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- EMDB-3536: 26S proteasome in presence of AMP-PNP (s3) -

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Basic information

Entry
Database: EMDB / ID: 3536
Title26S proteasome in presence of AMP-PNP (s3)
Sample26S proteasome of Saccharomyces cerevisiae in presence of AMP-PNP
SourceSaccharomyces cerevisiae s288c / yeast / image: Saccharomyces cerevisiae
Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Map data
Methodsingle particle reconstruction, at 7.8 Å 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: Mar 8, 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: 0.019
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.019
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5mpb
  • Surface level: 0.019
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_3536.map.gz (map file in CCP4 format, 287966 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
416 pix
1.35 Å/pix.
= 561.6 Å
416 pix
1.35 Å/pix.
= 561.6 Å
416 pix
1.35 Å/pix.
= 561.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.35 Å
Density
Contour Level:0.019 (by author), 0.019 (movie #1):
Minimum - Maximum-0.07371832 - 0.1133882
Average (Standard dev.)6.17737E-5 (0.0035366658)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions416416416
Origin000
Limit415415415
Spacing416416416
CellA=B=C: 561.60004 Å
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.351.351.35
M x/y/z416416416
origin x/y/z0.0000.0000.000
length x/y/z561.600561.600561.600
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS416416416
D min/max/mean-0.0740.1130.000

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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 AMP-PNP

EntireName: 26S proteasome of Saccharomyces cerevisiae in presence of AMP-PNP
Number of components: 37
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 AMP-PNP
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: protein, 26S proteasome regulatory subunit RPN10

ProteinName: 26S proteasome regulatory subunit RPN10 / Recombinant expression: No
MassTheoretical: 29.776098 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Component #23: protein, Ubiquitin carboxyl-terminal hydrolase RPN11

ProteinName: Ubiquitin carboxyl-terminal hydrolase RPN11 / Recombinant expression: No
MassTheoretical: 34.442281 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Component #24: protein, 26S proteasome regulatory subunit RPN12

ProteinName: 26S proteasome regulatory subunit RPN12 / Recombinant expression: No
MassTheoretical: 31.952119 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Component #25: protein, 26S proteasome regulatory subunit RPN13

ProteinName: 26S proteasome regulatory subunit RPN13 / Recombinant expression: No
MassTheoretical: 17.919002 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Component #26: protein, 26S proteasome complex subunit SEM1

ProteinName: 26S proteasome complex subunit SEM1 / Recombinant expression: No
MassTheoretical: 10.397102 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Component #27: protein, 26S proteasome regulatory subunit RPN1

ProteinName: 26S proteasome regulatory subunit RPN1 / Recombinant expression: No
MassTheoretical: 109.601906 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Component #28: protein, 26S proteasome regulatory subunit RPN2

ProteinName: 26S proteasome regulatory subunit RPN2 / Recombinant expression: No
MassTheoretical: 104.351883 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Component #29: protein, 26S proteasome regulatory subunit RPN3

ProteinName: 26S proteasome regulatory subunit RPN3 / Recombinant expression: No
MassTheoretical: 60.464605 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Component #30: protein, 26S proteasome regulatory subunit RPN5

ProteinName: 26S proteasome regulatory subunit RPN5 / Recombinant expression: No
MassTheoretical: 51.840352 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Component #31: protein, 26S proteasome regulatory subunit RPN6

ProteinName: 26S proteasome regulatory subunit RPN6 / Recombinant expression: No
MassTheoretical: 49.839812 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Component #32: protein, 26S proteasome regulatory subunit RPN7

ProteinName: 26S proteasome regulatory subunit RPN7 / Recombinant expression: No
MassTheoretical: 49.016367 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Component #33: protein, 26S proteasome regulatory subunit RPN8

ProteinName: 26S proteasome regulatory subunit RPN8 / Recombinant expression: No
MassTheoretical: 38.365508 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Component #34: protein, 26S proteasome regulatory subunit RPN9

ProteinName: 26S proteasome regulatory subunit RPN9 / Recombinant expression: No
MassTheoretical: 45.839348 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /

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Component #35: ligand, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

LigandName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 0.506196 kDa

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Component #36: ligand, MAGNESIUM ION

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

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Component #37: 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

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 45 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD / Defocus: 1500 - 3500 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 67500
3D reconstructionSoftware: RELION / Resolution: 7.8 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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