☰ Navigation Tabs
Cryo-EM structure of PCMTD1-ELOBC-CUL5-RBX2 (CRL5-PCMTD1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold experimental model PDB 6V9I experimental model PDB 8FVI
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.333 f_angle_d 0.646 f_chiral_restr 0.04 f_bond_d 0.005 f_plane_restr 0.005
Sample Pentameric complex of PCMTD1, Elongins B and C, Cullin-5, and RING-box protein 2 (CRL5-PCMTD1) Sample Components PCMTD1-ELOBC substrate receptor complex PCMTD1 CUL5-RBX2 catalytic core
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument SPT LABTECH CHAMELEON Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 352937 Reported Resolution (Å) 4.14 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (6V9I, 6V9I, 8FVI, 8FVI) Refinement Space REAL Refinement Protocol OTHER Refinement Target Overall B Value Fitting Procedure Details After initial fitting in ChimeraX, model was energy minimized against the 3D map with Rosetta FastRelax, adjusted in Coot, and refined in Phenix.
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1500 Maximum Defocus (nm) 2500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4 MODEL FITTING UCSF ChimeraX MODEL FITTING Rosetta MODEL FITTING Coot INITIAL EULER ASSIGNMENT cryoSPARC 4 FINAL EULER ASSIGNMENT cryoSPARC 4 RECONSTRUCTION cryoSPARC 4 MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE 1302046