CryoEM of E. coli RNA polymerase Sigma N bound to full duplex DNA fragment dhsU36 (-12T)

REL 2023-04-06 2023-05-16 2023-05-16 CryoEM of E. coli RNA polymerase Sigma N bound to full duplex DNA fragment dhsU36 (-12T) 0000-0003-3002-3695 Andreas Mueller The Rockefeller University 1230 York Avenue New York New York United States 10065 0000-0002-8241-3153 Seth Darst The Rockefeller University 1230 York Avenue New York New York United States 10065 Mueller AU Chen J Wu M Chiu C Nixon BT Campbell EA Darst SA National Institutes of Health (NIH) R35 GM118130 United States 2.4 10.6019/EMPIAR-11522 EMDB molecule EMD-28786 EMD-28790 EMD-28791 Mueller AU Chen J Wu M Chiu C Nixon BT Campbell EA Darst SA A general mechanism for transcription bubble nucleation in bacteria Proceedings of the National Academy of Sciences of the United States of America Proc Natl Acad Sci U S A 14 120 2023 English 10.1073/pnas.2220874120 36972428 Unaligned micrographs (raw movies) /data/micrographs_multiframe micrographs - multiframe TIFF TIFF 6088 40 UNSIGNED BYTE 5760 1.083 4092 1.083

FEI Titan Krios + Gatan K3, super-resolution, image shift, BioQuantum energy filter 20 eV slit; accelerating voltage 300 kV; dose 25.7 e-/px; pixel size 1.083 A/px; exposure 2.0 s; dose/frame 0.87647 e-/A^2/frame; frame time 0.05 s; total dose 43.82 e-/A^2; total frames 40; defocus range -0.8 to -2.5um Gain references can be found in the "references" subfolder. Picked particles star file "EsN-dhsU36full_particles_picked.star" ("aux_files" folder) contains all particles picked initially and is only provided for reference.

data/micrographs_multiframe/21apr19d_*enn.frames.tif data/aux_files/EsN-dhsU36full_particles_picked.star Motion-corrected micrographs (dose-weighted) /data/micrographs_singleframe micrographs - single frame MRC MRC 6088 1 32 BIT FLOAT 5760 1.083 4092 1.083

See also the "corrected_micrographs.star" file in the "aux_files" folder. Picked particles star file "EsN-dhsU36full_particles_picked.star" ("aux_files" folder) contains all particles picked initially and is only provided for reference.

data/micrographs_singleframe/21apr19d_*enn_frames.mrc data/aux_files/EsN-dhsU36full_particles_picked.star Particle images for map 1 /data/particles_shiny_map1 picked particles - single frame - processed MRCS MRCS 5836 1 32 BIT FLOAT 324 1.083 324 1.083

Particle stack for map 1 after Bayesian polishing (see "EsN-dhsU36full_particles_map1.star" (final refinement parameters) and "EsN-dhsU36full_particles_shiny.star" (output from Bayesian Polishing) in "aux_files" folder)

data/particles_shiny_map1/21apr19d_*enn_frames_shiny.mrcs data/aux_files/EsN-dhsU36full_particles_shiny.star data/particles_shiny_map1 Particle images for map 2 (subtracted particles) /data/particles_subtracted_map2 picked particles - single frame - processed MRCS MRCS 558 1 32 BIT FLOAT 324 1.083 324 1.083

Particle stack for map 2 after masked subtraction (see "EsN-dhsU36full_particles_map2.star" (final refinement parameters) and "EsN-dhsU36full_particles_original_map2.star" (original particles) in "aux_files" folder)

data/particles_subtracted_map2/subtracted_particles_batch_*.mrcs data/aux_files/EsN-dhsU36full_particles_map2.star data/particles_subtracted_map2