8K0G | pdb_00008k0g

Cryo-EM structure of human 26S RP (Ed state) bound to K11/K48-branched ubiquitin (Ub) chain composed of four Ub.

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6MSK

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.5131
f_angle_d	0.8821
f_chiral_restr	0.0519
f_bond_d	0.0079
f_plane_restr	0.0064

Sample
Human 26S proteasome
Sample Components
19S regulatory particle (RP) of human 26S proteasome
AAA+-ATPase of 19S regulatory particle (RP) of human 26S proteasome
alpha subunits of the 20S core particle (CP) of human 26S proteasome
Ubiquitinated substrate
K11/K48-branched ubiquitin (Ub) chain composed of four Ub.
Sic1_PY substrate polypeptide

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	incubation time= 3 s blotting time= 2.5 s

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	84476
Reported Resolution (Å)	3.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Performed in cryoSPARC using Non-uniform Refinement job type. Some parts of the map were then improved by using focused local refinement.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (6MSK)
Refinement Space	REAL
Refinement Protocol	OTHER
Refinement Target	0.83
Overall B Value	107.54
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)	49

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1200
Maximum Defocus (nm)	1800
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	70000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	Topaz
IMAGE ACQUISITION	EPU
CTF CORRECTION	CTFFIND	4.1
MODEL FITTING	UCSF ChimeraX	1.3
MODEL REFINEMENT	ISOLDE	1.3
MODEL REFINEMENT	Coot	0.9.4.1 EL
MODEL REFINEMENT	PHENIX	1.19.2
INITIAL EULER ASSIGNMENT	RELION	3.1
FINAL EULER ASSIGNMENT	cryoSPARC	3.1
CLASSIFICATION	RELION	3.1
RECONSTRUCTION	cryoSPARC	3.1

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		2695911