EMD-9045 Experiments and Validation

Yeast 26S proteasome bound to ubiquitinated substrate (4D motor state)

Single particle reconstruction
Overview of EMD-9045
Sample name: Substrate-engaged 26S proteasome in the 4D state
Organisms: Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Homo sapiens, Saccharomyces cerevisiae S288c
Fitted atomic model: 6ef3
Related EM entries by publication: EMD-9042, EMD-9043, EMD-9044

Map parameters

Recommended contour level: 0.045 (author)
Number of grid points: 340 × 340 × 340
Voxel size: 1.03 × 1.03 × 1.03 Å
Minimum density: 0.00
Maximum density: 0.222
Average density: 0.001
Standard deviation: 0.008

Sample information

Sample name: Substrate-engaged 26S proteasome in the 4D state
Ligands: ADENOSINE-5'-TRIPHOSPHATE, ADENOSINE-5'-DIPHOSPHATE
Proteins: Substrate-engaged 26S proteasome in the 4D state, Proteasome, substrate, Proteasome subunit beta type-1, Proteasome subunit beta type-2, Proteasome subunit beta type-3, Proteasome subunit beta type-4, Proteasome subunit beta type-5, Proteasome subunit beta type-6, Proteasome subunit beta type-7, Proteasome subunit alpha type-1, Proteasome subunit alpha type-2, Proteasome subunit alpha type-3, Proteasome subunit alpha type-4, Proteasome subunit alpha type-5, Proteasome subunit alpha type-6, Probable proteasome subunit alpha type-7, 26S proteasome regulatory subunit 7 homolog, 26S proteasome regulatory subunit 4 homolog, 26S proteasome regulatory subunit 8 homolog, 26S proteasome regulatory subunit 6B homolog, 26S proteasome subunit RPT4, 26S proteasome regulatory subunit 6A, Proteasome subunit beta type-7, Ubiquitin carboxyl-terminal hydrolase RPN11, Model substrate polypeptide, Ubiquitin-60S ribosomal protein L40

Validation information

Experimental information

 

Image processing

Applied symmetry: C1
Software: RELION
Number of particles: 48335
CTF correction: CTF correction was performed by Relion during reconstruction

Fitting

Initial atomic model: 5MPC
Fitting protocol: rigid body
Refinement space: REAL

Imaging

Session
Microscope model: FEI TITAN KRIOS
Electron source: FIELD EMISSION GUN
Electron dose (e/A**2): 50.0
Nominal CS (mm): 2.70
Nominal magnification: 29000.0
Defocus max (nm): -2,500.00
Defocus min (nm): -1,000.00
Holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Details: images were acquired in nanoprobe mode
Acquisition
Number of images: 11656
Sampling interval (μm): 5.0

Specimen

Preparation
Specimen state: particle
Specimen concentration (mg/mL): 25.00
Specimen support: unspecified
Vitrification
Apparatus: HOMEMADE PLUNGER
Cryogen: ETHANE
Humidity: 90
Details: specimens were manually blotted with Whatman #1 filter paper.