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Cryo-EM structure of human 26S RP (Eb state) bound to K11/K48-branched ubiquitin (Ub) chain composed of four Ub.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6MSB
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.672 f_angle_d 0.997 f_chiral_restr 0.056 f_bond_d 0.011 f_plane_restr 0.007
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 K11/K48-branched ubiquitin (Ub) chain composed of four Ub.
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 52216 Reported Resolution (Å) 3.8 Resolution Method FSC 0.143 CUT-OFF Other Details Performed in cryoSPARC using Non-uniform Refinment 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 (6MSB) Refinement Space REAL Refinement Protocol OTHER Refinement Target 0.83 Overall B Value 110.45 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 cryoSPARC 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