RNA polymerase sigma factor RpoD
OrganismNot specified
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein–DNA Heteromer Protein × 6 DNA 2 PDB declaration: octameric（8） Consistent with all polymer counts | Chain F； UniProt 8–613 | Not recorded | DNA-directed RNA polymerase subunit beta × 1 （A0A0A0GWV9） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A0A369F490） DNA-directed RNA polymerase subunit alpha × 1 （P0A7Z4） DNA-directed RNA polymerase subunit alpha × 1 （P0A7Z4） DNA-directed RNA polymerase subunit omega × 1 （P0A800） DNA (94-MER) × 1 DNA (94-MER) × 1 | ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 | Resolution 17.00 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 6N4C | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1SIG CRYSTAL STRUCTURE OF A SIGMA70 SUBUNIT FRAGMENT FROM ESCHERICHIA COLI RNA POLYMERASE Deposited 1997-02-18 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
114–448（335 aa）
Fragment：RESIDUES 114 - 448
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.1；PROTEIN CRYSTALLIZED FROM 50 MM SODIUM ACETATE, 0.5-0.7 M LI2SO4, 5-7% (W/V) PEG 8000, 5 MM DTT, PH 5.1; TRANSFERRED IN EIGHT STEPS TO 50 MM SODIUM ACETATE, 0.5 M LI2SO4, 15% (W/V) PEG 8000, 17.5% GLYCEROL AND 10MM DTT, PH 5.1
|
Resolution 2.60 Å R-free 0.315 |
| 1TLH T4 AsiA bound to sigma70 region 4 Deposited 2004-06-09 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
533–613（81 aa）
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7；312 K；Ionic strength (raw mmCIF value) 150 mM NaCl；Pressure 1
NMR sample composition
0.7 mM protein, phosphate buffered saline, 50 mM sodium azide, 1 mM benzamidine hydrochloride | 97% H2O, 3% D2O
|
Resolution not provided |
| 2P7V Crystal structure of the Escherichia coli regulator of sigma 70, Rsd, in complex with sigma 70 domain 4 Deposited 2007-03-20 | 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 B
546–613（68 aa）
Fragment：domain 4
|
Not recorded | MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M KCl, 0.05 M MgCl2, 0.05 M Tris-HCl, pH 7.5, and 10% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.60 Å R-free 0.273 |
| 2P7V Crystal structure of the Escherichia coli regulator of sigma 70, Rsd, in complex with sigma 70 domain 4 Deposited 2007-03-20 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
546–613（68 aa）
Fragment：domain 4
|
Not recorded | MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M KCl, 0.05 M MgCl2, 0.05 M Tris-HCl, pH 7.5, and 10% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.60 Å R-free 0.273 |
| 3IYD Three-dimensional EM structure of an intact activator-dependent transcription initiation complex Deposited 2009-08-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain F
1–613（613 aa）
|
Not recorded | 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 |
| 3T72 PhoB(E)-Sigma70(4)-(RNAP-Betha-flap-tip-helix)-DNA Transcription Activation Sub-Complex Deposited 2011-07-29 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: pentameric |
Chain q
533–609（77 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；8-10% PEG 4000, 100 mM KCl, 10 mM magnesium chloride, 50 mM MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 4.33 Å |
| 3T72 PhoB(E)-Sigma70(4)-(RNAP-Betha-flap-tip-helix)-DNA Transcription Activation Sub-Complex Deposited 2011-07-29 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Insufficient information Heteromer；Protein × 3 PDB declaration: pentameric |
Chain o
533–609（77 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；8-10% PEG 4000, 100 mM KCl, 10 mM magnesium chloride, 50 mM MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 4.33 Å |
| 4JK1 X-ray crystal structure of Escherichia coli sigma70 holoenzyme in complex with Guanosine tetraphosphate (ppGpp) Deposited 2013-03-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain X
1–613（613 aa）
|
Not recorded | 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 construct 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 Y
1–613（613 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain X
1–613（613 aa）
|
Not recorded | 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 construct 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 Y
1–613（613 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 |
| 4JKR Crystal Structure of E. coli RNA Polymerase in complex with ppGpp Deposited 2013-03-11 | Different construct 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 F
1–613（613 aa）
|
Not recorded | SR STRONTIUM ION × 6 G4P GUANOSINE-5',3'-TETRAPHOSPHATE × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；20% PEG400, 0.18M strontium chloride, 0.1M HEPES , pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 4.20 Å R-free 0.318 |
| 4JKR Crystal Structure of E. coli RNA Polymerase in complex with ppGpp Deposited 2013-03-11 | Different construct 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 L
1–613（613 aa）
|
Not recorded | SR STRONTIUM ION × 2 G4P GUANOSINE-5',3'-TETRAPHOSPHATE × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；20% PEG400, 0.18M strontium chloride, 0.1M HEPES , pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 4.20 Å R-free 0.318 |
| 4KMU X-ray crystal structure of the Escherichia coli RNA polymerase in complex with Rifampin Deposited 2013-05-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain X
1–613（613 aa）
|
Not recorded | 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 construct 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 Y
1–613（613 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain X
1–613（613 aa）
|
Not recorded | 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 construct 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 Y
1–613（613 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain X
1–613（613 aa）
|
Not recorded | 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 construct 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 Y
1–613（613 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 |
| 4LJZ Crystal Structure Analysis of the E.coli holoenzyme Deposited 2013-07-05 | Different construct 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 F
92–613（522 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；0.1 M MES, 0.1 M calcium acetate, 12-15% PEG 400, 5 mM dithiothreitol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 3.59 Å R-free 0.288 |
| 4LJZ Crystal Structure Analysis of the E.coli holoenzyme Deposited 2013-07-05 | Different construct 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 L
92–613（522 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；0.1 M MES, 0.1 M calcium acetate, 12-15% PEG 400, 5 mM dithiothreitol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 3.59 Å R-free 0.288 |
| 4LK0 Crystal Structure Analysis of the E.coli holoenzyme/T7 Gp2 complex Deposited 2013-07-05 | Different construct 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 F
92–613（522 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；0.1 M MES, 0.1 M calcium acetate, 12-15% PEG 400, 5 mM dithiothreitol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 3.91 Å R-free 0.260 |
| 4LK0 Crystal Structure Analysis of the E.coli holoenzyme/T7 Gp2 complex Deposited 2013-07-05 | Different construct 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 L
92–613（522 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；0.1 M MES, 0.1 M calcium acetate, 12-15% PEG 400, 5 mM dithiothreitol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 3.91 Å R-free 0.260 |
| 4LK1 Crystal Structure Analysis of the E.coli holoenzyme Deposited 2013-07-05 | Different construct 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 F
1–613（613 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；0.1 M MES, pH 6, 0.1 M calcium acetate, 12-15% PEG 400, 5 mM dithiothreitol, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 3.84 Å R-free 0.272 |
| 4LK1 Crystal Structure Analysis of the E.coli holoenzyme Deposited 2013-07-05 | Different construct 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 L
1–613（613 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；0.1 M MES, pH 6, 0.1 M calcium acetate, 12-15% PEG 400, 5 mM dithiothreitol, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 3.84 Å R-free 0.272 |
| 4LLG Crystal Structure Analysis of the E.coli holoenzyme/Gp2 complex Deposited 2013-07-09 | Different construct 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 F
1–613（613 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；0.1 M MES, 0.1 M calcium acetate, 12-15% PEG 400, 5 mM dithiothreitol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 3.79 Å R-free 0.282 |
| 4LLG Crystal Structure Analysis of the E.coli holoenzyme/Gp2 complex Deposited 2013-07-09 | Different construct 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 L
1–613（613 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；0.1 M MES, 0.1 M calcium acetate, 12-15% PEG 400, 5 mM dithiothreitol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 3.79 Å R-free 0.282 |
| 4MEX Crystal structure of Escherichia coli RNA polymerase in complex with salinamide A Deposited 2013-08-27 | Different construct 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 F
1–613（613 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 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 construct 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 L
1–613（613 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 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 construct 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 F
1–613（613 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 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 construct 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 L
1–613（613 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 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 |
| 4XSX Crystal structure of CBR 703 bound to Escherichia coli RNA polymerase holoenzyme Deposited 2015-01-22 | Different construct 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 F
92–613（522 aa）
Fragment：unp residues 92-613
|
Not recorded | 42S 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 6；295 K；MES, calcium acetate, PEG 400
|
Resolution 3.71 Å R-free 0.273 |
| 4XSX Crystal structure of CBR 703 bound to Escherichia coli RNA polymerase holoenzyme Deposited 2015-01-22 | Different construct 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 L
92–613（522 aa）
Fragment：unp residues 92-613
|
Not recorded | 42S 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 6；295 K；MES, calcium acetate, PEG 400
|
Resolution 3.71 Å R-free 0.273 |
| 4XSY Crystal structure of CBR 9379 bound to Escherichia coli RNA polymerase holoenzyme Deposited 2015-01-22 | Different construct 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 F
92–613（522 aa）
Fragment：unp residues 92-613
|
Not recorded | 42T 3-{[(2,6-dichlorophenyl)carbamoyl]amino}-N-hydroxy-N'-phenyl-5-(trifluoromethyl)benzenecarboximidamide × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；MES, calcium acetate, PEG 400
|
Resolution 4.01 Å R-free 0.270 |
| 4XSY Crystal structure of CBR 9379 bound to Escherichia coli RNA polymerase holoenzyme Deposited 2015-01-22 | Different construct 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 L
92–613（522 aa）
Fragment：unp residues 92-613
|
Not recorded | 42T 3-{[(2,6-dichlorophenyl)carbamoyl]amino}-N-hydroxy-N'-phenyl-5-(trifluoromethyl)benzenecarboximidamide × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；MES, calcium acetate, PEG 400
|
Resolution 4.01 Å R-free 0.270 |
| 4XSZ Crystal structure of CBR 9393 bound to Escherichia coli RNA polymerase holoenzyme Deposited 2015-01-22 | Different construct 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 F
92–613（522 aa）
Fragment：unp residues 92-613
|
Not recorded | 42U 4-[3-(4-fluorophenyl)-1H-pyrazol-4-yl]-N-[2-(piperazin-1-yl)ethyl]-2-(trifluoromethyl)aniline × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；MES, calcium acetate, PEG 400
|
Resolution 3.68 Å R-free 0.286 |
| 4XSZ Crystal structure of CBR 9393 bound to Escherichia coli RNA polymerase holoenzyme Deposited 2015-01-22 | Different construct 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 L
92–613（522 aa）
Fragment：unp residues 92-613
|
Not recorded | 42U 4-[3-(4-fluorophenyl)-1H-pyrazol-4-yl]-N-[2-(piperazin-1-yl)ethyl]-2-(trifluoromethyl)aniline × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；MES, calcium acetate, PEG 400
|
Resolution 3.68 Å R-free 0.286 |
| 4YFK Escherichia coli RNA polymerase in complex with squaramide compound 8. Deposited 2015-02-25 | Different construct 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 F
1–613（613 aa）
|
Not recorded | MG MAGNESIUM ION × 2 ZN ZINC ION × 2 4C6 3,5-dimethyl-N-{2-[4-(4-methylbenzyl)piperidin-1-yl]-3,4-dioxocyclobut-1-en-1-yl}-1,2-oxazole-4-sulfonamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；300 K；0.1M HEPES-HCL, 0.2M CaACETATE, 15% PEG400
|
Resolution 3.57 Å R-free 0.252 |
| 4YFK Escherichia coli RNA polymerase in complex with squaramide compound 8. Deposited 2015-02-25 | Different construct 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 L
1–613（613 aa）
|
Not recorded | MG MAGNESIUM ION × 2 ZN ZINC ION × 2 4C6 3,5-dimethyl-N-{2-[4-(4-methylbenzyl)piperidin-1-yl]-3,4-dioxocyclobut-1-en-1-yl}-1,2-oxazole-4-sulfonamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；300 K；0.1M HEPES-HCL, 0.2M CaACETATE, 15% PEG400
|
Resolution 3.57 Å R-free 0.252 |
| 4YFN Escherichia coli RNA polymerase in complex with squaramide compound 14 (N-[3,4-dioxo-2-(4-{[4-(trifluoromethyl)benzyl]amino}piperidin-1-yl)cyclobut-1-en-1-yl]-3,5-dimethyl-1,2-oxazole-4-sulfonamide) Deposited 2015-02-25 | Different construct 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 F
1–613（613 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 4C2 N-[3,4-dioxo-2-(4-{[4-(trifluoromethyl)benzyl]amino}piperidin-1-yl)cyclobut-1-en-1-yl]-3,5-dimethyl-1,2-oxazole-4-sulfonamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；300 K；0.1M HEPES-HCL (PH7), 0.2M CaACETATE, 15% PEG400
|
Resolution 3.82 Å R-free 0.270 |
| 4YFN Escherichia coli RNA polymerase in complex with squaramide compound 14 (N-[3,4-dioxo-2-(4-{[4-(trifluoromethyl)benzyl]amino}piperidin-1-yl)cyclobut-1-en-1-yl]-3,5-dimethyl-1,2-oxazole-4-sulfonamide) Deposited 2015-02-25 | Different construct 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 L
1–613（613 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 4C2 N-[3,4-dioxo-2-(4-{[4-(trifluoromethyl)benzyl]amino}piperidin-1-yl)cyclobut-1-en-1-yl]-3,5-dimethyl-1,2-oxazole-4-sulfonamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；300 K；0.1M HEPES-HCL (PH7), 0.2M CaACETATE, 15% PEG400
|
Resolution 3.82 Å R-free 0.270 |
| 4YFX Escherichia coli RNA polymerase in complex with Myxopyronin B Deposited 2015-02-25 | Different construct 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 F
1–613（613 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 4C4 Myxopyronin B × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；300 K；0.1M HEPES-HCL , 0.2M CaACETATE, 15% PEG400
|
Resolution 3.84 Å R-free 0.300 |
| 4YFX Escherichia coli RNA polymerase in complex with Myxopyronin B Deposited 2015-02-25 | Different construct 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 L
1–613（613 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；300 K；0.1M HEPES-HCL , 0.2M CaACETATE, 15% PEG400
|
Resolution 3.84 Å R-free 0.300 |
| 4YG2 X-ray crystal structur of Escherichia coli RNA polymerase sigma70 holoenzyme Deposited 2015-02-25 | Different construct 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 F
1–613（613 aa）
|
Not recorded | MG MAGNESIUM ION × 2 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；300 K；0.1M HEPES-HCL (PH7), 0.2M CaACETATE, 15% PEG400
|
Resolution 3.70 Å R-free 0.260 |
| 4YG2 X-ray crystal structur of Escherichia coli RNA polymerase sigma70 holoenzyme Deposited 2015-02-25 | Different construct 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 L
1–613（613 aa）
|
Not recorded | MG MAGNESIUM ION × 2 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；300 K；0.1M HEPES-HCL (PH7), 0.2M CaACETATE, 15% PEG400
|
Resolution 3.70 Å R-free 0.260 |
| 4YLN E. coli Transcription Initiation Complex - 17-bp spacer and 4-nt RNA Deposited 2015-03-05 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric |
Chain F
1–613（613 aa）
|
Not recorded | ZN ZINC ION × 2 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；7% PEG3350, 150 mM magnesium chloride, 100 mM HEPES sodium, pH 7.0
|
Resolution 5.50 Å R-free 0.328 |
| 4YLN E. coli Transcription Initiation Complex - 17-bp spacer and 4-nt RNA Deposited 2015-03-05 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 6 PDB declaration: nonameric |
Chain L
1–613（613 aa）
|
Not recorded | ZN ZINC ION × 2 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；7% PEG3350, 150 mM magnesium chloride, 100 mM HEPES sodium, pH 7.0
|
Resolution 5.50 Å R-free 0.328 |
| 4YLN E. coli Transcription Initiation Complex - 17-bp spacer and 4-nt RNA Deposited 2015-03-05 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Other combination Heteromer；Protein × 6 PDB declaration: nonameric |
Chain R
1–613（613 aa）
|
Not recorded | ZN ZINC ION × 2 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；7% PEG3350, 150 mM magnesium chloride, 100 mM HEPES sodium, pH 7.0
|
Resolution 5.50 Å R-free 0.328 |
| 4YLO E. coli Transcription Initiation Complex - 16-bp spacer and 4-nt RNA Deposited 2015-03-05 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric |
Chain F
1–613（613 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；7% PEG3350, 150 mM magnesium chloride, 100 mM HEPES sodium, pH 7.0
|
Resolution 6.00 Å R-free 0.314 |
| 4YLO E. coli Transcription Initiation Complex - 16-bp spacer and 4-nt RNA Deposited 2015-03-05 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 6 PDB declaration: nonameric |
Chain L
1–613（613 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；7% PEG3350, 150 mM magnesium chloride, 100 mM HEPES sodium, pH 7.0
|
Resolution 6.00 Å R-free 0.314 |
| 4YLO E. coli Transcription Initiation Complex - 16-bp spacer and 4-nt RNA Deposited 2015-03-05 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Other combination Heteromer；Protein × 6 PDB declaration: nonameric |
Chain R
1–613（613 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；7% PEG3350, 150 mM magnesium chloride, 100 mM HEPES sodium, pH 7.0
|
Resolution 6.00 Å R-free 0.314 |
| 4YLP E. coli Transcription Initiation Complex - 16-bp spacer and 5-nt RNA Deposited 2015-03-05 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric |
Chain F
1–613（613 aa）
|
Not recorded | ZN ZINC ION × 2 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；7% PEG3350, 150 mM magnesium chloride, 100 mM HEPES sodium, pH 7.0
|
Resolution 5.50 Å R-free 0.313 |
| 4YLP E. coli Transcription Initiation Complex - 16-bp spacer and 5-nt RNA Deposited 2015-03-05 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 6 PDB declaration: nonameric |
Chain L
1–613（613 aa）
|
Not recorded | ZN ZINC ION × 2 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；7% PEG3350, 150 mM magnesium chloride, 100 mM HEPES sodium, pH 7.0
|
Resolution 5.50 Å R-free 0.313 |
| 4YLP E. coli Transcription Initiation Complex - 16-bp spacer and 5-nt RNA Deposited 2015-03-05 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Other combination Heteromer；Protein × 6 PDB declaration: nonameric |
Chain R
1–613（613 aa）
|
Not recorded | ZN ZINC ION × 2 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；7% PEG3350, 150 mM magnesium chloride, 100 mM HEPES sodium, pH 7.0
|
Resolution 5.50 Å R-free 0.313 |
| 4ZH2 Crystal structure of Escherichia coli RNA polymerase in complex with CBR703 Deposited 2015-04-24 | Different construct 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 F
1–613（613 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 construct 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 L
1–613（613 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 construct 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 F
1–613（613 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 construct 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 L
1–613（613 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 construct 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 F
1–613（613 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 construct 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 L
1–613（613 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 |
| 5UAC Escherichia coli RNA polymerase and Rifampin complex, wild-type Deposited 2016-12-19 | Different construct 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 F
1–613（613 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 construct 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 L
1–613（613 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；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 construct 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 F
1–613（613 aa）
|
Not recorded | 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 construct 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 L
1–613（613 aa）
|
Not recorded | 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 construct 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 F
1–613（613 aa）
|
Not recorded | 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 construct 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 L
1–613（613 aa）
|
Not recorded | 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 construct 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 F
1–613（613 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；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 construct 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 L
1–613（613 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；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 construct 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 F
1–613（613 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；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 construct 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 L
1–613（613 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；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 construct 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 F
1–613（613 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；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 construct 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 L
1–613（613 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；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 construct 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 F
1–613（613 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 construct 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 L
1–613（613 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 6 PDB declaration: heptameric |
Chain L
94–613（520 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 construct 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 F
1–613（613 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 construct 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 L
1–613（613 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 construct 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 F
1–613（613 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 construct 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 L
1–613（613 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 |
| 6B6H The cryo-EM structure of a bacterial class I transcription activation complex Deposited 2017-10-02 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: dodecameric |
Chain F
1–613（613 aa）
|
Not recorded | ZN ZINC ION × 2 MG MAGNESIUM ION × 1 CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20 mM TRIS pH 7.5, 50 mM sodium chloride, 0.1mM EDTA, 5 mM MgCl2, 5 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE；3 second blotting
|
Resolution 3.90 Å |
| 6BYU X-ray crystal structure of Escherichia coli RNA polymerase (RpoB-H526Y) and ppApp complex Deposited 2017-12-21 | Different construct 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 F
1–613（613 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 construct 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 L
1–613（613 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 |
| 6C9Y Cryo-EM structure of E. coli RNAP sigma70 holoenzyme Deposited 2018-01-29 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain F
1–613（613 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.25 Å |
| 6CA0 Cryo-EM structure of E. coli RNAP sigma70 open complex Deposited 2018-01-29 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: decameric |
Chain F
1–613（613 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.75 Å |
| 6CUX Escherichia coli RpoB S531L mutant RNA polymerase holoenzyme in complex with Kanglemycin A Deposited 2018-03-26 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain F
1–613（613 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 construct 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 L
1–613（613 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；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 |
| 6JNX Cryo-EM structure of a Q-engaged arrested complex Deposited 2019-03-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: undecameric |
Chain F
1–613（613 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.08 Å |
| 6K4Y CryoEM structure of sigma appropriation complex Deposited 2019-05-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain F
1–613（613 aa）
|
Not recorded | 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 |
| 6LDI The cryo-EM structure of E. coli CueR transcription activation complex Deposited 2019-11-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: undecameric |
Chain F
1–613（613 aa）
|
Not recorded | ZN ZINC ION × 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 |
| 6P18 Q21 transcription antitermination complex: loading complex Deposited 2019-05-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: undecameric |
Chain F
1–613（613 aa）
|
Mutation：R541C, L607P | 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 |
| 6PB4 The E. coli class-II CAP-dependent transcription activation complex with de novo RNA transcript at the state 2 Deposited 2019-06-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: undecameric |
Chain F
1–613（613 aa）
|
Not recorded | ZN ZINC ION × 2 MG MAGNESIUM ION × 1 CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 3 seconds before plunging
|
Resolution 4.35 Å |
| 6PB5 The E. coli class-II CAP-dependent transcription activation complex at the state 1 architecture Deposited 2019-06-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain F
1–613（613 aa）
|
Not recorded | ZN ZINC ION × 2 MG MAGNESIUM ION × 1 CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 3 seconds before plunging
|
Resolution 4.52 Å |
| 6PB6 The E. coli class-II CAP-dependent transcription activation complex at the state 2 Deposited 2019-06-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain F
1–613（613 aa）
|
Not recorded | ZN ZINC ION × 2 MG MAGNESIUM ION × 1 CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 3 seconds before plunging
|
Resolution 4.29 Å |
| 6XH7 CueR-TAC without RNA Deposited 2020-06-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain F
1–613（613 aa）
|
Not recorded | ZN ZINC ION × 2 CU COPPER (II) ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 6XH8 CueR-transcription activation complex with RNA transcript Deposited 2020-06-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: undecameric |
Chain F
1–613（613 aa）
|
Not recorded | ZN ZINC ION × 2 CU COPPER (II) ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 6XL5 Cryo-EM structure of EcmrR-RNAP-promoter open complex (EcmrR-RPo) Deposited 2020-06-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain F
1–613（613 aa）
|
Not recorded | 1N7 CHAPSO × 5 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 118 TETRAPHENYLANTIMONIUM ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.50 Å |
| 6XL9 Cryo-EM structure of EcmrR-RNAP-promoter initial transcribing complex with 3-nt RNA transcript (EcmrR-RPitc-3nt) Deposited 2020-06-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: decameric |
Chain F
1–613（613 aa）
|
Not recorded | ZN ZINC ION × 2 MG MAGNESIUM ION × 2 118 TETRAPHENYLANTIMONIUM ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.50 Å |
| 6XLJ Cryo-EM structure of EcmrR-RNAP-promoter initial transcribing complex with 4-nt RNA transcript (EcmrR-RPitc-4nt) Deposited 2020-06-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: undecameric |
Chain F
1–613（613 aa）
|
Not recorded | 1N7 CHAPSO × 5 118 TETRAPHENYLANTIMONIUM ION × 3 MG MAGNESIUM ION × 2 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 6XLL Cryo-EM structure of E. coli RNAP-promoter initial transcribing complex with 5-nt RNA transcript (RPitc-5nt) Deposited 2020-06-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric |
Chain F
1–613（613 aa）
|
Not recorded | 1N7 CHAPSO × 2 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 6XLM Cryo-EM structure of E.coli RNAP-DNA elongation complex 1 (RDe1) in EcmrR-dependent transcription Deposited 2020-06-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric |
Chain F
1–613（613 aa）
|
Not recorded | 1N7 CHAPSO × 2 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 |
| 7BEF Structures of class II bacterial transcription complexes Deposited 2020-12-23 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric |
Chain F
1–613（613 aa）
|
Not recorded | 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain F
1–613（613 aa）
|
Not recorded | 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 |
| 7DY6 A refined cryo-EM structure of an Escherichia coli RNAP-promoter open complex (RPo) with SspA Deposited 2021-01-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain F
1–613（613 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 |
| 7KHB Escherichia coli RNA polymerase and rrnBP1 promoter open complex Deposited 2020-10-20 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric |
Chain F
1–613（613 aa）
|
Not recorded | 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: decameric |
Chain F
1–613（613 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric |
Chain F
1–613（613 aa）
|
Not recorded | 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric |
Chain F
1–613（613 aa）
|
Not recorded | 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 |
| 7SZJ Cryo-EM structure of Rifamycin bound to E. coli RNAP and rrnBP1 promoter complex Deposited 2021-11-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric |
Chain F
1–613（613 aa）
|
Not recorded | 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 construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric |
Chain F
1–613（613 aa）
|
Not recorded | 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric |
Chain F
1–613（613 aa）
|
Not recorded | 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain F
1–613（613 aa）
|
Not recorded | 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric |
Chain F
1–613（613 aa）
|
Not recorded | 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 construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric |
Chain F
1–613（613 aa）
|
Not recorded | 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 construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric |
Chain F
1–613（613 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 7XUI Cryo-EM structure of sigma70 bound HK022 putRNA-associated E.coli RNA polymerase elongation complex Deposited 2022-05-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: octameric |
Chain L
1–613（613 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 |
| 8AD1 RNA polymerase at U-rich pause bound to RNA putL triple mutant - pause prone, closed clamp state Deposited 2022-07-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric |
Chain F
1–613（613 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 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 |
| 8IGR Cryo-EM structure of CII-dependent transcription activation complex Deposited 2023-02-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain L
1–613（613 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 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 L
1–613（613 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 |
| 8K59 The cryo-EM map of TIC-TIEA complex Deposited 2023-07-21 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: decameric |
Chain F
90–612（523 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 |
| 8TO8 Escherichia coli RNA polymerase unwinding intermediate (I1b) at the lambda PR promoter Deposited 2023-08-03 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric |
Chain L
1–613（613 aa）
|
Not recorded | 4QM (3R,5S,7R,8R,9S,10S,12S,13R,14S,17R)-10,13-dimethyl-17-[(2R)-pentan-2-yl]-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthrene-3,7,12-triol × 4 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；CHAPSO was added (from 80 mM stock) to 8 mM final in each sample just prior to spray mixing.
|
Resolution 2.90 Å |
| 8U3B Cryo-EM structure of E. coli NarL-transcription activation complex at 3.2A Deposited 2023-09-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: 11-meric |
Chain F
1–613（613 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 |
| 9L0X Cryo-EM structure of E.coli transcription initiation complex with Escherichia phage Mu late transcription activator C Deposited 2024-12-13 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric |
Chain F
1–613（613 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 construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric |
Chain F
1–613（613 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 |
| 9W3G Cryo-EM structure of E. coli RNA polymerase in complex with VP1 Deposited 2025-07-29 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain F
1–613（613 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 9YMU De novo initial transcribing RNA polymerase with 2-mer RNA and bound CTP / Michaelis complex (RPitc2+CTP) Deposited 2025-10-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric |
Chain L
1–613（613 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric |
Chain L
1–613（613 aa）
|
Not recorded | ATP ADENOSINE-5'-TRIPHOSPHATE × 1 POP PYROPHOSPHATE 2- × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 9YMW De novo initial transcribing RNA polymerase with 5-mer RNA CCAUC (RPitc5a) Deposited 2025-10-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric |
Chain L
1–613（613 aa）
|
Not recorded | POP PYROPHOSPHATE 2- × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 9YMX De novo initial transcribing RNA polymerase with 5-mer RNA AUCUA (RPitc5b) Deposited 2025-10-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric |
Chain L
1–613（613 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric |
Chain L
1–613（613 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric |
Chain L
1–613（613 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric |
Chain F
1–613（613 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric |
Chain F
1–613（613 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 |
91 other PDB entries and 132 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | RPOD_ECOLI |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain F； PDBConstruct 1–558； UniProt 8–613 |
