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- EMDB-1866: Structure of the yeast eisosome core component Lsp1 filament -

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Basic information

Entry
Database: EMDB / ID: EMD-1866
TitleStructure of the yeast eisosome core component Lsp1 filament
Map dataThis is a map of Lsp1 filament with helical symmetry parameters turn -136 degrees, rise 5.2 A
Sample
  • Sample: Lsp1
  • Protein or peptide: Yeast eisosome core component Lsp1 filament
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodhelical reconstruction / cryo EM / Resolution: 29.0 Å
AuthorsKarotki L / Huiskonen JT / Stefan CJ / Roth R / Surma MA / Aguilar PS / Krogan NJ / Emr SD / Heuser J / Gruenewald K / Walther TC
CitationJournal: J Cell Biol / Year: 2011
Title: Eisosome proteins assemble into a membrane scaffold.
Authors: Lena Karotki / Juha T Huiskonen / Christopher J Stefan / Natasza E Ziółkowska / Robyn Roth / Michal A Surma / Nevan J Krogan / Scott D Emr / John Heuser / Kay Grünewald / Tobias C Walther /
Abstract: Spatial organization of membranes into domains of distinct protein and lipid composition is a fundamental feature of biological systems. The plasma membrane is organized in such domains to ...Spatial organization of membranes into domains of distinct protein and lipid composition is a fundamental feature of biological systems. The plasma membrane is organized in such domains to efficiently orchestrate the many reactions occurring there simultaneously. Despite the almost universal presence of membrane domains, mechanisms of their formation are often unclear. Yeast cells feature prominent plasma membrane domain organization, which is at least partially mediated by eisosomes. Eisosomes are large protein complexes that are primarily composed of many subunits of two Bin-Amphiphysin-Rvs domain-containing proteins, Pil1 and Lsp1. In this paper, we show that these proteins self-assemble into higher-order structures and bind preferentially to phosphoinositide-containing membranes. Using a combination of electron microscopy approaches, we generate structural models of Pil1 and Lsp1 assemblies, which resemble eisosomes in cells. Our data suggest that the mechanism of membrane organization by eisosomes is mediated by self-assembly of its core components into a membrane-bound protein scaffold with lipid-binding specificity.
History
DepositionJan 26, 2011-
Header (metadata) releaseNov 11, 2011-
Map releaseJan 27, 2012-
UpdateApr 20, 2016-
Current statusApr 20, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.94
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.94
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_1866.map.gz / Format: CCP4 / Size: 12.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a map of Lsp1 filament with helical symmetry parameters turn -136 degrees, rise 5.2 A
Voxel sizeX=Y=Z: 4.42 Å
Density
Contour LevelBy AUTHOR: 1.94 / Movie #1: 1.94
Minimum - Maximum-5.80455923 - 7.03617477
Average (Standard dev.)0.000000001658808 (±0.99999982)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 663.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.424.424.42
M x/y/z150150150
origin x/y/z0.0000.0000.000
length x/y/z663.000663.000663.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ454586
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS150150150
D min/max/mean-5.8057.0360.000

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Supplemental data

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Sample components

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Entire : Lsp1

EntireName: Lsp1
Components
  • Sample: Lsp1
  • Protein or peptide: Yeast eisosome core component Lsp1 filament

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Supramolecule #1000: Lsp1

SupramoleculeName: Lsp1 / type: sample / ID: 1000 / Oligomeric state: Filament / Number unique components: 1

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Macromolecule #1: Yeast eisosome core component Lsp1 filament

MacromoleculeName: Yeast eisosome core component Lsp1 filament / type: protein_or_peptide / ID: 1 / Name.synonym: Lsp1 filament / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's Yeast / Cell: Yeast
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant plasmid: pGEX-6P-1

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.4
Details: 150mM KoAc, 2mM MgAc, 20mM HEPES pH 7.4, 5% Glycerol
GridDetails: Cflat CF-2/1-2C
VitrificationCryogen name: NITROGEN / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 68180 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal magnification: 50000
Sample stageSpecimen holder: Side entry / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 80 K
Detailslow dose imaging
Image recordingCategory: CCD / Film or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 20 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Phase flip for each particle
Final reconstructionApplied symmetry - Helical parameters - Δz: 5.2 Å
Applied symmetry - Helical parameters - Δ&Phi: 136.0 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 29.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IHRSR

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