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- EMDB-1994: Negative stain reconstruction of the Saccharomyces cerevisiae pro... -

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Basic information

Entry
Database: EMDB / ID: 1994
TitleNegative stain reconstruction of the Saccharomyces cerevisiae proteasome lid
Keywords26S / 19S / proteasome / yeast lid / regulatory particle / ubiquitin recognition / deubiquitination / AAA-ATPase
SampleSaccharomyces cerevisiae proteasome lid subcomplex
SourceSaccharomyces cerevisiae / yeast / Baker's Yeast / サッカロミセス・セレビシエ /
Map datamap of endogenous Saccharomyces cerevisiae proteasome lid
Methodsingle particle reconstruction, at 15 Å resolution
AuthorsLander GC / Estrin E / Matyskiela M / Bashore C / Nogales E / Martin A
CitationNature, 2012, 482, 186-191

Nature, 2012, 482, 186-191 Yorodumi Papers
Complete subunit architecture of the proteasome regulatory particle.
Gabriel C Lander / Eric Estrin / Mary E Matyskiela / Charlene Bashore / Eva Nogales / Andreas Martin

DateDeposition: Nov 18, 2011 / Header (metadata) release: Jan 6, 2012 / Map release: Jan 6, 2012 / Last update: Feb 3, 2012

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 5
  • Imaged by UCSF CHIMERA
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Supplemental images

Downloads & links

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Map

Fileemd_1994.map.gz (map file in CCP4 format, 8193 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
2.76 Å/pix.
= 353.28 Å
128 pix
2.76 Å/pix.
= 353.28 Å
128 pix
2.76 Å/pix.
= 353.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.76 Å
Density
Contour Level:5 (by author), 5 (movie #1):
Minimum - Maximum-5.48156 - 17.3354
Average (Standard dev.)-5.82217e-09 (1)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128128128
Origin-64-64-64
Limit636363
Spacing128128128
CellA=B=C: 353.28 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.762.762.76
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z353.280353.280353.280
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-5.48217.335-0.000

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Supplemental data

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Sample components

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Entire Saccharomyces cerevisiae proteasome lid subcomplex

EntireName: Saccharomyces cerevisiae proteasome lid subcomplex / Details: monodisperse / Number of components: 1 / Oligomeric State: 8 subunit complex
MassTheoretical: 361 kDa / Experimental: 361 kDa / Measured by: Mass Spectrometry

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Component #1: protein, lid

ProteinName: lid / a.k.a: lid / Oligomeric Details: monomer
Details: lid was purified from endogenous proteasome holoenzyme using a 1M salt wash
Recombinant expression: No / Number of Copies: 1
MassTheoretical: 361 kDa / Experimental: 361 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / Baker's Yeast / サッカロミセス・セレビシエ /
Strain: YYS40
External referencesInterPro: InterPro: 002015 / Gene Ontology: GO: 0008541

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.009 mg/ml
Buffer solution: 60mM HEPES, 50mM NaCl, 50mM KCl, 5 mM MgCl2, 0.5mM EDTA, 1mM DTT, 10% glycerol
pH: 7.6
Support film200 mesh Cu grid
StainingProtein adsorbed to grid for 1 minute, then passed over four 50uL drops of 2% w/v uranyl formate, 5 seconds on each drop
VitrificationInstrument: NONE / Cryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 20 / Date: Apr 2, 2011 / Details: Data acquired using Leginon
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 20 e/Å2 / Electron beam tilt params: 0 / Illumination mode: FLOOD BEAM
LensMagnification: 80000 X (nominal), 80000 X (calibrated)
Astigmatism: objective lens astigmatism was corrected at 210,000 times magnification
Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 500 - 1200 nm
Specimen HolderHolder: Room temp single tilt / Model: SIDE ENTRY, EUCENTRIC / Temperature: 78 K ( 78 - 78 K)
CameraDetector: GENERIC GATAN (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 250

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 33478
Details: Image processing performed in the Appion processing environment. 3D reconstruction performed using EMAN2 and SPARX libraries
Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: Projection matching / Software: EMAN2 SPARX / CTF correction: whole micrograph / Resolution: 15 Å / Resolution method: FSC 0.5

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