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- EMDB-3534: 26S proteasome in presence of ATP (s1) -

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Basic information

Entry
Database: EMDB / ID: 3534
Title26S proteasome in presence of ATP (s1)
Sample26S proteasome of Saccharomyces cerevisiae in presence of ATP (s1)
SourceSaccharomyces cerevisiae s288c / yeast / image: Saccharomyces cerevisiae
Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Map data
Methodsingle particle reconstruction, at 4.1 A resolution
AuthorsWehmer M / Rudack T
CitationProc. Natl. Acad. Sci. U.S.A., 2017, 114, 1305-1310

Proc. Natl. Acad. Sci. U.S.A., 2017, 114, 1305-1310 StrPapers
Structural insights into the functional cycle of the ATPase module of the 26S proteasome.
Marc Wehmer / Till Rudack / Florian Beck / Antje Aufderheide / Günter Pfeifer / Jürgen M Plitzko / Friedrich Förster / Klaus Schulten / Wolfgang Baumeister / Eri Sakata

DateDeposition: Dec 16, 2016 / Header (metadata) release: Jan 25, 2017 / Map release: Mar 8, 2017 / Last update: Dec 16, 2016

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF CHIMERA
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3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_3534.map.gz (map file in CCP4 format, 226493 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
384 pix
1.38 A/pix
= 529.92 A
384 pix
1.38 A/pix
= 529.92 A
384 pix
1.38 A/pix
= 529.92 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.38 A
Density
Contour Level:0.02 (by author), 0.02 (movie #1):
Minimum - Maximum-0.13271986 - 0.21069339
Average (Standard dev.)-5.665332E-6 (0.0063910563)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions384384384
Origin000
Limit383383383
Spacing384384384
CellA=B=C: 529.92 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.381.381.38
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z529.920529.920529.920
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.1330.211-0.000

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Supplemental data

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Sample components

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Entire 26S proteasome of Saccharomyces cerevisiae in presence of ATP (s1)

EntireName: 26S proteasome of Saccharomyces cerevisiae in presence of ATP (s1)
Number of components: 24
MassTheoretical: 1.7 MDa

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Component #1: protein, 26S proteasome of Saccharomyces cerevisiae in presence o...

ProteinName: 26S proteasome of Saccharomyces cerevisiae in presence of ATP (s1)
Recombinant expression: No
MassTheoretical: 1.7 MDa
SourceSpecies: Saccharomyces cerevisiae s288c / yeast / image: Saccharomyces cerevisiae

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Component #2: protein, Proteasome subunit alpha type-1

ProteinName: Proteasome subunit alpha type-1 / Recombinant expression: No
MassTheoretical: 28.03383 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Component #3: protein, Proteasome subunit alpha type-2

ProteinName: Proteasome subunit alpha type-2 / Recombinant expression: No
MassTheoretical: 27.191828 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Component #4: protein, Proteasome subunit alpha type-3

ProteinName: Proteasome subunit alpha type-3 / Recombinant expression: No
MassTheoretical: 28.74823 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Component #5: protein, Proteasome subunit alpha type-4

ProteinName: Proteasome subunit alpha type-4 / Recombinant expression: No
MassTheoretical: 28.478111 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Component #6: protein, Proteasome subunit alpha type-5

ProteinName: Proteasome subunit alpha type-5 / Recombinant expression: No
MassTheoretical: 28.649086 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Component #7: protein, Proteasome subunit alpha type-6

ProteinName: Proteasome subunit alpha type-6 / Recombinant expression: No
MassTheoretical: 25.634 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Component #8: protein, Probable proteasome subunit alpha type-7

ProteinName: Probable proteasome subunit alpha type-7 / Recombinant expression: No
MassTheoretical: 31.575068 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Component #9: protein, Proteasome subunit beta type-1

ProteinName: Proteasome subunit beta type-1 / Recombinant expression: No
MassTheoretical: 23.573604 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Component #10: protein, Proteasome subunit beta type-2

ProteinName: Proteasome subunit beta type-2 / Recombinant expression: No
MassTheoretical: 28.299889 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Component #11: protein, Proteasome subunit beta type-3

ProteinName: Proteasome subunit beta type-3 / Recombinant expression: No
MassTheoretical: 22.627842 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Component #12: protein, Proteasome subunit beta type-4

ProteinName: Proteasome subunit beta type-4 / Recombinant expression: No
MassTheoretical: 22.545676 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Component #13: protein, Proteasome subunit beta type-5

ProteinName: Proteasome subunit beta type-5 / Recombinant expression: No
MassTheoretical: 31.670539 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Component #14: protein, Proteasome subunit beta type-6

ProteinName: Proteasome subunit beta type-6 / Recombinant expression: No
MassTheoretical: 26.905076 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Component #15: protein, Proteasome subunit beta type-7

ProteinName: Proteasome subunit beta type-7 / Recombinant expression: No
MassTheoretical: 29.471289 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Component #16: protein, 26S protease regulatory subunit 7 homolog

ProteinName: 26S protease regulatory subunit 7 homolog / Recombinant expression: No
MassTheoretical: 52.054891 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Component #17: protein, 26S protease regulatory subunit 4 homolog

ProteinName: 26S protease regulatory subunit 4 homolog / Recombinant expression: No
MassTheoretical: 48.89816 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Component #18: protein, 26S protease regulatory subunit 6B homolog

ProteinName: 26S protease regulatory subunit 6B homolog / Recombinant expression: No
MassTheoretical: 47.953676 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Component #19: protein, 26S protease subunit RPT4

ProteinName: 26S protease subunit RPT4 / Recombinant expression: No
MassTheoretical: 49.480137 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Component #20: protein, 26S protease regulatory subunit 6A

ProteinName: 26S protease regulatory subunit 6A / Recombinant expression: No
MassTheoretical: 48.315727 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Component #21: protein, 26S protease regulatory subunit 8 homolog

ProteinName: 26S protease regulatory subunit 8 homolog / Recombinant expression: No
MassTheoretical: 45.342742 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Component #22: ligand, ADENOSINE-5'-TRIPHOSPHATE

LigandName: ADENOSINE-5'-TRIPHOSPHATE / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 0.507181 kDa

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Component #23: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #24: ligand, ADENOSINE-5'-DIPHOSPHATE

LigandName: ADENOSINE-5'-DIPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.427201 kDa

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 1 mg/ml / pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE MIXTURE / Temperature: 277 K / Humidity: 95 %

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Electron microscopy imaging

ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 45 e/A2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD / Defocus: 1500 - 3500 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 286500
3D reconstructionSoftware: RELION / Resolution: 4.1 A / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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