas / Maria G Tettamanti / Jelena Gajić / Caroline Gabus / Pablo Campomanes / Leandro F Estrozi / Nesli E Sen ...Authors: Jennifer M Kefauver / Markku Hakala / Luoming Zou / Josephine Alba / Javier Espadas / Maria G Tettamanti / Jelena Gajić / Caroline Gabus / Pablo Campomanes / Leandro F Estrozi / Nesli E Sen / Stefano Vanni / Aurélien Roux / Ambroise Desfosses / Robbie Loewith /
Abstract: Biological membranes are partitioned into functional zones termed membrane microdomains, which contain specific lipids and proteins. The composition and organization of membrane microdomains remain ...Biological membranes are partitioned into functional zones termed membrane microdomains, which contain specific lipids and proteins. 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. 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. 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, 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.
History
DepositionAug 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2024Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year / _em_admin.last_update
Revision 1.2Aug 7, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.3Aug 28, 2024Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sphingolipid long chain base-responsive protein PIL1
J: Sphingolipid long chain base-responsive protein PIL1
F: Sphingolipid long chain base-responsive protein PIL1
B: Sphingolipid long chain base-responsive protein PIL1
C: Sphingolipid long chain base-responsive protein PIL1
I: Sphingolipid long chain base-responsive protein PIL1
D: Sphingolipid long chain base-responsive protein PIL1
E: Sphingolipid long chain base-responsive protein PIL1
K: Sphingolipid long chain base-responsive protein PIL1
L: Sphingolipid long chain base-responsive protein PIL1
G: Sphingolipid long chain base-responsive protein PIL1
M: Sphingolipid long chain base-responsive protein PIL1
H: Sphingolipid long chain base-responsive protein PIL1
N: Sphingolipid long chain base-responsive protein PIL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)543,38428
Polymers537,50314
Non-polymers5,88114
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "J"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "F"
d_7ens_1chain "G"
d_8ens_1chain "H"
d_9ens_1chain "I"
d_10ens_1chain "A"
d_11ens_1chain "K"
d_12ens_1chain "L"
d_13ens_1chain "M"
d_14ens_1chain "N"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11METMETTHRTHRJB1 - 2711 - 271
d_12I3PI3PI3PI3PJP401
d_21METMETTHRTHRBD1 - 2711 - 271
d_22I3PI3PI3PI3PBR401
d_31METMETTHRTHRCE1 - 2711 - 271
d_32I3PI3PI3PI3PCS401
d_41METMETTHRTHRDG1 - 2711 - 271
d_42I3PI3PI3PI3PDU401
d_51METMETTHRTHREH1 - 2711 - 271
d_52I3PI3PI3PI3PEV401
d_61METMETTHRTHRFC1 - 2711 - 271
d_62I3PI3PI3PI3PFQ401
d_71METMETTHRTHRGK1 - 2711 - 271
d_72I3PI3PI3PI3PGY401
d_81METMETTHRTHRHM1 - 2711 - 271
d_82I3PI3PI3PI3PHAA401
d_91METMETTHRTHRIF1 - 2711 - 271
d_92I3PI3PI3PI3PIT401
d_101METMETTHRTHRAA1 - 2711 - 271
d_102I3PI3PI3PI3PAO401
d_111METMETTHRTHRKI1 - 2711 - 271
d_112I3PI3PI3PI3PKW401
d_121METMETTHRTHRLJ1 - 2711 - 271
d_122I3PI3PI3PI3PLX401
d_131METMETTHRTHRML1 - 2711 - 271
d_132I3PI3PI3PI3PMZ401
d_141METMETTHRTHRNN1 - 2711 - 271
d_142I3PI3PI3PI3PNBA401

NCS oper:
IDCodeMatrixVector
1given(0.801862704086, 0.597505959378, 0.00168294500383), (-0.597506757974, 0.801863874328, -3.49761622902E-5), (-0.00137039126646, -0.000977524933016, 0.999998583235)-106.705024203, 211.320433298, -13.8526078361
2given(-0.891450644715, -0.453116986467, -0.000862909107722), (-0.453117769322, 0.8914481638, 0.00211148816634), (-0.000187512415286, 0.00227328693721, -0.999997398499)623.094262717, 148.563416538, 589.027978872
3given(-0.284422183155, -0.958697529725, -0.00175163615034), (-0.958699057026, 0.284422399331, 0.000129678911841), (0.000373881704195, 0.0017161754848, -0.999998457476)596.292656539, 444.671921956, 559.850268996
4given(-0.117795836062, -0.993037397822, -0.00093141433058), (-0.993037271159, 0.11779671659, -0.000954803485009), (0.00105787311811, 0.000812457270366, -0.999999110408)560.896563529, 498.32908263, 516.159586292
5given(-0.688485970089, -0.725249088835, -0.000910019417744), (-0.725248869374, 0.688486530261, -0.000612470962474), (0.00107073011887, 0.000238312889077, -0.999999398372)641.333273444, 275.540305852, 501.704337014
6given(-0.999999773803, 0.000227448830613, -0.000632977992194), (0.000226589929356, 0.999999054062, 0.0013566622685), (0.000633285964682, 0.00135651853519, -0.999998879403)531.310247343, -0.43660628626, 530.761716804
7given(-0.985446952322, 0.169982209626, 0.000593775930334), (0.169983148632, 0.985444123812, 0.00236812701897), (-0.000182593538049, 0.00243459545578, -0.999997019698)482.06746388, -41.9946919507, 574.473612801
8given(0.688275830151, 0.72544756279, 0.00148837893881), (-0.725448295958, 0.688276663406, -6.70936132586E-5), (-0.0010730893881, -0.00103356305253, 0.999998890113)-110.248731232, 275.473512045, 29.6049778823
9given(-0.804336675541, -0.594154501523, 0.00478964506554), (-0.594173195568, 0.804298155137, -0.00791778453223), (0.000852084631942, -0.00921444320253, -0.999957183077)636.602870236, 212.030031353, 546.662061067
10given(0.985452623018, -0.169949840798, -0.000423556698019), (0.169950366539, 0.985449162363, 0.00261176401201), (-2.64752847673E-5, -0.00264575331242, 0.999996499638)49.0689929673, -42.0730253775, -43.1704948693
11given(0.891410117233, 0.453196238957, 0.0010825388337), (-0.453197493838, 0.891406520731, 0.00253897177705), (0.000185670284874, -0.00275386901584, 0.999996190859)-91.9433694502, 148.472077179, -57.7596512701
12given(0.284632949115, 0.958634199441, 0.00213446486654), (-0.958636483401, 0.284633193245, 0.00019492424147), (-0.000420678506658, -0.0021016577553, 0.999997703029)-65.2871472605, 444.606663642, -28.5795582337
13given(0.117770821463, 0.993040131225, 0.00115385806694), (-0.993040049348, 0.117772082939, -0.00109401630234), (-0.0012222943604, -0.00101698407312, 0.999998735869)-29.7712028867, 498.382773722, 15.1265609274

-
Components

#1: Protein
Sphingolipid long chain base-responsive protein PIL1


Mass: 38393.043 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: TB50 / Gene: PIL1 / Plasmid: pCoofy6
Details (production host): gift from Sabine Suppmann, Addgene plasmid #43990
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P53252
#2: Chemical
ChemComp-I3P / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE


Mass: 420.096 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C6H15O15P3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

-
Sample preparation

ComponentName: Helical assembly of recombinant Pil1 protein tubulating +PIP2/-sterol lipid mixture (DOPC,DOPE,DOPS,PI(4,5)P2 50:20:20:10)
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: TB50
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Plasmid: pCoofy6
Buffer solutionpH: 7.4 / Details: 20 mM HEPES, pH 7.4, 150 mM KoAc, 2 mM MgAc
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: EMS Lacey Carbon
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 291 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

-
Processing

EM softwareName: PHENIX / Version: 1.21_5207 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -83.25 ° / Axial rise/subunit: 14.547 Å / Axial symmetry: D3
3D reconstructionResolution: 3.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 85456 / Symmetry type: HELICAL
Atomic model buildingSpace: REAL
Atomic model buildingAccession code: P53252 / Source name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 116.46 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002530912
ELECTRON MICROSCOPYf_angle_d0.509641874
ELECTRON MICROSCOPYf_chiral_restr0.03164676
ELECTRON MICROSCOPYf_plane_restr0.00295432
ELECTRON MICROSCOPYf_dihedral_angle_d4.2674289
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BJELECTRON MICROSCOPYNCS constraints7.78023122511E-13
ens_1d_3BJELECTRON MICROSCOPYNCS constraints7.65495372191E-13
ens_1d_4BJELECTRON MICROSCOPYNCS constraints1.26914499721E-12
ens_1d_5BJELECTRON MICROSCOPYNCS constraints2.04517735164E-10
ens_1d_6BJELECTRON MICROSCOPYNCS constraints1.66247596886E-11
ens_1d_7BJELECTRON MICROSCOPYNCS constraints6.89361826372E-13
ens_1d_8BJELECTRON MICROSCOPYNCS constraints5.51566518642E-13
ens_1d_9BJELECTRON MICROSCOPYNCS constraints2.6897582607E-10
ens_1d_10BJELECTRON MICROSCOPYNCS constraints2.8439481205E-11
ens_1d_11BJELECTRON MICROSCOPYNCS constraints1.2536170416E-12
ens_1d_12BJELECTRON MICROSCOPYNCS constraints7.64415841424E-13
ens_1d_13BJELECTRON MICROSCOPYNCS constraints1.06924767396E-12
ens_1d_14BJELECTRON MICROSCOPYNCS constraints4.27972733875E-10

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more