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- EMDB-1992: The Saccharomyces cerevisiae 26S proteasome at subnanometer resolution -

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Basic information

Entry
Database: EMDB / ID: 1992
TitleThe Saccharomyces cerevisiae 26S proteasome at subnanometer resolution
Keywords26S / 19S / proteasome / regulatory particle / ubiquitin recognition / deubiquitination / AAA-ATPase
Sample26S Proteasome
SourceSaccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Map data26 proteasome
Methodsingle particle reconstruction, at 9 A resolution
AuthorsLander GC / Estrin E / Matyskiela M / Bashore C / Nogales E / Martin A
CitationNature, 2012, 482, 186-191

Nature, 2012, 482, 186-191 StrPapers
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: Nov 18, 2011

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

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Map

Fileemd_1992.map.gz (map file in CCP4 format, 65537 KB)
Projections & slices
Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
2.17 A/pix
= 555.52 A
256 pix
2.17 A/pix
= 555.52 A
256 pix
2.17 A/pix
= 555.52 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.17 A
Density
Contour Level:3 (by author), 3 (movie #1):
Minimum - Maximum-21.592 - 33.7328
Average (Standard dev.)0.0686551 (1.12869)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin161616
Limit271271271
Spacing256256256
CellA=B=C: 555.52 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z2.172.172.17
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z555.520555.520555.520
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS161616
NC/NR/NS256256256
D min/max/mean-21.59233.7330.069

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Supplemental data

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Sample components

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Entire 26S Proteasome

EntireName: 26S Proteasome / Details: monodisperse / Number of components: 1 / Oligomeric State: holoenzyme
MassTheoretical: 1.5 MDa / Experimental: 1.5 MDa / Measured by: Mass Spectrometry

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Component #1: protein, 26S Proteasome

ProteinName: 26S Proteasome / a.k.a: 26S Proteasome / Oligomeric Details: monomer / Details: Endogenous proteasome was purified from yeast / Recombinant expression: No / Number of Copies: 1
MassTheoretical: 1.5 MDa / Experimental: 1.5 MDa
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Strain: YYS40
External referencesInterPro: InterPro: 001353 / Gene Ontology: GO: 0005838

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 1.7 mg/ml
Buffer solution: 20mM HEPES, 50mM NaCl, 50mM KCl, 1mM ATP, 1mM DTT, 0.05% NP40
pH: 7.6
Support film400-mesh C-flats, 2um holes with 2um spacing (Protochips Inc.)
StainingC-flat grids made hydrophilic with Solarus Plasma cleaner, 4 uL of sample applied, blotted in Vitrobot for 3 seconds with offset -1, plunged into liquid ethane
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 86 K / Humidity: 100 % / Method: Blot 3 seconds with -2 offset / Details: Vitrification instrument: Vitrobot

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 20 / Date: Sep 11, 2011 / Details: Data acquired using Leginon
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 20 e/A2 / Electron beam tilt params: 0 / Illumination mode: FLOOD BEAM
LensMagnification: 100000 X (nominal)
Astigmatism: objective lens astigmatism was corrected at 210,000 times magnification
Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200 - 2600 nm
Specimen HolderHolder: Side-entry cryostage / Model: GATAN LIQUID NITROGEN / Temperature: 78 K ( 78 - 78 K)
CameraDetector: GENERIC GATAN (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 9153

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 93679
Details: Image processing performed in the Appion processing environment. 3D reconstruction performed using EMAN2 and SPARX libraries
Applied symmetry: C2 (2 fold cyclic)
3D reconstructionAlgorithm: Projection matching / Software: EMAN2 SPARX / CTF correction: whole micrograph
Details: Final map filtered to local resolution using the blocfilt function in Bsoft
Resolution: 9 A / Resolution method: FSC 0.5

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