KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and Virus Strains
E. coli BL21(DE3)	Novagen/EMD Millipore	N/A
E. coli BL21(DE3)T-X234-241H	Twist et al., 2011	N/A
E. coli BL2-AI	Invitrogen	Cat# C6070-03
E. coli Rosetta (DE3) pLysS	Novagen	N/A
E. coli BL21-CodonPlus	Agilent	Cat# 230280
E. coli Rosetta (DE3)	Novagen	Cat# 70954-3
SARS-CoV-2 infected Vero E6 cells	Blanco-Melo et al., 2020	N/A
Chemicals, Peptides, and Recombinant Proteins
Ammonium Acetate, TraceSELECT	Sigma-Aldrich	Cat#373432-100G-F; CAS: 631-61-8
Tween-20 Surfact-Amps (20% v/v) Detergent Solution	Thermo Scientific	Cat#28320; CAS: 9005-64-5
Polyethyleneimine	Fisher Scientific	Cat#AC178572500; CAS: 9002-98-6
Glutaraldehyde (50% v/v) solution	Sigma Aldrich	Cat#G7651-10ML; CAS: 111-30-8
E. coli DdRp core (full-length subunits)	Chen et al., 2019; Kang et al., 2020	N/A
E. coli σ70	Chen et al., 2019	N/A
E. coli TraR	Chen et al., 2019	N/A
E. coli DdRp core (ΔCTD for α subunit)	Twist et al., 2011	N/A
HK022 Nun	Kang et al., 2017	N/A
E. coli Mfd	Deaconescu and Darst, 2005; Kang et al., 2020	N/A
SARS-CoV-2 nsp12	Chen et al., 2020b	N/A
SARS-CoV-2 nsp7/8	Chen et al., 2020b	N/A
SARS-CoV-2 nsp13	Chen et al., 2020b	N/A
Deposited Data
native MS RAW files	This paper; Mendeley Data	http://dx.doi.org/10.17632/nbyz8j4j34.1
Oligonucleotides
The promoters used for the screening of transcription initiation complexes (DNA sequences shown in Figure S1A)	Integrated DNA Technologies	N/A
Template DNA for TEC/Nun assembly: 5’-GGGTATTCGCCGTGTACCTCTCC-3’	Integrated DNA Technologies	N/A
Non-template DNA for TEC/Nun assembly: 5’-GGGCTACCTCTCCATGACGGCGAATACCC-3’	Integrated DNA Technologies	N/A
Pre-translocated RNA for TEC/Nun assembly: 5’-GGAGAGGUAC-3’	Dharmacon	N/A
Post-translocated RNA for TEC/Nun assembly: 5’-GGAGAGGUA-3’	Dharmacon	N/A
The template and non-template DNA constructs used for the screening of Mfd-TEC (DNA sequences shown in Figure S2A)	Integrated DNA Technologies	N/A
The RNA transcripts used for the screening of Mfd-TEC (RNA sequences shown in Figure S2A)	Dharmacon	N/A
The RNA constructs used for the nsp13-RTC screening (Figure S4A)	Horizon Discovery Ltd./Dharmacon	N/A
Recombinant DNA
pACYCDuet-1_Ec_rpoZ	Twist et al., 2011	N/A
pEcrpoABC(-XH)Z	Twist et al., 2011	N/A
pET28a	EMD Millipore	N/A
pET28a-His10-SUMO rpoD	Chen et. al., 2017	N/A
pET28a-His10-SUMO traR	Chen et al., 2019	pRLG15142
pVS10 plasmid harboring genes encoding for E.coli RNAP α-X234-241, β, β’, and ω	Twist et al., 2011	N/A
pET21d plasmid harboring HK022 Nun	Kang et al., 2017	N/A
pET21d	Novagen	N/A
pAD6 (pET28a plasmid harboring Mfd)	Deaconescu et. al., 2005	N/A
pET28a-His10-SUMO nsp12	Chen et al., 2020b	N/A
pCDFDuet-1	Novagen	Cat#71340-3
pCDFDuet-1-His6-SARS-CoV-2-nsp7_nsp8	Chen et al., 2020b	N/A
pRSFDuet-1	Novagen	Cat#71341-3
pRSFDuet-1-His6-SUMO-SARS-CoV-2-nsp12	Chen et al., 2020b	N/A
pET28-His6-SARS-CoV-2-nsp13	GenScript	N/A
Software and Algorithms
UniDec version 3.2 & 4.1	Marty et al., 2015; Reid et al., 2019	https://github.com/michaelmarty/UniDec/releases
Qual Browser Thermo Xcalibur version 3.0.63 & 4.2.47	Thermo Fisher Scientific Inc.	Thermo Scientific MS instruments
m/z- Knexus edition	Proteometrics, LLC	N/A
PyMOL Molecular Graphics System	Schrödinger, LLC	http://www.pymol.org
Other
cOmplete Protease Inhibitor Cocktail	Roche	Cat#11697498001
Bio-Rex 70 cation exchange resin, analytical grade, 100-200 mesh	Bio-Rad	Cat#1425842
HiLoad 26/600 Superdex 200 pg	GE Healthcare Life Sciences	Cat#28989336
HiTrap IMAC HP	GE Healthcare Life Sciences	Cat#17092003
HiLoad 16/600 Superdex 200 pg	GE Healthcare Life Sciences	Cat#GE28-9893-3
HiLoad 16/600 Superdex 75 pg	GE Healthcare Life Sciences	Cat#GE28-9893-33
HisTrap HP	GE Healthcare Life Sciences	Cat#GE17-5248-02
HiTrap Heparin HP	GE Healthcare Life Sciences	Cat#GE17-0407-03
HiTrapSP	GE Healthcare Life Sciences	Cat#17115201
MonoS 10/100 GL	GE Healthcare Life Sciences	Cat#17516901
Superose 6 Increase 10/300 GL column	GE Healthcare Life Sciences	Cat#GE29-0915-96
Zeba Micro Spin Desalting Columns, 40K MWCO	Thermo Pierce	Cat#87765
Amicon Ultra-0.5 Centrifugal Filter Unit with Ultracel-100 membrane, 100 kDa MWCO	EMD Millipore	Cat#UFC510096
Quartz tubing without filament: 1.0mm O.D., 0.70mm I.D., 10cm length	Sutter	Cat#Q100-70-10