← Back to search
7c97

Cryo-EM structure of an Escherichia coli RNAP-promoter open complex (RPo) with SspA

Method: ELECTRON MICROSCOPY Dmax: 179.8 Å Quality: GOOD
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Stringent starvation protein A

Escherichia coli

UniProt H4IXP2

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 9 DNA 2 PDB declaration: undecameric（11） Consistent with all polymer counts Chain I； UniProt 1–212 Chain J； UniProt 1–212 Not recorded DNA (63-mer) × 1 DNA-directed RNA polymerase subunit alpha × 3 （F4VJT6） DNA-directed RNA polymerase subunit beta × 1 （P0A8V2） ;DNA-directed RNA polymerase subunit beta' ; × 1 （M9GTE2） DNA-directed RNA polymerase subunit omega × 1 （T9C803） RNA polymerase sigma factor RpoD × 1 （Q0P6L9） DNA (63-mer) × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.68 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name H4IXP2_ECOLX
Isoform —
PDB entities 2
Chains and sequence ranges Author chain I； PDBConstruct 1–212； UniProt 1–212 Author chain J； PDBConstruct 1–212； UniProt 1–212

DNA-directed RNA polymerase subunit alpha

Escherichia coli

UniProt F4VJT6

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 9 DNA 2 PDB declaration: undecameric（11） Consistent with all polymer counts Chain A； UniProt 1–329 Chain B； UniProt 1–329 Chain K； UniProt 1–329 Not recorded DNA (63-mer) × 1 Stringent starvation protein A × 2 （H4IXP2） DNA-directed RNA polymerase subunit beta × 1 （P0A8V2） ;DNA-directed RNA polymerase subunit beta' ; × 1 （M9GTE2） DNA-directed RNA polymerase subunit omega × 1 （T9C803） RNA polymerase sigma factor RpoD × 1 （Q0P6L9） DNA (63-mer) × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.68 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name F4VJT6_ECOLX
Isoform —
PDB entities 3
Chains and sequence ranges Author chain A； PDBConstruct 1–329； UniProt 1–329 Author chain B； PDBConstruct 1–329； UniProt 1–329 Author chain K； PDBConstruct 1–329； UniProt 1–329

DNA-directed RNA polymerase subunit beta

Escherichia coli (strain K12)

UniProt P0A8V2

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 9 DNA 2 PDB declaration: undecameric（11） Consistent with all polymer counts Chain C； UniProt 1–1342 Mutation：D516V DNA (63-mer) × 1 Stringent starvation protein A × 2 （H4IXP2） DNA-directed RNA polymerase subunit alpha × 3 （F4VJT6） ;DNA-directed RNA polymerase subunit beta' ; × 1 （M9GTE2） DNA-directed RNA polymerase subunit omega × 1 （T9C803） RNA polymerase sigma factor RpoD × 1 （Q0P6L9） DNA (63-mer) × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.68 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 7C97 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
10MA Closed Eco-ePEC: Cryo-EM structure of Eco RNAP his-elemental paused elongation complex with a closed active site (closed TL, SI3 and RH-FL) Deposited 2026-01-27 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain I 1–1342（1342 aa）
Not recorded 1N7 CHAPSO × 2 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
10MB Open1 Eco-ePEC: Cryo-EM structure of Eco RNAP his-elemental paused elongation complex with an open active site (open TL, SI3 and RH-FL) Deposited 2026-01-27 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain I 1–1342（1342 aa）
Not recorded 1N7 CHAPSO × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
10MC Open2 Eco-ePEC: Cryo-EM structure of Eco RNAP his-elemental paused elongation complex with an open active site (open TL, SI3 and RH-FL) Deposited 2026-01-27 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain I 1–1342（1342 aa）
Not recorded 1N7 CHAPSO × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
10MD Open3 Eco-ePEC: Cryo-EM structure of Eco RNAP his-elemental paused elongation complex with an open active site (open TL, SI3 and RH-FL) Deposited 2026-01-27 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain I 1–1342（1342 aa）
Not recorded 1N7 CHAPSO × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
3IYD Three-dimensional EM structure of an intact activator-dependent transcription initiation complex Deposited 2009-08-01 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–1342（1342 aa）
Not recorded CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer 25 mM HEPES, 100 mM KCl, 10 mM MgCl2, 1 mM DTT, 0.2 mM cAMP；pH 8；25 mM HEPES, 100 mM KCl, 10 mM MgCl2, 1 mM DTT, 0.2 mM cAMP
Resolution 19.80 Å
3LTI Crystal structure of the Escherichia coli RNA polymerase beta subunit beta2-betai4 domains Deposited 2010-02-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 152–443（292 aa） Fragment：beta2-beta-i-4 domains
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.2 M potassium-sodium tartrate, 20% PEG 3350, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.60 Å R-free 0.230
3LU0 Molecular model of Escherichia coli core RNA polymerase Deposited 2010-02-16 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer Tris-HCl；pH 8；Tris-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 11.20 Å
3TBI Crystal structure of T4 gp33 bound to E. coli RNAP beta-flap domain Deposited 2011-08-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 831–1057（227 aa） Fragment：beta-flap domain (UNP residues 831-1057)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；295 K；0.1 M triethylamine N-oxide, 20% PEG2000 MME, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, temperature 295K
Resolution 3.00 Å R-free 0.295
4JK1 X-ray crystal structure of Escherichia coli sigma70 holoenzyme in complex with Guanosine tetraphosphate (ppGpp) Deposited 2013-03-09 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 G4P GUANOSINE-5',3'-TETRAPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1 M Hepes-HCl (pH 7.0), 0.2 M CaAcetate, ~15 % PEG400, 10 mM Tri(2-carboxyethyl)phosphine (TCEP), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.90 Å R-free 0.320
4JK1 X-ray crystal structure of Escherichia coli sigma70 holoenzyme in complex with Guanosine tetraphosphate (ppGpp) Deposited 2013-03-09 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain H 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1 M Hepes-HCl (pH 7.0), 0.2 M CaAcetate, ~15 % PEG400, 10 mM Tri(2-carboxyethyl)phosphine (TCEP), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.90 Å R-free 0.320
4JK2 X-ray crystal structure of Escherichia coli sigma70 holoenzyme in complex with guanosine pentaphosphate (pppGpp) Deposited 2013-03-09 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 0O2 guanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen diphosphate) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1 M Hepes-HCl (pH 7.0), 0.2 M CaAcetate, ~15 % PEG400, 10 mM Tri(2-carboxyethyl)phosphine (TCEP), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 4.20 Å R-free 0.322
4JK2 X-ray crystal structure of Escherichia coli sigma70 holoenzyme in complex with guanosine pentaphosphate (pppGpp) Deposited 2013-03-09 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain H 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1 M Hepes-HCl (pH 7.0), 0.2 M CaAcetate, ~15 % PEG400, 10 mM Tri(2-carboxyethyl)phosphine (TCEP), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 4.20 Å R-free 0.322
4KMU X-ray crystal structure of the Escherichia coli RNA polymerase in complex with Rifampin Deposited 2013-05-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–1342（1342 aa）
Not recorded RFP RIFAMPICIN × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；300 K；0.1 M HEPES-HCl, pH 7.0, 0.2 M calcium acetate, ~15% PEG400, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Resolution 3.85 Å R-free 0.321
4KMU X-ray crystal structure of the Escherichia coli RNA polymerase in complex with Rifampin Deposited 2013-05-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain H 1–1342（1342 aa）
Not recorded RFP RIFAMPICIN × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；300 K；0.1 M HEPES-HCl, pH 7.0, 0.2 M calcium acetate, ~15% PEG400, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Resolution 3.85 Å R-free 0.321
4KN4 X-ray crystal structure of the Escherichia coli RNA polymerase in complex with Benzoxazinorifamycin-2b Deposited 2013-05-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–1342（1342 aa）
Not recorded 1RL Benzoxazinorifamycin-2b × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；300 K；0.1 M HEPES-HCl, pH 7.0, 0.2 M calcium acetate, ~15% PEG400, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Resolution 3.96 Å R-free 0.315
4KN4 X-ray crystal structure of the Escherichia coli RNA polymerase in complex with Benzoxazinorifamycin-2b Deposited 2013-05-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain H 1–1342（1342 aa）
Not recorded 1RL Benzoxazinorifamycin-2b × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；300 K；0.1 M HEPES-HCl, pH 7.0, 0.2 M calcium acetate, ~15% PEG400, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Resolution 3.96 Å R-free 0.315
4KN7 X-ray crystal structure of the Escherichia coli RNA polymerase in complex with Benzoxazinorifamycin-2c Deposited 2013-05-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–1342（1342 aa）
Not recorded 1RM Benzoxazinorifamycin-2c × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；300 K；0.1 M HEPES-HCl, pH 7.0, 0.2 M calcium acetate, ~15% PEG400, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Resolution 3.69 Å R-free 0.309
4KN7 X-ray crystal structure of the Escherichia coli RNA polymerase in complex with Benzoxazinorifamycin-2c Deposited 2013-05-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain H 1–1342（1342 aa）
Not recorded 1RM Benzoxazinorifamycin-2c × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；300 K；0.1 M HEPES-HCl, pH 7.0, 0.2 M calcium acetate, ~15% PEG400, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Resolution 3.69 Å R-free 0.309
4MEX Crystal structure of Escherichia coli RNA polymerase in complex with salinamide A Deposited 2013-08-27 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain C 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；0.1M HEPES, 0.2M calcium chloride, 18% PEG400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 3.90 Å R-free 0.325
4MEX Crystal structure of Escherichia coli RNA polymerase in complex with salinamide A Deposited 2013-08-27 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain I 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；0.1M HEPES, 0.2M calcium chloride, 18% PEG400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 3.90 Å R-free 0.325
4MEY Crystal structure of Escherichia coli RNA polymerase holoenzyme Deposited 2013-08-27 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；0.1M HEPES, 0.2M calcium chloride, 18% PEG400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 3.95 Å R-free 0.325
4MEY Crystal structure of Escherichia coli RNA polymerase holoenzyme Deposited 2013-08-27 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain I 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；0.1M HEPES, 0.2M calcium chloride, 18% PEG400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 3.95 Å R-free 0.325
4ZH2 Crystal structure of Escherichia coli RNA polymerase in complex with CBR703 Deposited 2015-04-24 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–1342（1342 aa）
Not recorded 4OB N-hydroxy-N'-phenyl-3-(trifluoromethyl)benzenecarboximidamide × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；0.1 M HEPES, 0.2 M calcium chloride, 18% PEG400
Resolution 4.20 Å R-free 0.288
4ZH2 Crystal structure of Escherichia coli RNA polymerase in complex with CBR703 Deposited 2015-04-24 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain I 1–1342（1342 aa）
Not recorded 4OB N-hydroxy-N'-phenyl-3-(trifluoromethyl)benzenecarboximidamide × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；0.1 M HEPES, 0.2 M calcium chloride, 18% PEG400
Resolution 4.20 Å R-free 0.288
4ZH3 Crystal structure of Escherichia coli RNA polymerase in complex with CBRH16-Br Deposited 2015-04-24 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 4OD N'-(3-bromophenyl)-4-fluoro-N-hydroxy-3-(trifluoromethyl)benzenecarboximidamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；0.1 M HEPES, 0.2 M calcium chloride, 18% PEG400
Resolution 4.08 Å R-free 0.267
4ZH3 Crystal structure of Escherichia coli RNA polymerase in complex with CBRH16-Br Deposited 2015-04-24 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain I 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 4OD N'-(3-bromophenyl)-4-fluoro-N-hydroxy-3-(trifluoromethyl)benzenecarboximidamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；0.1 M HEPES, 0.2 M calcium chloride, 18% PEG400
Resolution 4.08 Å R-free 0.267
4ZH4 Crystal structure of Escherichia coli RNA polymerase in complex with CBRP18 Deposited 2015-04-24 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–1342（1342 aa）
Not recorded 4OE 5-(4-fluorophenyl)-4-[4-fluoro-3-(trifluoromethyl)phenyl]-1H-pyrazole × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；0.1 M HEPES, 0.2 M calcium chloride, 18% PEG400
Resolution 3.99 Å R-free 0.283
4ZH4 Crystal structure of Escherichia coli RNA polymerase in complex with CBRP18 Deposited 2015-04-24 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain I 1–1342（1342 aa）
Not recorded 4OE 5-(4-fluorophenyl)-4-[4-fluoro-3-(trifluoromethyl)phenyl]-1H-pyrazole × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；0.1 M HEPES, 0.2 M calcium chloride, 18% PEG400
Resolution 3.99 Å R-free 0.283
5IPL SigmaS-transcription initiation complex with 4-nt nascent RNA Deposited 2016-03-09 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain C 1–1342（1342 aa）
Not recorded DPO DIPHOSPHATE × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；295 K；PEG3350, sodium chloride, HEPES
Resolution 3.60 Å R-free 0.293
5IPM SigmaS-transcription initiation complex with 4-nt nascent RNA Deposited 2016-03-09 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain C 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；295 K；PEG3350, sodium chloride, HEPES
Resolution 4.20 Å R-free 0.330
5IPN SigmaS-transcription initiation complex with 4-nt nascent RNA Deposited 2016-03-09 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain C 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；295 K；PEG3350, sodium chloride, HEPES
Resolution 4.61 Å R-free 0.345
5MS0 pseudo-atomic model of the RNA polymerase lambda-based antitermination complex solved by cryo-EM Deposited 2016-12-29 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tetradecameric
Chain C 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.80 Å
5NSR Cryo-EM structure of RNA polymerase-sigma54 holo enzyme with promoter DNA closed complex Deposited 2017-04-26 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain C 1–1342（1342 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
5NSS Cryo-EM structure of RNA polymerase-sigma54 holoenzyme with promoter DNA and transcription activator PspF intermedate complex Deposited 2017-04-26 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: octameric
Chain C 1–1342（1342 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.80 Å
5NWT Crystal Structure of Escherichia coli RNA polymerase - Sigma54 Holoenzyme complex Deposited 2017-05-08 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.9；291 K；9% PEG8000, 18% Ethylene glycol, 100mM Sodium HEPES/MOPS Buffer, 0.03M NaF, 0.03M NaBr, 0.03M NaI, 0-10mM DTT
Resolution 3.76 Å R-free 0.370
5UAC Escherichia coli RNA polymerase and Rifampin complex, wild-type Deposited 2016-12-19 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–1342（1342 aa）
Not recorded RFP RIFAMPICIN × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M HEPES-HCl (pH 6.7), 0.2 M Ca Acetate, 30% PEG400, 10 mM DTT
Resolution 3.80 Å R-free 0.295
5UAC Escherichia coli RNA polymerase and Rifampin complex, wild-type Deposited 2016-12-19 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain I 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M HEPES-HCl (pH 6.7), 0.2 M Ca Acetate, 30% PEG400, 10 mM DTT
Resolution 3.80 Å R-free 0.295
5UAG Escherichia coli RNA polymerase mutant - RpoB D516V Deposited 2016-12-19 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–1342（1342 aa）
Mutation：D516V MG MAGNESIUM ION × 2 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；300 K；0.1 M HEPES-HCl (pH 6.7), 0.2 M Ca Acetate, 30% PEG400, 10 mM DTT
Resolution 3.40 Å R-free 0.311
5UAG Escherichia coli RNA polymerase mutant - RpoB D516V Deposited 2016-12-19 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain I 1–1342（1342 aa）
Mutation：D516V MG MAGNESIUM ION × 2 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；300 K；0.1 M HEPES-HCl (pH 6.7), 0.2 M Ca Acetate, 30% PEG400, 10 mM DTT
Resolution 3.40 Å R-free 0.311
5UAH Escherichia coli RNA polymerase and Rifampin complex, RpoB D516V mutant Deposited 2016-12-19 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–1342（1342 aa）
Mutation：D516V RFP RIFAMPICIN × 1 MG MAGNESIUM ION × 2 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；300 K；0.1 M HEPES-HCl (pH 6.7), 0.2 M Ca Acetate, 30% PEG400, 10 mM DTT
Resolution 4.10 Å R-free 0.287
5UAH Escherichia coli RNA polymerase and Rifampin complex, RpoB D516V mutant Deposited 2016-12-19 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain I 1–1342（1342 aa）
Mutation：D516V MG MAGNESIUM ION × 2 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；300 K；0.1 M HEPES-HCl (pH 6.7), 0.2 M Ca Acetate, 30% PEG400, 10 mM DTT
Resolution 4.10 Å R-free 0.287
5UAJ Escherichia coli RNA polymerase RpoB S531L mutant Deposited 2016-12-19 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–1342（1342 aa）
Mutation：S531L MG MAGNESIUM ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；300 K；0.1 M HEPES-HCl (pH 6.7), 0.2 M Ca Acetate, 30% PEG400, 10 mM DTT
Resolution 3.92 Å R-free 0.307
5UAJ Escherichia coli RNA polymerase RpoB S531L mutant Deposited 2016-12-19 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain I 1–1342（1342 aa）
Mutation：S531L MG MAGNESIUM ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；300 K；0.1 M HEPES-HCl (pH 6.7), 0.2 M Ca Acetate, 30% PEG400, 10 mM DTT
Resolution 3.92 Å R-free 0.307
5UAL Escherichia coli RNA polymerase and Rifampin complex, RpoB S531L mutant Deposited 2016-12-19 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–1342（1342 aa）
Mutation：S531L RFP RIFAMPICIN × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；300 K；0.1 M HEPES-HCl (pH 6.7), 0.2 M Ca Acetate, 30% PEG400, 10 mM DTT
Resolution 3.89 Å R-free 0.286
5UAL Escherichia coli RNA polymerase and Rifampin complex, RpoB S531L mutant Deposited 2016-12-19 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain I 1–1342（1342 aa）
Mutation：S531L MG MAGNESIUM ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；300 K；0.1 M HEPES-HCl (pH 6.7), 0.2 M Ca Acetate, 30% PEG400, 10 mM DTT
Resolution 3.89 Å R-free 0.286
5UAQ Escherichia coli RNA polymerase RpoB H526Y mutant Deposited 2016-12-19 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–1342（1342 aa）
Mutation：H526Y MG MAGNESIUM ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；300 K；0.1 M HEPES-HCl (pH 6.7), 0.2 M Ca Acetate, 30% PEG400, 10 mM DTT
Resolution 3.60 Å R-free 0.305
5UAQ Escherichia coli RNA polymerase RpoB H526Y mutant Deposited 2016-12-19 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain I 1–1342（1342 aa）
Mutation：H526Y MG MAGNESIUM ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；300 K；0.1 M HEPES-HCl (pH 6.7), 0.2 M Ca Acetate, 30% PEG400, 10 mM DTT
Resolution 3.60 Å R-free 0.305
5VSW X-ray crystal structure of Escherichia coli RNA polymerase and DksA/ppGpp complex Deposited 2017-05-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain C 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 3 G4P GUANOSINE-5',3'-TETRAPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；300 K；0.1 M HEPES (pH 7.0), 0.2 M calcium acetate, 25 % PEG400, 10 mM DTT
Resolution 4.29 Å R-free 0.259
5VSW X-ray crystal structure of Escherichia coli RNA polymerase and DksA/ppGpp complex Deposited 2017-05-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain I 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 G4P GUANOSINE-5',3'-TETRAPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；300 K；0.1 M HEPES (pH 7.0), 0.2 M calcium acetate, 25 % PEG400, 10 mM DTT
Resolution 4.29 Å R-free 0.259
5VT0 Escherichia coli 6S RNA derivative in complex with Escherichia coli RNA polymerase sigma70-holoenzyme Deposited 2017-05-15 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 6 PDB declaration: heptameric
Chain I 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.78 Å
5W1S X-ray crystal structure of Escherichia coli RNA polymerase and TraR complex Deposited 2017-06-04 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain C 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1M HEPES-HCL (PH7), 0.2M Ca-ACETATE, 15% PEG400
Resolution 3.81 Å R-free 0.262
5W1S X-ray crystal structure of Escherichia coli RNA polymerase and TraR complex Deposited 2017-06-04 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain I 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1M HEPES-HCL (PH7), 0.2M Ca-ACETATE, 15% PEG400
Resolution 3.81 Å R-free 0.262
5W1T X-ray crystal structure of Escherichia coli RNA polymerase and DksA complex Deposited 2017-06-04 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain C 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M HEPES-HCL (PH7), 0.2M CA-ACETATE, 15% PEG400
Resolution 4.50 Å R-free 0.276
5W1T X-ray crystal structure of Escherichia coli RNA polymerase and DksA complex Deposited 2017-06-04 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain I 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M HEPES-HCL (PH7), 0.2M CA-ACETATE, 15% PEG400
Resolution 4.50 Å R-free 0.276
6ALF CryoEM structure of crosslinked E.coli RNA polymerase elongation complex Deposited 2017-08-07 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain I 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM Tris pH8.0, 150 mM KCl, 5mM MgCl2, 5mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6ALG CryoEM structure of HK022 Nun - E.coli RNA polymerase elongation complex Deposited 2017-08-07 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain I 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM Tris pH8.0, 150 mM Potassium Chloride, 5 mM Magnesium Chloride, 5 mM Dithreitol
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6ALH CryoEM structure of E.coli RNA polymerase elongation complex Deposited 2017-08-07 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain I 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM Tris pH8.0, 150 mM KCl, 5mM MgCl2, 5mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
6ASX CryoEM structure of E.coli his pause elongation complex Deposited 2017-08-25 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain I 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM Tris pH8.0, 150 mM potassium glutamate, 5 mM MgCl2, 5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6BJS CryoEM structure of E.coli his pause elongation complex without pause hairpin Deposited 2017-11-06 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain I 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM Tris pH8.0, 150 mM potassium glutamate, 5 mM MgCl2, 5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.50 Å
6BYU X-ray crystal structure of Escherichia coli RNA polymerase (RpoB-H526Y) and ppApp complex Deposited 2017-12-21 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–1342（1342 aa）
Not recorded ECJ (5R)-5-(6-amino-9H-purin-9-yl)-2-({[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}methyl)-4-oxo-4,5-dihydrofuran-3-yl trihydrogen diphosphate × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；300 K；0.1 M HEPES-HCl (pH 6.7), 0.2 M MgCl2, 30% PEG400, 10 mM DTT
Resolution 3.60 Å R-free 0.311
6BYU X-ray crystal structure of Escherichia coli RNA polymerase (RpoB-H526Y) and ppApp complex Deposited 2017-12-21 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain I 1–1342（1342 aa）
Not recorded ECJ (5R)-5-(6-amino-9H-purin-9-yl)-2-({[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}methyl)-4-oxo-4,5-dihydrofuran-3-yl trihydrogen diphosphate × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；300 K；0.1 M HEPES-HCl (pH 6.7), 0.2 M MgCl2, 30% PEG400, 10 mM DTT
Resolution 3.60 Å R-free 0.311
6C6S CryoEM structure of E.coli RNA polymerase elongation complex bound with RfaH Deposited 2018-01-19 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain I 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6C6T CryoEM structure of E.coli RNA polymerase elongation complex bound with RfaH Deposited 2018-01-19 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain I 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6C6U CryoEM structure of E.coli RNA polymerase elongation complex bound with NusG Deposited 2018-01-19 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain I 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6C9Y Cryo-EM structure of E. coli RNAP sigma70 holoenzyme Deposited 2018-01-29 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.25 Å
6CA0 Cryo-EM structure of E. coli RNAP sigma70 open complex Deposited 2018-01-29 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: decameric
Chain C 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.75 Å
6CUX Escherichia coli RpoB S531L mutant RNA polymerase holoenzyme in complex with Kanglemycin A Deposited 2018-03-26 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–1342（1342 aa）
Not recorded KNG Kanglemycin A × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M HEPES-HCl (pH 6.7), 0.2 M Ca Acetate, 30% PEG400, 10 mM DTT
Resolution 4.10 Å R-free 0.255
6CUX Escherichia coli RpoB S531L mutant RNA polymerase holoenzyme in complex with Kanglemycin A Deposited 2018-03-26 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain I 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M HEPES-HCl (pH 6.7), 0.2 M Ca Acetate, 30% PEG400, 10 mM DTT
Resolution 4.10 Å R-free 0.255
6FLP CryoEM structure of E.coli RNA polymerase paused elongation complex without RNA hairpin bound to NusA Deposited 2018-01-26 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain C 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6FLQ CryoEM structure of E.coli RNA polymerase paused elongation complex bound to NusA Deposited 2018-01-26 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: octameric
Chain C 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6GFW Cryo-EM structure of bacterial RNA polymerase-sigma54 holoenzyme initial transcribing complex Deposited 2018-05-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: nonameric
Chain C 1–1342（1342 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6GH5 Cryo-EM structure of bacterial RNA polymerase-sigma54 holoenzyme transcription open complex Deposited 2018-05-04 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain C 1–1342（1342 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6GH6 Cryo-EM structure of bacterial RNA polymerase-sigma54 holoenzyme intermediate partially loaded complex Deposited 2018-05-04 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain C 1–1342（1342 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6JBQ CryoEM structure of Escherichia coli sigmaE transcription initiation complex containing 5nt of RNA Deposited 2019-01-26 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain C 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.02 Å
6JNX Cryo-EM structure of a Q-engaged arrested complex Deposited 2019-03-18 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: undecameric
Chain C 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.08 Å
6K4Y CryoEM structure of sigma appropriation complex Deposited 2019-05-27 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.79 Å
6KJ6 cryo-EM structure of Escherichia coli Crl transcription activation complex Deposited 2019-07-21 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: decameric
Chain C 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot for 8 seconds before plunging
Resolution 3.80 Å
6LDI The cryo-EM structure of E. coli CueR transcription activation complex Deposited 2019-11-21 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: undecameric
Chain C 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 AG SILVER ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.69 Å
6N57 Cryo-EM structure of Escherichia coli RNAP polymerase bound with TraR in conformation I Deposited 2018-11-21 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain I 1–1342（1342 aa）
Not recorded 1N7 CHAPSO × 4 ZN ZINC ION × 3 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6N58 Cryo-EM structure of Escherichia coli RNAP polymerase bound with TraR in conformation II Deposited 2018-11-21 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain I 1–1342（1342 aa）
Not recorded 1N7 CHAPSO × 4 MG MAGNESIUM ION × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.78 Å
6N60 Escherichia coli RNA polymerase sigma70-holoenzyme bound to upstream fork promoter DNA and Microcin J25 (MccJ25) Deposited 2018-11-23 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain C 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；295 K；0.1 M HEPES, pH 6.7, 0.2 M magnesium chloride, 7% w/v PEG3350, 4% v/v glycerol
Resolution 3.68 Å R-free 0.306
6N61 Escherichia coli RNA polymerase sigma70-holoenzyme bound to upstream fork promoter DNA and Capistruin Deposited 2018-11-24 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain C 1–1342（1342 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；295 K；0.1 M HEPES, pH 6.8, 0.2 M magnesium chloride, 7% w/v PEG3350, 4% v/v glycerol, 4% v/v ethylene glycol
Resolution 3.25 Å R-free 0.316
6P18 Q21 transcription antitermination complex: loading complex Deposited 2019-05-19 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: undecameric
Chain C 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6P19 Q21 transcription antitermination complex: loaded complex Deposited 2019-05-19 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain C 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6R9B Cryo-EM structure of bacterial RNAP with a DNA mimic protein Ocr from T7 phage Deposited 2019-04-03 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain C 1–1342（1342 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6R9G Structural basis of transcription inhibition by the DNA mimic Ocr protein of bacteriophage T7 Deposited 2019-04-03 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain C 1–1342（1342 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6RH3 Cryo-EM structure of E. coli RNA polymerase elongation complex bound to CTP substrate Deposited 2019-04-18 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain C 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 CTP CYTIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6RI7 Cryo-EM structure of E. coli RNA polymerase elongation complex bound to GreB transcription factor Deposited 2019-04-23 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: nonameric
Chain C 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6RI9 Cryo-EM structure of E. coli RNA polymerase backtracked elongation complex in non-swiveled state Deposited 2019-04-23 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain C 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6RIN Cryo-EM structure of E. coli RNA polymerase backtracked elongation complex bound to GreB transcription factor Deposited 2019-04-24 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain C 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6RIP Cryo-EM structure of E. coli RNA polymerase backtracked elongation complex in swiveled state Deposited 2019-04-24 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain C 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6UTV E. coli sigma-S transcription initiation complex with a 6-nt RNA ("Fresh" crystal soaked with CTP, UTP, GTP, and ddATP for 150 seconds) Deposited 2019-10-30 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain CCC 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 2 DPO DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；PEG3350, sodium chloride, HEPES
Resolution 3.45 Å R-free 0.348
6XAS CryoEM Structure of E. coli Rho-dependent Transcription Pre-termination Complex Deposited 2020-06-04 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain I 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6XAV CryoEM Structure of E. coli Rho-dependent Transcription Pre-termination Complex bound with NusG Deposited 2020-06-04 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain I 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.70 Å
6ZTL E. coli 70S-RNAP expressome complex in collided state bound to NusG Deposited 2020-07-20 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 54 PDB declaration: 62-meric
Chain CC 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 441 PHE PHENYLALANINE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7BEF Structures of class II bacterial transcription complexes Deposited 2020-12-23 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain C 1–1342（1342 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM Tris pH 8, 50 mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7C17 The cryo-EM structure of E. coli CueR transcription activation complex with fully duplex promoter DNA Deposited 2020-05-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 AG SILVER ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.22 Å
7CHW Cryo-EM structure of an Escherichia coli RNAP-promoter open complex (RPo) Deposited 2020-07-06 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain C 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
Resolution 3.58 Å
7DY6 A refined cryo-EM structure of an Escherichia coli RNAP-promoter open complex (RPo) with SspA Deposited 2021-01-20 Different mutation/modification Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.68 Å
7EGS The crystal structure of lobe domain of E. coli RNA polymerase complexed with the C-terminal domain of UvrD Deposited 2021-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 152–443（292 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M HEPES pH 7.0, 10% w/v polyethylene glycol 4000, 10 % (v/v) isopropanol
Resolution 1.70 Å R-free 0.234
7KHB Escherichia coli RNA polymerase and rrnBP1 promoter open complex Deposited 2020-10-20 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain C 1–1342（1342 aa）
Not recorded 1N7 CHAPSO × 2 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.53 Å
7KHC Escherichia coli RNA polymerase and rrnBP1 promoter closed complex Deposited 2020-10-20 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: decameric
Chain C 1–1342（1342 aa）
Not recorded POP PYROPHOSPHATE 2- × 1 1N7 CHAPSO × 2 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.14 Å
7KHE Escherichia coli RNA polymerase and rrnBP1 promoter pre-open complex with DksA/ppGpp Deposited 2020-10-21 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain C 1–1342（1342 aa）
Not recorded 1N7 CHAPSO × 4 MG MAGNESIUM ION × 1 ZN ZINC ION × 3 G4P GUANOSINE-5',3'-TETRAPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.58 Å
7KHI Escherichia coli RNA polymerase and rrnBP1 promoter complex with DksA/ppGpp Deposited 2020-10-21 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain C 1–1342（1342 aa）
Not recorded 1N7 CHAPSO × 4 MG MAGNESIUM ION × 1 ZN ZINC ION × 3 G4P GUANOSINE-5',3'-TETRAPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å
7QV9 CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF Deposited 2022-01-20 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 1–1342（1342 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 5 AF3 ALUMINUM FLUORIDE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7QWP CryoEM structure of bacterial transcription close complex (RPc) Deposited 2022-01-25 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain C 1–1342（1342 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM Tris-HCl pH 8.0, 150 mM KCl, 10 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7QXI Cryo-EM structure of RNA polymerase-sigma54 holo enzyme with promoter DNA closed complex Deposited 2022-01-26 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain C 1–1342（1342 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM Tris-HCl pH 8.0, 150 mM KCl, 10 mM MgCl2,8 mM CHAPSO
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7SZJ Cryo-EM structure of Rifamycin bound to E. coli RNAP and rrnBP1 promoter complex Deposited 2021-11-28 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain C 1–1342（1342 aa）
Not recorded RFP RIFAMPICIN × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.11 Å
7SZK Cryo-EM structure of 27a bound to E. coli RNAP and rrnBP1 promoter complex Deposited 2021-11-28 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain C 1–1342（1342 aa）
Not recorded D9X (2S,7R,7aR,13aP,16Z,18E,20S,21S,22R,23R,24R,25S,26R,27S,28E)-5,21,23-trihydroxy-27-methoxy-2,4,16,20,22,24,26-heptamethyl-10-[4-(2-methylpropyl)piperazin-1-yl]-12-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1,6,15-trioxo-1,2,7,7a-tetrahydro-6H-2,7-(epoxypentadeca[1,11,13]trienoimino)[1]benzofuro[4,5-a]phenoxazin-25-yl acetate × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.94 Å
7VWY Cryo-EM structure of Rob-dependent transcription activation complex in a unique conformation Deposited 2021-11-12 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain C 1–1342（1342 aa）
Mutation：D516V ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.57 Å
7VWZ Cryo-EM structure of Rob-dependent transcription activation complex in a unique conformation Deposited 2021-11-12 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7W5W Cryo-EM structure of SoxS-dependent transcription activation complex with micF promoter DNA Deposited 2021-11-30 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain C 1–1342（1342 aa）
Mutation：D516V ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.55 Å
7W5X Cryo-EM structure of SoxS-dependent transcription activation complex with zwf promoter DNA Deposited 2021-11-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain C 1–1342（1342 aa）
Mutation：D516V No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7W5Y Cryo-EM structure of SoxS-dependent transcription activation complex with fpr promoter DNA Deposited 2021-11-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain C 1–1342（1342 aa）
Mutation：D516V No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7XUE Cryo-EM structure of HK022 putRNA-associated E.coli RNA polymerase elongation complex Deposited 2022-05-18 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain I 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；pH adjustment at 4'C
cryo-EM vitrification conditions Cryogen ETHANE；using two layers of blot papers
Resolution 3.17 Å
7XUG cryo-EM structure of HK022 putRNA-less E.coli RNA polymerase elongation complex Deposited 2022-05-18 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain I 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；pH adjustment at 4'C
cryo-EM vitrification conditions Cryogen ETHANE；using two layers of blot papers
Resolution 3.57 Å
7XUI Cryo-EM structure of sigma70 bound HK022 putRNA-associated E.coli RNA polymerase elongation complex Deposited 2022-05-18 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: octameric
Chain I 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；pH adjustment at 4'C
cryo-EM vitrification conditions Cryogen ETHANE；using two layers of blot papers
Resolution 3.61 Å
7YP9 Cryo-EM structure of Escherichia coli paused complex of transcription termination (TTC-pause) Deposited 2022-08-03 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain C 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.58 Å
7YPA Cryo-EM structure of Escherichia coli hairpin-nucleation complex of transcription termination (TTC-hairpin) Deposited 2022-08-03 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: nonameric
Chain C 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
7YPB Cryo-EM structure of Escherichia coli release complex of transcription termination (TTC-release) Deposited 2022-08-03 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: nonameric
Chain C 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.48 Å
8ABY RNA polymerase bound to purified in vitro transcribed regulatory RNA putL - pause prone, closed clamp state Deposited 2022-07-05 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain C 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM Tris-glutamate pH 8.0, 50 mM K-glutamate, 10 mM Mg-glutamate, 0.001 mM ZnCl2, 2mM DTT
cryo-EM vitrification conditions Cryogen ETHANE；Quantifoil UltrAuFoil R1.2/1.3 300 mesh holey gold grids were plasma cleaned on a Model 1070 (Fischione Instruments) for 30 sec at 70% power and with an 80% Argon and 20% Oxygen mixture prior to the application of 0.004 ml of sample. Grids were plunge frozen into liquid ethane using a Vitrobot mark IV (FEI) with 95% chamber humidity at 283K.
Resolution 3.70 Å
8ABZ RNA polymerase at U-rich pause bound to non-regulatory RNA - pause prone, closed clamp state Deposited 2022-07-05 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain C 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM Tris-glutamate pH 8.0, 50 mM K-glutamate, 10 mM Mg-glutamate, 0.001 mM ZnCl2, 2mM DTT
cryo-EM vitrification conditions Cryogen ETHANE；Quantifoil UltrAuFoil R1.2/1.3 300 mesh holey gold grids were plasma cleaned on a Model 1070 (Fischione Instruments) for 30 sec at 70% power and with an 80% Argon and 20% Oxygen mixture prior to the application of 0.004 ml of sample. Grids were plunge frozen into liquid ethane using a Vitrobot mark IV (FEI) with 95% chamber humidity at 283K.
Resolution 3.40 Å
8AC0 RNA polymerase at U-rich pause bound to regulatory RNA putL - active, closed clamp state Deposited 2022-07-05 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain C 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM Tris-glutamate pH 8.0, 50 mM K-glutamate, 10 mM Mg-glutamate, 0.001 mM ZnCl2, 2mM DTT
cryo-EM vitrification conditions Cryogen ETHANE；Quantifoil UltrAuFoil R1.2/1.3 300 mesh holey gold grids were plasma cleaned on a Model 1070 (Fischione Instruments) for 30 sec at 70% power and with an 80% Argon and 20% Oxygen mixture prior to the application of 0.004 ml of sample. Grids were plunge frozen into liquid ethane using a Vitrobot mark IV (FEI) with 95% chamber humidity at 283K.
Resolution 4.10 Å
8AC1 RNA polymerase at U-rich pause bound to non-regulatory RNA - inactive, open clamp state Deposited 2022-07-05 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain C 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM Tris-glutamate pH 8.0, 50 mM K-glutamate, 10 mM Mg-glutamate, 0.001 mM ZnCl2, 2mM DTT
cryo-EM vitrification conditions Cryogen ETHANE；Quantifoil UltrAuFoil R1.2/1.3 300 mesh holey gold grids were plasma cleaned on a Model 1070 (Fischione Instruments) for 30 sec at 70% power and with an 80% Argon and 20% Oxygen mixture prior to the application of 0.004 ml of sample. Grids were plunge frozen into liquid ethane using a Vitrobot mark IV (FEI) with 95% chamber humidity at 283K.
Resolution 4.06 Å
8AC2 RNA polymerase- post-terminated, open clamp state Deposited 2022-07-05 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric
Chain C 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM Tris-glutamate pH 8.0, 50 mM K-glutamate, 10 mM Mg-glutamate, 0.001 mM ZnCl2, 2mM DTT
cryo-EM vitrification conditions Cryogen ETHANE；Quantifoil UltrAuFoil R1.2/1.3 300 mesh holey gold grids were plasma cleaned on a Model 1070 (Fischione Instruments) for 30 sec at 70% power and with an 80% Argon and 20% Oxygen mixture prior to the application of 0.004 ml of sample. Grids were plunge frozen into liquid ethane using a Vitrobot mark IV (FEI) with 95% chamber humidity at 283K.
Resolution 3.70 Å
8ACP RNA polymerase at U-rich pause bound to regulatory RNA putL - inactive, open clamp state Deposited 2022-07-06 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain C 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM Tris-glutamate pH 8.0, 50 mM K-glutamate, 10 mM Mg-glutamate, 0.001 mM ZnCl2, 2mM DTT
cryo-EM vitrification conditions Cryogen ETHANE；Quantifoil UltrAuFoil R1.2/1.3 300 mesh holey gold grids were plasma cleaned on a Model 1070 (Fischione Instruments) for 30 sec at 70% power and with an 80% Argon and 20% Oxygen mixture prior to the application of 0.004 ml of sample. Grids were plunge frozen into liquid ethane using a Vitrobot mark IV (FEI) with 95% chamber humidity at 283K.
Resolution 4.50 Å
8AD1 RNA polymerase at U-rich pause bound to RNA putL triple mutant - pause prone, closed clamp state Deposited 2022-07-07 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain C 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM Tris-glutamate pH 8.0, 50 mM K-glutamate, 10 mM Mg-glutamate, 0.001 mM ZnCl2, 2mM DTT
cryo-EM vitrification conditions Cryogen ETHANE；Quantifoil UltrAuFoil R1.2/1.3 300 mesh holey gold grids were plasma cleaned on a Model 1070 (Fischione Instruments) for 30 sec at 70% power and with an 80% Argon and 20% Oxygen mixture prior to the application of 0.004 ml of sample. Grids were plunge frozen into liquid ethane using a Vitrobot mark IV (FEI) with 95% chamber humidity at 283K.
Resolution 4.10 Å
8F1I SigN RNA polymerase early-melted intermediate bound to mismatch fragment dhsU36mm1 (-12T) Deposited 2022-11-05 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: decameric
Chain I 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8F1J SigN RNA polymerase early-melted intermediate bound to mismatch DNA fragment dhsU36mm2 (-12A) Deposited 2022-11-05 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: decameric
Chain I 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8F1K SigN RNA polymerase early-melted intermediate bound to full duplex DNA fragment dhsU36 (-12T) Deposited 2022-11-05 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: decameric
Chain I 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8F3C Cryo-EM consensus structure of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase minus preQ1 ligand Deposited 2022-11-09 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain I 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION WAS CARRIED OUT IN A CHAMBER WITH THE TEMPERATURE SET TO 4 DEGREES CELSIUS.
Resolution 3.40 Å
8FIX Cryo-EM structure of E. coli RNA polymerase backtracked elongation complex harboring a terminal mismatch Deposited 2022-12-17 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain C 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8FIY Cryo-EM structure of E. coli RNA polymerase Elongation complex in the Transcription-Translation Complex (RNAP in an anti-swiveled conformation) Deposited 2022-12-17 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: heptameric
Chain C 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.30 Å
8FTD Structure of Escherichia coli CedA in complex with transcription initiation complex Deposited 2023-01-11 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain I 1–1342（1342 aa）
Not recorded 1N7 CHAPSO × 3 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.76 Å
8FVR CryoEM structure of E.coli transcription elongation complex Deposited 2023-01-19 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain F 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM HEPES, pH 8.0, 150 mM NaCl, 10 mM MgCl2, 10 uM ZnCl2, 5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.42 Å
8FVW CryoEM structure of E.coli transcription elongation complex bound to ppGpp Deposited 2023-01-19 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain F 1–1342（1342 aa）
Not recorded G4P GUANOSINE-5',3'-TETRAPHOSPHATE × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 2 NA SODIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM HEPES, pH 8.0, 150 mM NaCl, 10 mM MgCl2, 10 uM ZnCl2, 5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.10 Å
8G00 Cryo-EM structure of 3DVA component 0 of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase minus preQ1 ligand Deposited 2023-01-31 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain I 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION WAS CARRIED OUT IN A CHAMBER WITH THE TEMPERATURE SET TO 4 DEGREES CELSIUS.
Resolution 3.40 Å
8G1S Cryo-EM structure of 3DVA component 1 of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase minus preQ1 ligand Deposited 2023-02-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain I 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM TRIS-HCl, pH 7.5; 100 mM potassium chloride, 1mM
cryo-EM vitrification conditions Cryogen ETHANE；Vitrification was carried out in a chamber with the temperature set to 4 C.
Resolution 3.70 Å
8HKC Cryo-EM structure of E. coli RNAP sigma32 complex Deposited 2022-11-25 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric
Chain C 2–1342（1341 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.49 Å
8IGR Cryo-EM structure of CII-dependent transcription activation complex Deposited 2023-02-21 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain I 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8IGS Cryo-EM structure of RNAP-promoter open complex at lambda promoter PRE Deposited 2023-02-21 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric
Chain I 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8K58 The cryo-EM map of close TIEA-TEC complex Deposited 2023-07-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain C 3–1342（1340 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.15 Å
8K59 The cryo-EM map of TIC-TIEA complex Deposited 2023-07-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: decameric
Chain C 3–1342（1340 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8K5A The cryo-EM map of open TIEA-TEC complex Deposited 2023-07-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain C 3–1342（1340 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8PDY E. coli RNA polymerase paused at ops site Deposited 2023-06-13 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain I 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8PEN fully recruited RfaH bound to E. coli transcription complex paused at ops site (alternative state of RfaH) Deposited 2023-06-14 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain I 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8PFG autoinhibited RfaH bound to E. coli transcription complex paused at ops site (encounter complex), not fully complementary scaffold Deposited 2023-06-15 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain I 1–1342（1342 aa）
Not recorded ZN ZINC ION × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8PFJ fully recruited RfaH bound to E. coli transcription complex paused at ops site (not fully complementary scaffold; alternative state of RfaH) Deposited 2023-06-16 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain I 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8PH9 E. coli RNA polymerase paused at ops site (non-complementary scaffold) Deposited 2023-06-19 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain I 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8PHK fully recruited RfaH bound to E. coli transcription complex paused at ops site Deposited 2023-06-20 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain I 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8PIB autoinhibited RfaH bound to E. coli transcription complex paused at ops site (encounter complex) Deposited 2023-06-21 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain I 1–1342（1342 aa）
Not recorded ZN ZINC ION × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8PID backtracked E. coli transcription complex paused at ops site and bound to RfaH Deposited 2023-06-21 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain I 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8PIL E. coli transcription complex paused at ops site and bound to RfaH and NusA Deposited 2023-06-22 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: decameric
Chain I 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8PIM fully recruited RfaH bound to E. coli transcription complex paused at ops site (not complementary scaffold) Deposited 2023-06-22 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain I 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8RE4 Cryo-EM structure of bacterial RNA polymerase-sigma54 initial transcribing complex - 5nt pre-translocated complex Deposited 2023-12-10 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain C 1–1341（1341 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8REA Cryo-EM structure of bacterial RNA polymerase-sigma54 initial transcribing complex - 5nt post-translocated complex Deposited 2023-12-10 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain C 1–1341（1341 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8REB Cryo-EM structure of bacterial RNA polymerase-sigma54 initial transcribing complex - 6nt complex Deposited 2023-12-10 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain C 1–1341（1341 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8REC Cryo-EM structure of bacterial RNA polymerase-sigma54 initial transcribing complex - 7nt complex Deposited 2023-12-10 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain C 1–1341（1341 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8RED Cryo-EM structure of bacterial RNA polymerase-sigma54 initial transcribing complex - 8nt complex Deposited 2023-12-10 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain C 1–1341（1341 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8REE Cryo-EM structure of bacterial RNA polymerase-sigma54 initial transcribing complex - 9nt complex Deposited 2023-12-10 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain C 1–1341（1341 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8SY5 E. coli DNA-directed RNA polymerase transcription elongation complex bound the unnatural dS-BTP base pair in the active site Deposited 2023-05-24 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain I 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 X0F 2-oxo-2-hydroadenosine 5'-(tetrahydrogen triphosphate) × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20mM Tris (pH 8.0), 40mM KCl, 5mM DTT and 5mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8SY6 E. coli DNA-directed RNA polymerase transcription elongation complex bound the unnatural dB-UTP base pair in the active site Deposited 2023-05-24 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain I 1–1342（1342 aa）
Not recorded DGP 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 1 UTP URIDINE 5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20mM Tris (pH 8.0), 40mM KCl, 5mM DTT and 5mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.28 Å
8SY7 E. coli DNA-directed RNA polymerase transcription elongation complex bound the unnatural dB-STP base pair in the active site Deposited 2023-05-24 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain I 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 X0O [[(2~{R},3~{S},4~{R},5~{S})-5-(4-azanyl-1-methyl-2-oxidanylidene-pyrimidin-5-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20mM Tris (pH 8.0), 40mM KCl, 5mM DTT and 5mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.65 Å
8SZW Reconstituted E. coli RNA polymerase post-termination complex on negatively-supercoiled DNA: open duplex DNA (rPTCo) Deposited 2023-05-30 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric
Chain I 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.63 Å
8T02 Reconstituted E. coli RNA polymerase post-termination complex on negatively-supercoiled DNA: unwinding duplex DNA (rPTCi) Deposited 2023-05-31 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric
Chain I 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.79 Å
8TO1 Escherichia coli RNA polymerase unwinding intermediate (I1a) at the lambda PR promoter Deposited 2023-08-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain I 1–1342（1342 aa）
Not recorded 4QM (3R,5S,7R,8R,9S,10S,12S,13R,14S,17R)-10,13-dimethyl-17-[(2R)-pentan-2-yl]-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthrene-3,7,12-triol × 4 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；CHAPSO was added (from 80 mM stock) to 8 mM final in each sample just prior to spray mixing.
Resolution 2.80 Å
8TO6 Escherichia coli RNA polymerase unwinding intermediate (I1d) at the lambda PR promoter Deposited 2023-08-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain I 1–1342（1342 aa）
Not recorded 4QM (3R,5S,7R,8R,9S,10S,12S,13R,14S,17R)-10,13-dimethyl-17-[(2R)-pentan-2-yl]-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthrene-3,7,12-triol × 3 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；CHAPSO was added (from 80 mM stock) to 8 mM final in each sample just prior to spray mixing.
Resolution 2.90 Å
8TO8 Escherichia coli RNA polymerase unwinding intermediate (I1b) at the lambda PR promoter Deposited 2023-08-03 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain I 1–1342（1342 aa）
Not recorded 4QM (3R,5S,7R,8R,9S,10S,12S,13R,14S,17R)-10,13-dimethyl-17-[(2R)-pentan-2-yl]-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthrene-3,7,12-triol × 4 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；CHAPSO was added (from 80 mM stock) to 8 mM final in each sample just prior to spray mixing.
Resolution 2.90 Å
8TOE Escherichia coli RNA polymerase unwinding intermediate (I1c) at the lambda PR promoter Deposited 2023-08-03 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain I 1–1342（1342 aa）
Not recorded 1N7 CHAPSO × 3 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；CHAPSO was added (from 80 mM stock) to 8 mM final in each sample just prior to spray mixing.
Resolution 2.90 Å
8TOM Escherichia coli RNA polymerase closed complex intermediate at the lambda PR promoter Deposited 2023-08-03 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain I 1–1342（1342 aa）
Not recorded 1N7 CHAPSO × 4 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；CHAPSO was added (from 80 mM stock) to 8 mM final.
Resolution 3.10 Å
8TXO E. coli DNA-directed RNA polymerase transcription elongation complex bound to the unnatural dZ-PTP base pair in the active site Deposited 2023-08-23 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: heptameric
Chain I 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 S9F [[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-1$l^{4},3,5,7-tetrazabicyclo[4.3.0]nona-1(6),3,8-trien-7-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8U3B Cryo-EM structure of E. coli NarL-transcription activation complex at 3.2A Deposited 2023-09-07 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: 11-meric
Chain C 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
8UPO Escherichia coli transcription-translation coupled complex class A (TTC-A) containing RfaH bound to ops signal, mRNA with a 21 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome Deposited 2023-10-23 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 58 PDB declaration: 66-meric
Chain AA 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.50 Å
8UPR Escherichia coli transcription-translation coupled complex class A (TTC-A) containing RfaH bound to ops signal, mRNA with a 21 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome Deposited 2023-10-23 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 59 PDB declaration: 67-meric
Chain AA 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.30 Å
8UQL Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH in loaded state, mRNA with a 24 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome Deposited 2023-10-24 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 59 PDB declaration: 67-meric
Chain AA 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8UQM Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH in loaded state, NusA, mRNA with a 24 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome Deposited 2023-10-24 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 60 PDB declaration: 68-meric
Chain AA 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.30 Å
8UQP Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, mRNA with a 24 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome Deposited 2023-10-24 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 59 PDB declaration: 67-meric
Chain AA 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8UR0 Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, NusA, mRNA with a 24 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome Deposited 2023-10-25 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 60 PDB declaration: 68-meric
Chain AA 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8URH Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, mRNA with a 27 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome Deposited 2023-10-26 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 59 PDB declaration: 67-meric
Chain AA 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.70 Å
8URI Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, NusA, mRNA with a 27 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome Deposited 2023-10-26 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 60 PDB declaration: 68-meric
Chain AA 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.30 Å
8URX Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, mRNA with a 30 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome Deposited 2023-10-27 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 59 PDB declaration: 67-meric
Chain AA 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.60 Å
8URY Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, NusA, mRNA with a 30 nt long spacer, and fMet-tRNA in E-site and P-site of the ribosome Deposited 2023-10-27 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 60 PDB declaration: 68-meric
Chain AA 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8VKV Escherichia coli transcription-translation coupled complex (TTC-B) containing mRNA with a 33 nt long spacer, ops signal, RfaH, NusA, and fMet-tRNAs in E-site and P-site Deposited 2024-01-10 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 60 PDB declaration: 68-meric
Chain AA 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8VL1 Escherichia coli transcription-translation loosely coupled complex (TTC-LC) containing mRNA with a 36 nt long spacer, ops signal, RfaH, NusA, and fMet-tRNAs in E-site and P-site Deposited 2024-01-11 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 60 PDB declaration: 68-meric
Chain AA 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.30 Å
8VOO Escherichia coli transcription-translation loosely coupled complex (TTC-LC) containing mRNA with a 39 nt long spacer, ops signal, RfaH, NusA, and fMet-tRNAs in E-site and P-site Deposited 2024-01-15 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 60 PDB declaration: 68-meric
Chain AA 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8VOP Escherichia coli transcription-translation coupled complex (TTC-B) containing mRNA with a 36 nt long spacer, NusG, NusA, and fMet-tRNAs in E-site and P-site Deposited 2024-01-15 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 60 PDB declaration: 68-meric
Chain AA 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.00 Å
8VOQ Escherichia coli transcription-translation loosely coupled complex (TTC-LC) containing mRNA with a 39 nt long spacer, NusG, NusA, and fMet-tRNAs in E-site and P-site Deposited 2024-01-15 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 60 PDB declaration: 68-meric
Chain AA 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.30 Å
8VOR Escherichia coli transcription-translation loosely coupled complex (TTC-LC) containing mRNA with a 51 nt long spacer, NusG, NusA, and fMet-tRNAs in E-site and P-site Deposited 2024-01-15 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 60 PDB declaration: 68-meric
Chain AA 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8VOS Escherichia coli transcription-translation loosely coupled complex (TTC-LC) containing mRNA with a 60 nt long spacer, NusG, NusA, and fMet-tRNAs in E-site and P-site Deposited 2024-01-15 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 60 PDB declaration: 68-meric
Chain AA 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8Y5K E.coli transcription translation coupling complex in TTC-A state 2 containing mRNA with 27-mer spacer, NusG, NusA, fMet-tRNA(iMet), Phe-tRNA(Phe), and viomycin Deposited 2024-01-31 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 59 PDB declaration: 67-meric
Chain B2 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å
8Y5L E.coli transcription translation coupling complex in TTC-B state 1 (subclass1) containing mRNA with 30-mer spacer, NusG, NusA, fMet-tRNA(iMet), Phe-tRNA(Phe), and viomycin Deposited 2024-01-31 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 58 PDB declaration: 67-meric
Chain B2 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8Y5M E.coli transcription translation coupling complex in TTC-B state 2 containing mRNA with 27-mer spacer, NusG, NusA, fMet-tRNA(iMet), Phe-tRNA(Phe), and viomycin Deposited 2024-01-31 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 60 PDB declaration: 68-meric
Chain B2 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
8Y5N E.coli transcription translation coupling complex in TTC-A state 3 containing mRNA with 21-mer spacer, NusG, NusA, fMet-tRNA(iMet), Phe-tRNA(Phe), and viomycin Deposited 2024-01-31 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 59 PDB declaration: 67-meric
Chain B2 1–1342（1342 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
8Y5O E.coli transcription translation coupling complex in TTC-B state 3 (subclass1) containing mRNA with 30-mer spacer, NusG, NusA, fMet-tRNA(iMet), Phe-tRNA(Phe), and viomycin Deposited 2024-01-31 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 60 PDB declaration: 68-meric
Chain B2 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
8Y5P E.coli transcription translation coupling complex in TTC-B state 4 (subclass 1) containing mRNA with 24-mer spacer, NusG, NusA, fMet-tRNA(iMet), Phe-tRNA(Phe), and viomycin Deposited 2024-01-31 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 60 PDB declaration: 67-meric
Chain B2 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.50 Å
8Y5Q E.coli transcription translation coupling complex in TTC-B state 4 (subclass 2) containing mRNA with 27-mer spacer, NusG, NusA, fMet-tRNA(iMet), Phe-tRNA(Phe), and GDPCP Deposited 2024-01-31 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 59 PDB declaration: 66-meric
Chain B2 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8Y5R E.coli Transcription translation coupling complex in TTC-B state 5 (subclass 1) containing mRNA with 27-mer spacer, NusG, NusA, fMet-tRNA(iMet), Phe-tRNA(Phe), and fusidic acid Deposited 2024-01-31 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 58 PDB declaration: 66-meric
Chain B2 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 FUA FUSIDIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
8Y5S E.coli Transcription translation coupling complex in TTC-B state 5 (subclass 2) containing mRNA with 27-mer spacer, NusG, NusA, fMet-tRNA(iMet), Phe-tRNA(Phe), and GDPCP Deposited 2024-01-31 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 58 PDB declaration: 66-meric
Chain B2 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
8Y5T E.coli Transcription translation coupling complex in TTC-B state 5 (subclass 3) containing mRNA with 27-mer spacer, NusG, NusA, fMet-tRNA(iMet), Phe-tRNA(Phe), and fusidic acid Deposited 2024-01-31 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 58 PDB declaration: 66-meric
Chain B2 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 FUA FUSIDIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
8Y6U Cryo-EM structure of E.coli transcription initiation complex with transcription factor GcvA Deposited 2024-02-03 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain C 1–1342（1342 aa）
Mutation：D516V No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.97 Å
8YDE E.coli transcription translation coupling complex in TTC-B state 1 (subclass 3) containing mRNA with 39-mer spacer, NusG, NusA, fMet-tRNA(iMet), Phe-tRNA(Phe), and viomycin Deposited 2024-02-20 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 58 PDB declaration: 67-meric
Chain B2 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.00 Å
8YDF E.coli transcription translation coupling complex in TTC-B state 1 (subclass 2) containing mRNA with 39-mer spacer, NusG, NusA, fMet-tRNA(iMet), Phe-tRNA(Phe), and viomycin Deposited 2024-02-20 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 58 PDB declaration: 67-meric
Chain B2 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8YDG E.coli transcription translation coupling complex in TTC-B state 3 (subclass2) containing mRNA with 39-mer spacer, NusG, NusA, fMet-tRNA(iMet), Phe-tRNA(Phe), and viomycin Deposited 2024-02-20 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 60 PDB declaration: 68-meric
Chain B2 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
8YDH E.coli transcription translation coupling complex in TTC-P state 1 (subclass1) containing mRNA with 39-mer spacer, NusG, NusA, fMet-tRNA(iMet), Phe-tRNA(Phe), and viomycin Deposited 2024-02-20 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 58 PDB declaration: 67-meric
Chain B2 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.55 Å
8YDI E.coli transcription translation coupling complex in TTC-P state 1 (subclass 2) containing mRNA with 39-mer spacer, NusG, NusA, fMet-tRNA(iMet), Phe-tRNA(Phe), and viomycin Deposited 2024-02-20 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 58 PDB declaration: 67-meric
Chain B2 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8YDJ E.coli transcription translation coupling complex in TTC-P containing mRNA with 39-mer spacer, NusG, NusA, fMet-tRNA(iMet), Phe-tRNA(Phe), and viomycin Deposited 2024-02-20 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 60 PDB declaration: 68-meric
Chain B2 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
9GDA RNAP-TopoI complex on duplex scaffold Deposited 2024-08-05 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain C 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
9GDB RNAP-TopoI complex on bubble scaffold - consensus reconstruction Deposited 2024-08-05 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain C 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9GDC RNAP-TopoI complex on bubble scaffold - single-bubble configuration Deposited 2024-08-05 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain C 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
9GDD RNAP-TopoI complex on bubble scaffold - two-bubble configuration Deposited 2024-08-05 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain C 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
9GDE RNAP-TopoI complex on long-overhang scaffold - orientation 1 Deposited 2024-08-05 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain C 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
9GDH RNAP-TopoI complex on long-overhang scaffold - orientation 2 Deposited 2024-08-05 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain C 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
9GUR 30S mRNA delivery complex TEC resolved (TEC only) Deposited 2024-09-20 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain 3 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
9GUW 30S-TEC (TEC in expressome position) Inactive state 2 Deposited 2024-09-20 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 30-meric
Chain 3 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 118 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9GUX 30S-TEC (TEC in expressome position) Inactive state 1 Deposited 2024-09-20 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 27 PDB declaration: 31-meric
Chain 3 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 132 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9L0X Cryo-EM structure of E.coli transcription initiation complex with Escherichia phage Mu late transcription activator C Deposited 2024-12-13 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain C 1–1342（1342 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
9L0Y Cryo-EM structure of E.coli transcription initiation complex with Escherichia phage Mu middle transcription activator Mor Deposited 2024-12-13 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain C 1–1342（1342 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.78 Å
9MSE de novo SigN RNA polymerase transcription initiation intermediate with pre-catalytic bEBP state (RPi1 open ring) Deposited 2025-01-09 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 16-meric
Chain I 1–1342（1342 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 3 POP PYROPHOSPHATE 2- × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；40 mM Tris-HCl, pH 8/RT, 200 mM KCl, 10 mM MgCl2, 1 mM DTT; fluorinated fos-choline-8 (FC8F) added to a final concentration of 1.5 mM during grid preparation
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
9MSF de novo SigN RNA polymerase transcription initiation intermediate with post-catalytic bEBP state (RPi1 closed ring) Deposited 2025-01-09 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 16-meric
Chain I 1–1342（1342 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 5 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 POP PYROPHOSPHATE 2- × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；40 mM Tris-HCl, pH 8/RT, 200 mM KCl, 10 mM MgCl2, 1 mM DTT; fluorinated fos-choline-8 (FC8F) added to a final concentration of 1.5 mM during grid preparation
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
9MSG De novo SigN RNA polymerase transcription initiation intermediate with bound SigN-RII Deposited 2025-01-09 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain I 1–1342（1342 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 5 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 POP PYROPHOSPHATE 2- × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；40 mM Tris-HCl, pH 8/RT, 200 mM KCl, 10 mM MgCl2, 1 mM DTT; fluorinated fos-choline-8 (FC8F) added to a final concentration of 1.5 mM during grid preparation
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
9MSH de novo SigN RNA polymerase open complex (RPo) Deposited 2025-01-09 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain I 1–1342（1342 aa）
Not recorded POP PYROPHOSPHATE 2- × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；40 mM Tris-HCl, pH 8/RT, 200 mM KCl, 10 mM MgCl2, 1 mM DTT; fluorinated fos-choline-8 (FC8F) added to a final concentration of 1.5 mM during grid preparation
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9MSJ de novo SigN RNA polymerase NTP-bound open complex (RPo+2A) Deposited 2025-01-09 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain I 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；40 mM Tris-HCl, pH 8/RT, 200 mM KCl, 10 mM MgCl2, 1 mM DTT; fluorinated fos-choline-8 (FC8F) added to a final concentration of 1.5 mM during grid preparation
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9Q90 CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF Deposited 2025-02-26 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain C 1–1342（1342 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 5 AF3 ALUMINUM FLUORIDE × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9Q91 CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 6 Deposited 2025-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain C 1–1341（1341 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
9Q92 CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 5 Deposited 2025-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain C 1–1341（1341 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 5 AF3 ALUMINUM FLUORIDE × 5 MG MAGNESIUM ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.80 Å
9Q93 CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 4 Deposited 2025-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain C 1–1341（1341 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 5 AF3 ALUMINUM FLUORIDE × 5 MG MAGNESIUM ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.60 Å
9Q94 CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 3 Deposited 2025-02-26 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 1–1342（1342 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 5 AF3 ALUMINUM FLUORIDE × 5 MG MAGNESIUM ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.80 Å
9Q95 CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -10 to -1 Deposited 2025-02-26 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 1–1342（1342 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 5 AF3 ALUMINUM FLUORIDE × 5 MG MAGNESIUM ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.80 Å
9Q96 Cryo-EM Structure of Bacterial RNA polymerase-sigma54 transcription open complex with wild type sigma54, from RPi(-10-1) Deposited 2025-02-26 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain C 1–1342（1342 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
9Q97 CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 2 Deposited 2025-02-26 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 1–1342（1342 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 5 AF3 ALUMINUM FLUORIDE × 5 MG MAGNESIUM ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
9Q98 CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 1 Deposited 2025-02-26 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 1–1342（1342 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 5 AF3 ALUMINUM FLUORIDE × 5 MG MAGNESIUM ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.30 Å
9Y79 Escherichia coli transcription-translation loosely coupled complex (TTC-LC^walked) containing mRNA with a 39 nt long spacer, NusG, NusA, and fMet-tRNAs in E-site and P-site Deposited 2025-09-09 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 60 PDB declaration: 68-meric
Chain AA 1–1342（1342 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.20 Å
9YMU De novo initial transcribing RNA polymerase with 2-mer RNA and bound CTP / Michaelis complex (RPitc2+CTP) Deposited 2025-10-10 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain I 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 2 CTP CYTIDINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
9YMV De novo initial transcribing RNA polymerase with pretranslocated 3-mer RNA / product complex (RPitc3) Deposited 2025-10-10 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain I 1–1342（1342 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 POP PYROPHOSPHATE 2- × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
9YMW De novo initial transcribing RNA polymerase with 5-mer RNA CCAUC (RPitc5a) Deposited 2025-10-10 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain I 1–1342（1342 aa）
Not recorded POP PYROPHOSPHATE 2- × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
9YMX De novo initial transcribing RNA polymerase with 5-mer RNA AUCUA (RPitc5b) Deposited 2025-10-10 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain I 1–1342（1342 aa）
Not recorded POP PYROPHOSPHATE 2- × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
9YMY De novo initial transcribing RNA polymerase with 9-mer RNA (RPitc9) Deposited 2025-10-10 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain I 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9YN0 De novo initial transcribing RNA polymerase with sigma 70 region 1.1 bound (RPitc-s70_1.1) Deposited 2025-10-10 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain I 1–1342（1342 aa）
Not recorded POP PYROPHOSPHATE 2- × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9YNP Cryo-EM structure of Escherichia coli transcription initiation complex with GpA and pseudouridimycin (PUM) Deposited 2025-10-11 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain C 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 PUM (1S)-1,4-anhydro-5-[(N-carbamimidoylglycyl-N~2~-hydroxy-L-glutaminyl)amino]-5-deoxy-1-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-D-ribitol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.06 Å
9YNQ Cryo-EM structure of Escherichia coli transcription initiation complex with GpA and des-hydroxy pseudouridimycin (des-hydroxy PUM) Deposited 2025-10-11 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain C 1–1342（1342 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 A1CYH (1S)-1,4-anhydro-5-[(N-carbamimidoylglycyl-L-glutaminyl)amino]-5-deoxy-1-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-D-ribitol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.32 Å

219 other PDB entries and 240 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPOB_ECOLI
Isoform —
PDB entities 4
Chains and sequence ranges Author chain C； PDBConstruct 1–1342； UniProt 1–1342

;DNA-directed RNA polymerase subunit beta' ;

Escherichia coli

UniProt M9GTE2

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 9 DNA 2 PDB declaration: undecameric（11） Consistent with all polymer counts Chain D； UniProt 1–1407 Not recorded DNA (63-mer) × 1 Stringent starvation protein A × 2 （H4IXP2） DNA-directed RNA polymerase subunit alpha × 3 （F4VJT6） DNA-directed RNA polymerase subunit beta × 1 （P0A8V2） DNA-directed RNA polymerase subunit omega × 1 （T9C803） RNA polymerase sigma factor RpoD × 1 （Q0P6L9） DNA (63-mer) × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.68 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name M9GTE2_ECOLX
Isoform —
PDB entities 5
Chains and sequence ranges Author chain D； PDBConstruct 1–1407； UniProt 1–1407

DNA-directed RNA polymerase subunit omega

Escherichia coli

UniProt T9C803

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 9 DNA 2 PDB declaration: undecameric（11） Consistent with all polymer counts Chain E； UniProt 1–91 Not recorded DNA (63-mer) × 1 Stringent starvation protein A × 2 （H4IXP2） DNA-directed RNA polymerase subunit alpha × 3 （F4VJT6） DNA-directed RNA polymerase subunit beta × 1 （P0A8V2） ;DNA-directed RNA polymerase subunit beta' ; × 1 （M9GTE2） RNA polymerase sigma factor RpoD × 1 （Q0P6L9） DNA (63-mer) × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.68 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 7C97 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6VZ3 Escherichia coli transcription-translation complex D2 (TTC-D2) containing mRNA with a 27 nt long spacer Deposited 2020-02-27 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 56 PDB declaration: 65-meric
Chain AF 2–84（83 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.90 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name T9C803_ECOLX
Isoform —
PDB entities 6
Chains and sequence ranges Author chain E； PDBConstruct 1–91； UniProt 1–91

RNA polymerase sigma factor RpoD

Escherichia coli

UniProt Q0P6L9

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 9 DNA 2 PDB declaration: undecameric（11） Consistent with all polymer counts Chain F； UniProt 1–613 Not recorded DNA (63-mer) × 1 Stringent starvation protein A × 2 （H4IXP2） DNA-directed RNA polymerase subunit alpha × 3 （F4VJT6） DNA-directed RNA polymerase subunit beta × 1 （P0A8V2） ;DNA-directed RNA polymerase subunit beta' ; × 1 （M9GTE2） DNA-directed RNA polymerase subunit omega × 1 （T9C803） DNA (63-mer) × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.68 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 7C97 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6N57 Cryo-EM structure of Escherichia coli RNAP polymerase bound with TraR in conformation I Deposited 2018-11-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain L 1–613（613 aa）
Not recorded 1N7 CHAPSO × 4 ZN ZINC ION × 3 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6N58 Cryo-EM structure of Escherichia coli RNAP polymerase bound with TraR in conformation II Deposited 2018-11-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain L 1–613（613 aa）
Not recorded 1N7 CHAPSO × 4 MG MAGNESIUM ION × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.78 Å
6N60 Escherichia coli RNA polymerase sigma70-holoenzyme bound to upstream fork promoter DNA and Microcin J25 (MccJ25) Deposited 2018-11-23 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain F 1–613（613 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；295 K；0.1 M HEPES, pH 6.7, 0.2 M magnesium chloride, 7% w/v PEG3350, 4% v/v glycerol
Resolution 3.68 Å R-free 0.306
6N61 Escherichia coli RNA polymerase sigma70-holoenzyme bound to upstream fork promoter DNA and Capistruin Deposited 2018-11-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain F 1–613（613 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；295 K；0.1 M HEPES, pH 6.8, 0.2 M magnesium chloride, 7% w/v PEG3350, 4% v/v glycerol, 4% v/v ethylene glycol
Resolution 3.25 Å R-free 0.316
6N62 Escherichia coli RNA polymerase sigma70-holoenzyme bound to upstream fork promoter DNA Deposited 2018-11-24 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain F 1–613（613 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；295 K；0.1 M HEPES, pH 6.8, 0.2 M magnesium chloride, 7% w/v PEG3350, 4% v/v glycerol, 4% v/v ethylene glycol
Resolution 3.80 Å R-free 0.334
6OUL Cryo-EM structure of Escherichia coli RNAP polymerase bound to rpsTP2 promoter DNA Deposited 2019-05-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain L 1–613（613 aa）
Not recorded 1N7 CHAPSO × 3 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6P1K Cryo-EM structure of Escherichia coli sigma70 bound RNAP polymerase holoenzyme Deposited 2019-05-20 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain L 1–613（613 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.05 Å
6PSQ Escherichia coli RNA polymerase closed complex (TRPc) with TraR and rpsT P2 promoter Deposited 2019-07-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain L 1–613（613 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 3 1N7 CHAPSO × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6PSR Escherichia coli RNA polymerase promoter unwinding intermediate (TRPi1) with TraR and rpsT P2 promoter Deposited 2019-07-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain L 1–613（613 aa）
Not recorded 1N7 CHAPSO × 4 MG MAGNESIUM ION × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6PSS Escherichia coli RNA polymerase promoter unwinding intermediate (TRPi1.5a) with TraR and mutant rpsT P2 promoter Deposited 2019-07-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain L 1–613（613 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6PST Escherichia coli RNA polymerase promoter unwinding intermediate (TRPi1.5b) with TraR and mutant rpsT P2 promoter Deposited 2019-07-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain L 1–613（613 aa）
Not recorded ZN ZINC ION × 3 1N7 CHAPSO × 4 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6PSU Escherichia coli RNA polymerase promoter unwinding intermediate (TRPi2) with TraR and rpsT P2 promoter Deposited 2019-07-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain L 1–613（613 aa）
Not recorded ZN ZINC ION × 3 1N7 CHAPSO × 4 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6PSV Escherichia coli RNA polymerase promoter unwinding intermediate (TpreRPo) with TraR and rpsT P2 promoter Deposited 2019-07-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain L 1–613（613 aa）
Not recorded ZN ZINC ION × 3 1N7 CHAPSO × 4 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6PSW Escherichia coli RNA polymerase promoter unwinding intermediate (TRPo) with TraR and rpsT P2 promoter Deposited 2019-07-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain L 1–613（613 aa）
Not recorded 1N7 CHAPSO × 2 MG MAGNESIUM ION × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6VJS Escherichia coli RNA polymerase and ureidothiophene-2-carboxylic acid complex Deposited 2020-01-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain X 1–613（613 aa）
Not recorded QZY 3-{[benzyl(ethyl)carbamoyl]amino}-5-(4-phenoxyphenyl)thiophene-2-carboxylic acid × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；300 K；0.1M Hepes-NaOH (pH 8), 0.2M CaAcetate, 15% PEG400
Resolution 4.02 Å R-free 0.276
6VJS Escherichia coli RNA polymerase and ureidothiophene-2-carboxylic acid complex Deposited 2020-01-17 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain Y 1–613（613 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；300 K；0.1M Hepes-NaOH (pH 8), 0.2M CaAcetate, 15% PEG400
Resolution 4.02 Å R-free 0.276
6WMU E. coli RNAPs70-SspA-gadA DNA complex Deposited 2020-04-21 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: dodecameric
Chain F 1–613（613 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.18 Å
7BEG Structures of class I bacterial transcription complexes Deposited 2020-12-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain F 1–613（613 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM Tris pH 8, 50 mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7CHW Cryo-EM structure of an Escherichia coli RNAP-promoter open complex (RPo) Deposited 2020-07-06 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain F 1–613（613 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
Resolution 3.58 Å
7MKD Cryo-EM structure of Escherichia coli RNA polymerase bound to lambda PR promoter DNA (class 1) Deposited 2021-04-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain L 1–613（613 aa）
Not recorded 1N7 CHAPSO × 3 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7MKE Cryo-EM structure of Escherichia coli RNA polymerase bound to lambda PR promoter DNA (class 2) Deposited 2021-04-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain L 1–613（613 aa）
Not recorded 1N7 CHAPSO × 4 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7MKI Cryo-EM structure of Escherichia coli RNA polymerase bound to lambda PR (-5G to C) promoter DNA Deposited 2021-04-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain L 1–613（613 aa）
Not recorded 1N7 CHAPSO × 3 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7MKJ Cryo-EM structure of Escherichia coli RNA polymerase bound to T7A1 promoter DNA Deposited 2021-04-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain L 1–613（613 aa）
Not recorded 1N7 CHAPSO × 3 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7N4E Escherichia coli sigma 70-dependent paused transcription elongation complex Deposited 2021-06-04 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain F 1–613（613 aa）
Mutation：R541C, L607P ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7UBM Transcription antitermination complex: "pre-engaged" Qlambda-loading complex Deposited 2022-03-15 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: decameric
Chain F 1–613（613 aa）
Not recorded ZN ZINC ION × 3 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
7UBN Transcription antitermination complex: NusA-containing "engaged" Qlambda-loading complex Deposited 2022-03-15 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: undecameric
Chain F 1–613（613 aa）
Not recorded ZN ZINC ION × 3 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.36 Å
8FTD Structure of Escherichia coli CedA in complex with transcription initiation complex Deposited 2023-01-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain L 1–613（613 aa）
Not recorded 1N7 CHAPSO × 3 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.76 Å
8JO2 Structural basis of transcriptional activation by the OmpR/PhoB-family response regulator PmrA Deposited 2023-06-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain F 1–613（613 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.74 Å
8TO1 Escherichia coli RNA polymerase unwinding intermediate (I1a) at the lambda PR promoter Deposited 2023-08-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain L 1–613（613 aa）
Not recorded 4QM (3R,5S,7R,8R,9S,10S,12S,13R,14S,17R)-10,13-dimethyl-17-[(2R)-pentan-2-yl]-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthrene-3,7,12-triol × 4 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；CHAPSO was added (from 80 mM stock) to 8 mM final in each sample just prior to spray mixing.
Resolution 2.80 Å
8TO6 Escherichia coli RNA polymerase unwinding intermediate (I1d) at the lambda PR promoter Deposited 2023-08-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain L 1–613（613 aa）
Not recorded 4QM (3R,5S,7R,8R,9S,10S,12S,13R,14S,17R)-10,13-dimethyl-17-[(2R)-pentan-2-yl]-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthrene-3,7,12-triol × 3 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；CHAPSO was added (from 80 mM stock) to 8 mM final in each sample just prior to spray mixing.
Resolution 2.90 Å
8TOE Escherichia coli RNA polymerase unwinding intermediate (I1c) at the lambda PR promoter Deposited 2023-08-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain L 1–613（613 aa）
Not recorded 1N7 CHAPSO × 3 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；CHAPSO was added (from 80 mM stock) to 8 mM final in each sample just prior to spray mixing.
Resolution 2.90 Å
8TOM Escherichia coli RNA polymerase closed complex intermediate at the lambda PR promoter Deposited 2023-08-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain L 1–613（613 aa）
Not recorded 1N7 CHAPSO × 4 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；CHAPSO was added (from 80 mM stock) to 8 mM final.
Resolution 3.10 Å
8Y6U Cryo-EM structure of E.coli transcription initiation complex with transcription factor GcvA Deposited 2024-02-03 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain F 1–613（613 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.97 Å

32 other PDB entries and 33 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q0P6L9_ECOLX
Isoform —
PDB entities 7
Chains and sequence ranges Author chain F； PDBConstruct 1–613； UniProt 1–613

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 7c97

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7c97
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id7c97
Deposition date deposition_date2020-06-05
Structure title titleCryo-EM structure of an Escherichia coli RNAP-promoter open complex (RPo) with SspA
Keywords keywordsStringent starvation protein A, RNA polymerase, promoter escape, zinc binding domain, GENE REGULATION, TRANSFERASE-DNA complex; TRANSFERASE/DNA
Experimental Method methodELECTRON MICROSCOPY
▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier55.74 Å
Radius of gyration Rg (electron density) rg_electron55.10 Å
Forward intensity I(0) i03934560000.00
Molecular weight molecular_weight501010.0 kDa
Excluded volume excluded_volume617180 ų
Envelope volume envelope_volume950610 ų
Hydration-shell volume shell_volume138630 ų
Envelope diameter envelope_diameter189.8 Å
Shell Rg shell_rg61.82 Å
Envelope Rg envelope_rg54.08 Å
Shape Rg shape_rg55.09 Å
Total Rg total_rg55.27 Å
Total atoms total_atoms35581
Residues n_residues4275
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax179.8 Å
Rg (real space) rg_real55.51 Å
Rg uncertainty (real space) rg_real_error1.15 Å
I(0) (real space) i0_real3.9350e+09
I(0) uncertainty (real space) i0_real_error7.1020e+07
Rg (reciprocal space) rg_reciprocal55.92 Å
I(0) (reciprocal space) i0_reciprocal3937000000.0000
Solution quality estimate total_estimate0.8757
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary70.6 Å
Skewness Skewness skewness0.209
Kurtosis Kurtosis kurtosis-0.373
Angular range angular_range— – 0.1400 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha569100000.0000
Real-space data points n_real_points29
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.871; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.959; Smooth: 0.806
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (10)

▼

7. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id7c97A01
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology120 — RNA Polymerase Alpha Subunit; Chain A, domain 2
Homologous superfamily homologous superfamily12 — DNA-directed RNA polymerase, insert domain
Domain ID domain_id7c97B01
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology120 — RNA Polymerase Alpha Subunit; Chain A, domain 2
Homologous superfamily homologous superfamily12 — DNA-directed RNA polymerase, insert domain
Domain ID domain_id7c97C01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily150 — RNA polymerase II, Rpb2 subunit, wall domain
Domain ID domain_id7c97D01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology132 — Topoisomerase I; Chain A, domain 4
Homologous superfamily homologous superfamily30 — RNA polymerase Rpb1 funnel domain
Domain ID domain_id7c97D02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain
▶

8. Citations (1)

▶

9. Files and Curves (10)