KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Bacterial and virus strains | ||
| E. coli BL21(DE3) | Novagen | N/A |
| E. coli BL21(DE3) pLysS | Novagen | N/A |
| Rosetta 2 (DE3) | Novagen | N/A |
| Biological samples | ||
| Chemicals, peptides, and recombinant proteins | ||
| n-Octyl-b-D-Glucopyranoside | Anatrace | Cat# O311 |
| Mtb RNAP (cryo-EM samples) | Boyaci et al., 2019a | N/A |
| Mtb CarD | Srivastava et al., 2013 | N/A |
| Mtb σA/WhiB7 | This paper | N/A |
| Mtb RbpA | Hubin et al., 2015 | N/A |
| Mtb σA/RbpA | Boyaci et al., 2018 | N/A |
| Mtb σA | Davis et al., 2015 | N/A |
| Polyethyleneimine | Fisher Scientific | Cat# AC178572500 |
| Desthiobiotin | Sigma Aldrich | Cat# D1411 |
| ULP-1 protease | Invitrogen | Cat# 12588018 |
| Critical commercial assays | ||
| Deposited data | ||
| Coordinates of Mtb W-RPo | This paper | PDB: 7KIF |
| Coordinates of Mtb W-RPc | This paper | PDB: 7KIM |
| Coordinates of Mtb RPo | This paper | PDB: 7KIN |
| Cryo-EM map of Mtb W-RPo | This paper | EMD-22886 |
| Cryo-EM map Mtb W-RPc | This paper | EMD-22887 |
| Cryo-EM map of Mtb RPo | This paper | EMD-22888 |
| Abortive initiation transcription gel | This paper; Mendeley Data | https://data.mendeley.com/datasets/jph6vjvhbs/draft?a=394ea63c-e6a8-4415-acda-1725bd491dd6 |
| EMSA gel shifts | This paper; Mendeley Data | https://data.mendeley.com/datasets/fh9639t5sc/draft?a=48f930a7-2899-494e-a494-eb7f3ae0ecac |
| Experimental models: cell lines | ||
| Experimental models: organisms/strains | ||
| Mycobacterium tuberculosis | N/A | N/A |
| Oligonucleotides | ||
| WhiB7 top strand: CTGTACCGGCAAACGCGCAGG TCAGAAAATCGGTTGTGGTCA GCTGCTGCCACCGGTTAACC TCCAGGTCGCATTCTGCTGC CAGCCTGGAGATGGCATT |
This paper, IDT | N/A |
| WhiB7 bottom strand: AATGCCATCTCCAGGCTGGCA GCAGAATGCGACCTGGAGGTT AACCGGTGGCAGCAGCTGACC ACAACCGATTTTCTGACCTGCG CGTTTGCCGGTACAG |
This paper, IDT | N/A |
| Recombinant DNA | ||
| Mtb RNAP, pMP61 | Boyaci et al., 2019a | N/A |
| pCDFDuet-1 | Novagen | N/A |
| pCDFDuet-1/ σA/WhiB7 | This paper | N/A |
| pET SUMO/CarD | Srivastava et al., 2013 | N/A |
| pET20b/RbpA | Hubin et al., 2015 | N/A |
| pAC27/ σA | Davis et al., 2015 | N/A |
| Software and algorithms | ||
| Bayesian Polishing | Zivanov et al., 2018 | https://github.com/3dem/relion |
| blocfilt | Cardone et al., 2013 | https://lsbr.niams.nih.gov/bsoft/programs/blocres.html |
| blocres | Cardone et al., 2013 | https://lsbr.niams.nih.gov/bsoft/programs/blocres.html |
| Coot | Emsley and Cowtan, 2004 | https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot |
| cryoSPARC | Punjani et al., 2017 | https://cryosparc.com/ |
| GraphPad Prism | GraphPad | http://www.graphpad.com/scientific-software/prism/ |
| ImageQuant 5.2 | GE Healthcare, Pittsburgh PA | N/A |
| MotionCor2 | Zheng et al., 2017 | N/A |
| MTRIAGE | Afonine et al. 2018 | https://www.phenix-online.org/documentation/reference/mtriage.html |
| PHENIX | Adams et al., 2010 | https://www.phenix-online.org/documentation/index.html |
| RELION | Scheres, 2012 | https://github.com/3dem/relion |
| SBGrid | Morin et al., 2013 | https://sbgrid.org/ |
| The PyMOL Molecular Graphics System | Schrïdinger, LLC | https://pymol.org/2/ |
| UCSF Chimera | Pettersen et al., 2004 | https://www.cgl.ucsf.edu/chimera |
| MegAlign Pro | DNASTAR | https://www.dnastar.com/?utm_source=software&utm_medium=MegAlignPro |
| Other | ||
| C-flat CF-1.2/1.3 400 mesh gold grids | Electron Microscopy Sciences | Cat# CF413-100-Au |
| HiLoad 16/600 Superdex 200 pg | Cytiva | Cat# 28989335 |
| HiTrap IMAC HP | Cytiva | Cat# 17092003 |
| StrepTrap HP | Cytiva | Cat# 28907547 |
| Isotope [α32P] CTP | Perkin Elmer | Cat # BLU013H250UCI |
| Superose 6 INCREASE 10/300 GL | Cytiva | Cat# 29091596 |
| Mono Q 5/50 GL | Cytiva | Cat# 17516601 |