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- EMDB-1868: Structure of the yeast eisosome core component Pil1 filament boun... -

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Basic information

Entry
Database: EMDB / ID: 1868
TitleStructure of the yeast eisosome core component Pil1 filament bound to a liposome membrane.
Map dataThis is a map of Pil1 filament bound to a liposome membrane with helical symmetry parameters turn 49.4 degrees, rise 5.1 A
SamplePil1
  • Yeast eisosome core component Pil1 filament
SourceSaccharomyces cerevisiae (baker's yeast)
Methodhelical reconstruction / cryo EM / 29 Å resolution
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
DateDeposition: Jan 26, 2011 / Header (metadata) release: Nov 11, 2011 / Map release: Jan 27, 2012 / Last update: Apr 20, 2016

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.36
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.36
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_1868.map.gz (map file in CCP4 format, 13185 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
150 pix
4.42 Å/pix.
= 663. Å
150 pix
4.42 Å/pix.
= 663. Å
150 pix
4.42 Å/pix.
= 663. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.42 Å
Density
Contour Level:1.36 (by author), 1.36 (movie #1):
Minimum - Maximum-5.5123835 - 6.0835776
Average (Standard dev.)1.7230859E-9 (0.9999999)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions150150150
Origin000
Limit149149149
Spacing150150150
CellA=B=C: 663.0 Å
α=β=γ: 90.0 deg.

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-5.5126.0840.000

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Supplemental data

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Sample components

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Entire Pil1

EntireName: Pil1 / Number of components: 1 / Oligomeric State: helical multimer

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Component #1: protein, Yeast eisosome core component Pil1 filament

ProteinName: Yeast eisosome core component Pil1 filament / a.k.a: Pil1 filament / Recombinant expression: Yes
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria) / Vector: pGEX-6P-1
Source (natural)Cell: Yeast

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Experimental details

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Sample preparation

SpecimenSpecimen state: filament / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Hand: RIGHT HANDED / Delta z: 5.1 Å / Delta phi: 49.4 deg.
Sample solutionBuffer solution: 150mM KAcetate, 2mM MgAcetate, 20mM HEPES pH 7.4, 5% Glycerol
pH: 7.4
Support filmCflat CF-2/1-2C
VitrificationInstrument: NONE / Cryogen name: NITROGEN

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20 / Details: Low dose imaging
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal), 68180 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD
Specimen HolderHolder: Side entry / Model: GATAN LIQUID NITROGEN / Temperature: 80 K
CameraDetector: FEI EAGLE (4k x 4k)

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionAlgorithm: IHRSR / Software: IHRSR / CTF correction: Phase flip for each particle / Resolution: 29 Å / Resolution method: FSC 0.5

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