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Structure of complete, activated transcription complex Pol II-DSIF-PAF-SPT6 uncovers allosteric elongation activation by RTF1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GMH experimental model PDB 4L1U experimental model PDB 6AFO
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 8.948 f_angle_d 1.342 f_chiral_restr 0.083 f_bond_d 0.025 f_plane_restr 0.008
Sample Complete EC* Sample Components Pig DNA/RNA polymerase subunits Human transcription factors and associated proteins DNA/RNA Transcription elongation factor SPT4 and SPT5
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details 2 microliters applied to both sides of grid. Sample incubated on grid for 10s prior to blotting. Blotting for 8.5s.
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 446195 Reported Resolution (Å) 3.1 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (6GMH, 4L1U, 6AFO) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value 115 Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 QUANTUM (4k x 4k) Electron Dose (electrons/Å**2) 40
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) Maximum Defocus (nm) Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 130000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Warp IMAGE ACQUISITION EPU CTF CORRECTION Warp MODEL FITTING UCSF Chimera MODEL FITTING NAMD INITIAL EULER ASSIGNMENT RELION 3.0 FINAL EULER ASSIGNMENT RELION 3.0 RECONSTRUCTION RELION 3.0 MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 611983