DNA-directed RNA polymerase subunit beta
Escherichia coli
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Other combination Heteromer Protein × 6 DNA 2 RNA 1 PDB declaration: nonameric（9） Consistent with all polymer counts | Chain I； UniProt 1–1342 | Not recorded | DNA-directed RNA polymerase subunit omega × 1 （P0A800） Nascent RNA × 1 T7A1 promoter fragment non-template strand × 1 DNA-directed RNA polymerase subunit alpha × 2 （P0A7Z4） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P0A8T7） RNA polymerase sigma factor RpoD × 1 （P00579） T7A1 promoter fragment template strand × 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 2.70 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 9YMW | 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 oligomeric state Different ligand/ion 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 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 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 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 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 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 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 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 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 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 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 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 × 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 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 × 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 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 |
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 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 |
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 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 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 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 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 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 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 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 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 | 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 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 | 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 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 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 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 |
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 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：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 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）
|
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 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：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 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）
|
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 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 | 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 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：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 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：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 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：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 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：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 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 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 oligomeric state Different ligand/ion 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 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 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 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 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 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 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 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 × 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 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 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 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 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 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 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 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 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 |
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 oligomeric state Different ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 × 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 oligomeric state Different ligand/ion 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 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 | 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 | 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 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 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 |
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 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 |
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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 oligomeric state Different ligand/ion 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 |
| 7C97 Cryo-EM structure of an Escherichia coli RNAP-promoter open complex (RPo) with SspA Deposited 2020-06-05 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain C
1–1342（1342 aa）
|
Mutation：D516V | 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 |
| 7CHW Cryo-EM structure of an Escherichia coli RNAP-promoter open complex (RPo) Deposited 2020-07-06 | 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 | 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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）
|
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 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 |
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 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）
|
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 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）
|
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 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）
|
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 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 |
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 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 |
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 oligomeric state Different ligand/ion 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 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 | 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 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 | 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 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 | 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 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 | 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 oligomeric state Different ligand/ion 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 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 | 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 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 × 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 | 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 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 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 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 oligomeric state Different ligand/ion Different experimental conditions 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 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 |
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 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 × 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 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 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 × 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 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 |
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 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 × 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 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 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 × 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 oligomeric state Different ligand/ion 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 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 × 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion Different experimental conditions | 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 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 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 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 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 | 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 oligomeric state Different ligand/ion 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 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 | 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 oligomeric state Different ligand/ion 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 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 | 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 oligomeric state Different ligand/ion 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 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 | 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 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 | 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 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 | 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 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 | 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 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 | 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 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 | 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 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 | 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 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 | 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 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 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 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 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 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 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 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 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 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 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions 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 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 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 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 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 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 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 ligand/ion Different experimental conditions | 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 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 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 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 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 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 ligand/ion 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 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion Different experimental conditions | 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 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 oligomeric state Different ligand/ion Different experimental conditions | 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 oligomeric state 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 ligand/ion | 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 ligand/ion 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 |
| 9YMX De novo initial transcribing RNA polymerase with 5-mer RNA AUCUA (RPitc5b) Deposited 2025-10-10 | Parsed fields agree | 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 ligand/ion 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 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 ligand/ion 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 ligand/ion 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 | 1 |
| Chains and sequence ranges | Author chain I； PDBConstruct 1–1342； UniProt 1–1342 |
