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6xll

Cryo-EM structure of E. coli RNAP-promoter initial transcribing complex with 5-nt RNA transcript (RPitc-5nt)

Method: ELECTRON MICROSCOPY Dmax: 171.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-directed RNA polymerase subunit alpha

Escherichia coli O157:H7

UniProt P0A7Z6

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 A； UniProt 1–329 Chain B； UniProt 1–329 Not recorded DNA-directed RNA polymerase subunit beta × 1 （B7MIX3） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P0A8T8） DNA-directed RNA polymerase subunit omega × 1 （B7MFL0） RNA polymerase sigma factor RpoD × 1 （P00579） synthetic non-template strand DNA (54-MER) × 1 synthetic template strand DNA (54-MER) × 1 RNA transcript (5-MER) × 1 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

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 6XLL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4YG2 X-ray crystal structur of Escherichia coli RNA polymerase sigma70 holoenzyme Deposited 2015-02-25 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 A 1–329（329 aa）
Chain B 1–329（329 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 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 G 1–329（329 aa）
Chain H 1–329（329 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
5EZK RNA polymerase model placed by Molecular replacement into X-ray diffraction map of DNA-bound RNA Polymerase-Sigma 54 holoenzyme complex. Deposited 2015-11-26 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–329（329 aa）
Chain B 1–329（329 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；8% PGA-LM, 300mM Ammonium Formate, 100mM Hepes
Resolution 8.50 Å R-free 0.470
5TBZ E. Coli RNA Polymerase complexed with NusG Deposited 2016-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–235（235 aa）
Chain B 1–235（235 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；298 K；0.1 M sodium dihydrogen phosphate pH 6.5, 12% (w/v) PEG 8000
Resolution 7.00 Å R-free 0.395
5TBZ E. Coli RNA Polymerase complexed with NusG Deposited 2016-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain F 1–235（235 aa）
Chain G 1–235（235 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；298 K；0.1 M sodium dihydrogen phosphate pH 6.5, 12% (w/v) PEG 8000
Resolution 7.00 Å R-free 0.395
5UI8 structure of sigmaN-holoenzyme Deposited 2017-01-13 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 G 1–329（329 aa）
Chain H 1–329（329 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP
Resolution 3.76 Å R-free 0.312
6AWB Structure of 30S ribosomal subunit and RNA polymerase complex in non-rotated state Deposited 2017-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 27-meric
Chain 01 6–234（229 aa）
Chain 02 6–234（229 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20 mM Tris-HCl, pH 7.0, 100 mM NH4Cl, 10 mM MgCl2, 0.5 mM EDTA, 6 mM BME
cryo-EM vitrification conditions Cryogen ETHANE；2.5 uL of 50 nM 30S and 150 nM RNAP was applied to the grid. After a 30 second incubation, the grid was blotted for 5 seconds at blotting power 8.
Resolution 6.70 Å
6AWC Structure of 30S ribosomal subunit and RNA polymerase complex in rotated state Deposited 2017-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 27-meric
Chain 01 6–234（229 aa）
Chain 02 6–234（229 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20 mM Tris-HCl, pH 7.0, 100 mM NH4Cl, 10 mM MgCl2, 0.5 mM EDTA, 6 mM BME
cryo-EM vitrification conditions Cryogen ETHANE；2.5 uL of 50 nM 30S and 150 nM RNAP was applied to the grid. After a 30 second incubation, the grid was blotted for 5 seconds at blotting power 8.
Resolution 7.90 Å
6AWD Structure of 30S (S1 depleted) ribosomal subunit and RNA polymerase complex Deposited 2017-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 25 PDB declaration: 26-meric
Chain 01 6–234（229 aa）
Chain 02 6–234（229 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20 mM Tris-HCl, pH 7.0, 100 mM NH4Cl, 10 mM MgCl2, 0.5 mM EDTA, 6 mM BME
cryo-EM vitrification conditions Cryogen ETHANE；2.5 uL of 50 nM 30S and 150 nM RNAP was applied to the grid. After a 30 second incubation, the grid was blotted for 5 seconds at blotting power 8.
Resolution 8.10 Å
6B6H The cryo-EM structure of a bacterial class I transcription activation complex Deposited 2017-10-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: dodecameric
Chain A 1–329（329 aa）
Chain B 1–329（329 aa）
Chain I 250–324（75 aa） Fragment：Alpha C-terminal domain (alpha-CTD) residues 250-324
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
6GOV Structure of THE RNA POLYMERASE LAMBDA-BASED ANTITERMINATION COMPLEX Deposited 2018-06-04 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain U 1–329（329 aa）
Chain V 1–329（329 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 3.70 Å
6N62 Escherichia coli RNA polymerase sigma70-holoenzyme bound to upstream fork promoter DNA Deposited 2018-11-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain A 1–234（234 aa） Fragment：N-terminal domain (UNP residues 1-234)
Chain B 1–234（234 aa） Fragment：N-terminal domain (UNP residues 1-234)
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；295 K；0.1 M HEPES, pH 6.8, 0.2 M magnesium chloride, 7% w/v PEG3350, 4% v/v glycerol, 4% v/v ethylene glycol
Resolution 3.80 Å R-free 0.334
6OMF CryoEM structure of SigmaS-transcription initiation complex with activator Crl Deposited 2019-04-18 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 A 1–234（234 aa）
Chain B 1–234（234 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 3.26 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: undecameric
Chain A 1–329（329 aa）
Chain B 1–329（329 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–329（329 aa）
Chain B 1–329（329 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–329（329 aa）
Chain B 1–329（329 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
6PMI Sigm28-transcription initiation complex with specific promoter at the state 1 Deposited 2019-07-02 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain A 1–329（329 aa）
Chain B 1–329（329 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 3 seconds before plunging
Resolution 3.86 Å
6PMJ Sigm28-transcription initiation complex with specific promoter at the state 2 Deposited 2019-07-02 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain A 1–329（329 aa）
Chain B 1–329（329 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 3 seconds before plunging
Resolution 3.91 Å
6XH7 CueR-TAC without RNA Deposited 2020-06-18 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–329（329 aa）
Chain B 1–329（329 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 oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: undecameric
Chain A 1–329（329 aa）
Chain B 1–329（329 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 oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–329（329 aa）
Chain B 1–329（329 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 oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: decameric
Chain A 1–329（329 aa）
Chain B 1–329（329 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 oligomeric state Different ligand/ion Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: undecameric
Chain A 1–329（329 aa）
Chain B 1–329（329 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
6XLM Cryo-EM structure of E.coli RNAP-DNA elongation complex 1 (RDe1) in EcmrR-dependent transcription Deposited 2020-06-28 Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain A 1–329（329 aa）
Chain B 1–329（329 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
6XLN Cryo-EM structure of E. coli RNAP-DNA elongation complex 2 (RDe2) in EcmrR-dependent transcription Deposited 2020-06-28 Different oligomeric state Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain A 1–329（329 aa）
Chain B 1–329（329 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 2.80 Å
8EG7 Cryo-EM structure of pre-consensus elemental paused elongation complex Deposited 2022-09-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain G 1–234（234 aa）
Chain H 1–234（234 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；blot force 0, blot time 3 s
Resolution 3.20 Å
8EG8 Cryo-EM structure of consensus elemental paused elongation complex with a folded TL Deposited 2022-09-12 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain G 1–234（234 aa）
Chain H 1–234（234 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；blot force 0, blot time 3 s
Resolution 3.30 Å
8EGB Cryo-EM structure of consensus elemental paused elongation complex with an unfolded TL Deposited 2022-09-12 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain G 1–234（234 aa）
Chain H 1–234（234 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；blot force 0, blot time 3 s
Resolution 3.80 Å
8EH8 Cryo-EM structure of his-elemental paused elongation complex with a folded TL and a rotated RH-FL (1) Deposited 2022-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain G 1–234（234 aa）
Chain H 1–234（234 aa）
Not recorded MG MAGNESIUM ION × 1 1N7 CHAPSO × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blot force 0, blot time 3.5 s
Resolution 3.40 Å
8EH9 Cryo-EM structure of his-elemental paused elongation complex with a folded TL and a rotated RH-FL (2) Deposited 2022-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain G 1–234（234 aa）
Chain H 1–234（234 aa）
Not recorded MG MAGNESIUM ION × 1 1N7 CHAPSO × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blot force 0, blot time 3.5 s
Resolution 3.90 Å
8EHA Cryo-EM structure of his-elemental paused elongation complex with a folded TL and a rotated RH-FL (out) Deposited 2022-09-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain G 1–234（234 aa）
Chain H 1–234（234 aa）
Not recorded MG MAGNESIUM ION × 1 1N7 CHAPSO × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blot force 0, blot time 3.5 s
Resolution 3.70 Å
8EHF Cryo-EM structure of his-elemental paused elongation complex with an unfolded TL (1) Deposited 2022-09-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain G 1–234（234 aa）
Chain H 1–234（234 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 × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blot force 0, blot time 3.5 s
Resolution 3.30 Å
8EHI Cryo-EM structure of his-elemental paused elongation complex with an unfolded TL (2) Deposited 2022-09-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain G 1–234（234 aa）
Chain H 1–234（234 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blot force 0, blot time 3.5 s
Resolution 5.50 Å
9DR1 E. coli RNA polymerase consensus volume with a bound fluoride riboswitch in the ligand-bound state Deposited 2024-09-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain G 5–234（230 aa）
Chain H 5–234（230 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；5 mM Tris-HCl, pH 7.5, 100 mM KCl, 1 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å

32 other PDB entries and 34 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPOA_ECO57
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–329； UniProt 1–329 Author chain B； PDBConstruct 1–329； UniProt 1–329

DNA-directed RNA polymerase subunit beta

Escherichia coli O157:H7

UniProt B7MIX3

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 C； UniProt 1–1342 Not recorded DNA-directed RNA polymerase subunit alpha × 2 （P0A7Z6） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P0A8T8） DNA-directed RNA polymerase subunit omega × 1 （B7MFL0） RNA polymerase sigma factor RpoD × 1 （P00579） synthetic non-template strand DNA (54-MER) × 1 synthetic template strand DNA (54-MER) × 1 RNA transcript (5-MER) × 1 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

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 6XLL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5TBZ E. Coli RNA Polymerase complexed with NusG Deposited 2016-09-13 Different oligomeric state Different ligand/ion Different experimental method 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 No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；298 K；0.1 M sodium dihydrogen phosphate pH 6.5, 12% (w/v) PEG 8000
Resolution 7.00 Å R-free 0.395
5TBZ E. Coli RNA Polymerase complexed with NusG Deposited 2016-09-13 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain H 1–1342（1342 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；298 K；0.1 M sodium dihydrogen phosphate pH 6.5, 12% (w/v) PEG 8000
Resolution 7.00 Å R-free 0.395
5UI8 structure of sigmaN-holoenzyme Deposited 2017-01-13 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 I 1–1342（1342 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP
Resolution 3.76 Å R-free 0.312
6AWB Structure of 30S ribosomal subunit and RNA polymerase complex in non-rotated state Deposited 2017-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 27-meric
Chain 03 2–1341（1340 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20 mM Tris-HCl, pH 7.0, 100 mM NH4Cl, 10 mM MgCl2, 0.5 mM EDTA, 6 mM BME
cryo-EM vitrification conditions Cryogen ETHANE；2.5 uL of 50 nM 30S and 150 nM RNAP was applied to the grid. After a 30 second incubation, the grid was blotted for 5 seconds at blotting power 8.
Resolution 6.70 Å
6AWC Structure of 30S ribosomal subunit and RNA polymerase complex in rotated state Deposited 2017-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 27-meric
Chain 03 2–1341（1340 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20 mM Tris-HCl, pH 7.0, 100 mM NH4Cl, 10 mM MgCl2, 0.5 mM EDTA, 6 mM BME
cryo-EM vitrification conditions Cryogen ETHANE；2.5 uL of 50 nM 30S and 150 nM RNAP was applied to the grid. After a 30 second incubation, the grid was blotted for 5 seconds at blotting power 8.
Resolution 7.90 Å
6AWD Structure of 30S (S1 depleted) ribosomal subunit and RNA polymerase complex Deposited 2017-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 25 PDB declaration: 26-meric
Chain 03 2–1341（1340 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20 mM Tris-HCl, pH 7.0, 100 mM NH4Cl, 10 mM MgCl2, 0.5 mM EDTA, 6 mM BME
cryo-EM vitrification conditions Cryogen ETHANE；2.5 uL of 50 nM 30S and 150 nM RNAP was applied to the grid. After a 30 second incubation, the grid was blotted for 5 seconds at blotting power 8.
Resolution 8.10 Å
6B6H The cryo-EM structure of a bacterial class I transcription activation complex Deposited 2017-10-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: dodecameric
Chain C 1–1342（1342 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
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 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 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 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 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 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 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
6PMI Sigm28-transcription initiation complex with specific promoter at the state 1 Deposited 2019-07-02 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 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot for 3 seconds before plunging
Resolution 3.86 Å
6PMJ Sigm28-transcription initiation complex with specific promoter at the state 2 Deposited 2019-07-02 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 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot for 3 seconds before plunging
Resolution 3.91 Å
6XH7 CueR-TAC without RNA Deposited 2020-06-18 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 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 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 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 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 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 oligomeric state Different ligand/ion 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 × 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 oligomeric state Different ligand/ion Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: undecameric
Chain C 1–1342（1342 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
6XLM Cryo-EM structure of E.coli RNAP-DNA elongation complex 1 (RDe1) in EcmrR-dependent transcription Deposited 2020-06-28 Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
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 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6XLN Cryo-EM structure of E. coli RNAP-DNA elongation complex 2 (RDe2) in EcmrR-dependent transcription Deposited 2020-06-28 Different oligomeric state Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 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 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å

18 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPOB_ECO45
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–1342； UniProt 1–1342

;DNA-directed RNA polymerase subunit beta' ;

Escherichia coli O157:H7

UniProt P0A8T8

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 D； UniProt 1–1407 Not recorded DNA-directed RNA polymerase subunit alpha × 2 （P0A7Z6） DNA-directed RNA polymerase subunit beta × 1 （B7MIX3） DNA-directed RNA polymerase subunit omega × 1 （B7MFL0） RNA polymerase sigma factor RpoD × 1 （P00579） synthetic non-template strand DNA (54-MER) × 1 synthetic template strand DNA (54-MER) × 1 RNA transcript (5-MER) × 1 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

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 6XLL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4YG2 X-ray crystal structur of Escherichia coli RNA polymerase sigma70 holoenzyme Deposited 2015-02-25 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 D 1–1407（1407 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 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 J 1–1407（1407 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
5EZK RNA polymerase model placed by Molecular replacement into X-ray diffraction map of DNA-bound RNA Polymerase-Sigma 54 holoenzyme complex. Deposited 2015-11-26 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 1–1407（1407 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；8% PGA-LM, 300mM Ammonium Formate, 100mM Hepes
Resolution 8.50 Å R-free 0.470
5TBZ E. Coli RNA Polymerase complexed with NusG Deposited 2016-09-13 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 1–1407（1407 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；298 K；0.1 M sodium dihydrogen phosphate pH 6.5, 12% (w/v) PEG 8000
Resolution 7.00 Å R-free 0.395
5TBZ E. Coli RNA Polymerase complexed with NusG Deposited 2016-09-13 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain I 1–1407（1407 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；298 K；0.1 M sodium dihydrogen phosphate pH 6.5, 12% (w/v) PEG 8000
Resolution 7.00 Å R-free 0.395
5UI8 structure of sigmaN-holoenzyme Deposited 2017-01-13 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 J 1–1407（1407 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP
Resolution 3.76 Å R-free 0.312
6AWB Structure of 30S ribosomal subunit and RNA polymerase complex in non-rotated state Deposited 2017-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 27-meric
Chain 04 8–1376（1369 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20 mM Tris-HCl, pH 7.0, 100 mM NH4Cl, 10 mM MgCl2, 0.5 mM EDTA, 6 mM BME
cryo-EM vitrification conditions Cryogen ETHANE；2.5 uL of 50 nM 30S and 150 nM RNAP was applied to the grid. After a 30 second incubation, the grid was blotted for 5 seconds at blotting power 8.
Resolution 6.70 Å
6AWC Structure of 30S ribosomal subunit and RNA polymerase complex in rotated state Deposited 2017-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 27-meric
Chain 04 8–1376（1369 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20 mM Tris-HCl, pH 7.0, 100 mM NH4Cl, 10 mM MgCl2, 0.5 mM EDTA, 6 mM BME
cryo-EM vitrification conditions Cryogen ETHANE；2.5 uL of 50 nM 30S and 150 nM RNAP was applied to the grid. After a 30 second incubation, the grid was blotted for 5 seconds at blotting power 8.
Resolution 7.90 Å
6AWD Structure of 30S (S1 depleted) ribosomal subunit and RNA polymerase complex Deposited 2017-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 25 PDB declaration: 26-meric
Chain 04 8–1376（1369 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20 mM Tris-HCl, pH 7.0, 100 mM NH4Cl, 10 mM MgCl2, 0.5 mM EDTA, 6 mM BME
cryo-EM vitrification conditions Cryogen ETHANE；2.5 uL of 50 nM 30S and 150 nM RNAP was applied to the grid. After a 30 second incubation, the grid was blotted for 5 seconds at blotting power 8.
Resolution 8.10 Å
6B6H The cryo-EM structure of a bacterial class I transcription activation complex Deposited 2017-10-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: dodecameric
Chain D 1–1407（1407 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
6GOV Structure of THE RNA POLYMERASE LAMBDA-BASED ANTITERMINATION COMPLEX Deposited 2018-06-04 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain Y 1–1407（1407 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 3.70 Å
6N62 Escherichia coli RNA polymerase sigma70-holoenzyme bound to upstream fork promoter DNA Deposited 2018-11-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain D 2–1407（1406 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；295 K；0.1 M HEPES, pH 6.8, 0.2 M magnesium chloride, 7% w/v PEG3350, 4% v/v glycerol, 4% v/v ethylene glycol
Resolution 3.80 Å R-free 0.334
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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: undecameric
Chain D 1–1407（1407 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–1407（1407 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–1407（1407 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
6PMI Sigm28-transcription initiation complex with specific promoter at the state 1 Deposited 2019-07-02 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain D 1–1407（1407 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 3 seconds before plunging
Resolution 3.86 Å
6PMJ Sigm28-transcription initiation complex with specific promoter at the state 2 Deposited 2019-07-02 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain D 1–1407（1407 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 3 seconds before plunging
Resolution 3.91 Å
6XH7 CueR-TAC without RNA Deposited 2020-06-18 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–1407（1407 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 oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: undecameric
Chain D 1–1407（1407 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 oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–1407（1407 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 oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: decameric
Chain D 1–1407（1407 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 oligomeric state Different ligand/ion Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: undecameric
Chain D 1–1407（1407 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
6XLM Cryo-EM structure of E.coli RNAP-DNA elongation complex 1 (RDe1) in EcmrR-dependent transcription Deposited 2020-06-28 Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain D 1–1407（1407 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
6XLN Cryo-EM structure of E. coli RNAP-DNA elongation complex 2 (RDe2) in EcmrR-dependent transcription Deposited 2020-06-28 Different oligomeric state Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain D 1–1407（1407 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 2.80 Å
6ZTJ E. coli 70S-RNAP expressome complex in NusG-coupled state (38 nt intervening mRNA) Deposited 2020-07-20 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 CD 1–1407（1407 aa）
Not recorded MG MAGNESIUM ION × 479 PHE PHENYLALANINE × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 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 experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 54 PDB declaration: 62-meric
Chain CD 1–1407（1407 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
6ZTM E. coli 70S-RNAP expressome complex in collided state without NusG Deposited 2020-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 52 PDB declaration: 60-meric
Chain CD 1–1407（1407 aa）
Not recorded MG MAGNESIUM ION × 421 PHE PHENYLALANINE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6ZTN E. coli 70S-RNAP expressome complex in NusG-coupled state (42 nt intervening mRNA) Deposited 2020-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 54 PDB declaration: 63-meric
Chain CD 1–1407（1407 aa）
Not recorded MG MAGNESIUM ION × 487 PHE PHENYLALANINE × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6ZTO E. coli 70S-RNAP expressome complex in uncoupled state 1 Deposited 2020-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 54 PDB declaration: 62-meric
Chain CD 1–1407（1407 aa）
Not recorded MG MAGNESIUM ION × 487 PHE PHENYLALANINE × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6ZTP E. coli 70S-RNAP expressome complex in uncoupled state 6 Deposited 2020-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 54 PDB declaration: 62-meric
Chain CD 1–1407（1407 aa）
Not recorded MG MAGNESIUM ION × 487 PHE PHENYLALANINE × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6ZU1 E. coli 70S-RNAP expressome complex in uncoupled state 2 Deposited 2020-07-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 54 PDB declaration: 62-meric
Chain CD 1–1407（1407 aa）
Not recorded MG MAGNESIUM ION × 487 PHE PHENYLALANINE × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7BEG Structures of class I bacterial transcription complexes Deposited 2020-12-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain D 1–1407（1407 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM Tris pH 8, 50 mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7PY0 CryoEM structure of E.coli RNA polymerase elongation complex bound to NusG (NusG-EC in more-swiveled conformation) Deposited 2021-10-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain D 1–1407（1407 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 4.50 Å
7PY1 CryoEM structure of E.coli RNA polymerase elongation complex bound to NusG (the consensus NusG-EC) Deposited 2021-10-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain D 1–1407（1407 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
7PY3 CryoEM structure of E.coli RNA polymerase elongation complex bound to NusA (the consensus NusA-EC) Deposited 2021-10-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain D 1–1407（1407 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
7PY5 CryoEM structure of E.coli RNA polymerase elongation complex bound to NusA and NusG (the consensus NusA-NusG-EC) Deposited 2021-10-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: decameric
Chain D 1–1407（1407 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
7PY6 CryoEM structure of E.coli RNA polymerase elongation complex bound to NusA and NusG (NusA and NusG elongation complex in less-swiveled conformation) Deposited 2021-10-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: decameric
Chain D 1–1407（1407 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
7PY7 CryoEM structure of E.coli RNA polymerase elongation complex bound to NusA and NusG (NusA and NusG elongation complex in more-swiveled conformation) Deposited 2021-10-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: decameric
Chain D 1–1407（1407 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
7PY8 CryoEM structure of E.coli RNA polymerase elongation complex bound to NusG (NusG-EC in less-swiveled conformation) Deposited 2021-10-09 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain D 1–1407（1407 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
7PYJ CryoEM structure of E.coli RNA polymerase elongation complex bound to NusA (NusA elongation complex in less-swiveled conformation) Deposited 2021-10-10 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain D 1–1407（1407 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 4.20 Å
7PYK CryoEM structure of E.coli RNA polymerase elongation complex bound to NusA (NusA elongation complex in more-swiveled conformation) Deposited 2021-10-10 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain D 1–1407（1407 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
7Q0J RNA polymerase elongation complex in more-swiveled conformation Deposited 2021-10-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain D 1–1407（1407 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 4.30 Å
7Q0K RNA polymerase elongation complex in less-swiveled conformation Deposited 2021-10-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain D 1–1407（1407 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 4.00 Å
8ABY RNA polymerase bound to purified in vitro transcribed regulatory RNA putL - pause prone, closed clamp state Deposited 2022-07-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain D 1–1406（1406 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
8AC0 RNA polymerase at U-rich pause bound to regulatory RNA putL - active, closed clamp state Deposited 2022-07-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain D 1–1406（1406 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain D 1–1406（1406 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 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 D 1–1406（1406 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain D 1–1406（1406 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 construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain D 1–1406（1406 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
8PBL E. coli RNA polymerase elongation complex stalled at thymine dimer lesion Deposited 2023-06-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain G 1–1407（1407 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
9GUW 30S-TEC (TEC in expressome position) Inactive state 2 Deposited 2024-09-20 Different construct 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 4 1–1406（1406 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 construct 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 4 1–1406（1406 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
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 J 1–1407（1407 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

51 other PDB entries and 53 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPOC_ECO57
Isoform —
PDB entities 3
Chains and sequence ranges Author chain D； PDBConstruct 1–1407； UniProt 1–1407

DNA-directed RNA polymerase subunit omega

Escherichia coli O157:H7

UniProt B7MFL0

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 E； UniProt 1–91 Not recorded DNA-directed RNA polymerase subunit alpha × 2 （P0A7Z6） DNA-directed RNA polymerase subunit beta × 1 （B7MIX3） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P0A8T8） RNA polymerase sigma factor RpoD × 1 （P00579） synthetic non-template strand DNA (54-MER) × 1 synthetic template strand DNA (54-MER) × 1 RNA transcript (5-MER) × 1 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

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 6XLL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5UI8 structure of sigmaN-holoenzyme Deposited 2017-01-13 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 K 1–91（91 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP
Resolution 3.76 Å R-free 0.312
6AWB Structure of 30S ribosomal subunit and RNA polymerase complex in non-rotated state Deposited 2017-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 27-meric
Chain 05 2–77（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20 mM Tris-HCl, pH 7.0, 100 mM NH4Cl, 10 mM MgCl2, 0.5 mM EDTA, 6 mM BME
cryo-EM vitrification conditions Cryogen ETHANE；2.5 uL of 50 nM 30S and 150 nM RNAP was applied to the grid. After a 30 second incubation, the grid was blotted for 5 seconds at blotting power 8.
Resolution 6.70 Å
6AWC Structure of 30S ribosomal subunit and RNA polymerase complex in rotated state Deposited 2017-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 27-meric
Chain 05 2–60（59 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20 mM Tris-HCl, pH 7.0, 100 mM NH4Cl, 10 mM MgCl2, 0.5 mM EDTA, 6 mM BME
cryo-EM vitrification conditions Cryogen ETHANE；2.5 uL of 50 nM 30S and 150 nM RNAP was applied to the grid. After a 30 second incubation, the grid was blotted for 5 seconds at blotting power 8.
Resolution 7.90 Å
6AWD Structure of 30S (S1 depleted) ribosomal subunit and RNA polymerase complex Deposited 2017-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 25 PDB declaration: 26-meric
Chain 05 2–60（59 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20 mM Tris-HCl, pH 7.0, 100 mM NH4Cl, 10 mM MgCl2, 0.5 mM EDTA, 6 mM BME
cryo-EM vitrification conditions Cryogen ETHANE；2.5 uL of 50 nM 30S and 150 nM RNAP was applied to the grid. After a 30 second incubation, the grid was blotted for 5 seconds at blotting power 8.
Resolution 8.10 Å
6B6H The cryo-EM structure of a bacterial class I transcription activation complex Deposited 2017-10-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: dodecameric
Chain E 1–91（91 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
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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: undecameric
Chain E 1–91（91 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain E 1–91（91 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain E 1–91（91 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
6PMI Sigm28-transcription initiation complex with specific promoter at the state 1 Deposited 2019-07-02 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain E 1–91（91 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 3 seconds before plunging
Resolution 3.86 Å
6PMJ Sigm28-transcription initiation complex with specific promoter at the state 2 Deposited 2019-07-02 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain E 1–91（91 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 3 seconds before plunging
Resolution 3.91 Å
6XH7 CueR-TAC without RNA Deposited 2020-06-18 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain E 1–91（91 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 oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: undecameric
Chain E 1–91（91 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 oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain E 1–91（91 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
6XLJ Cryo-EM structure of EcmrR-RNAP-promoter initial transcribing complex with 4-nt RNA transcript (EcmrR-RPitc-4nt) Deposited 2020-06-28 Different oligomeric state Different ligand/ion Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: undecameric
Chain E 1–91（91 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
6XLM Cryo-EM structure of E.coli RNAP-DNA elongation complex 1 (RDe1) in EcmrR-dependent transcription Deposited 2020-06-28 Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain E 1–91（91 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
6XLN Cryo-EM structure of E. coli RNAP-DNA elongation complex 2 (RDe2) in EcmrR-dependent transcription Deposited 2020-06-28 Different oligomeric state Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain E 1–91（91 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 2.80 Å

16 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPOZ_ECO45
Isoform —
PDB entities 4
Chains and sequence ranges Author chain E； PDBConstruct 1–91； UniProt 1–91

RNA polymerase sigma factor RpoD

Escherichia coli O157:H7

UniProt P00579

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 F； UniProt 1–613 Not recorded DNA-directed RNA polymerase subunit alpha × 2 （P0A7Z6） DNA-directed RNA polymerase subunit beta × 1 （B7MIX3） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P0A8T8） DNA-directed RNA polymerase subunit omega × 1 （B7MFL0） synthetic non-template strand DNA (54-MER) × 1 synthetic template strand DNA (54-MER) × 1 RNA transcript (5-MER) × 1 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

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 6XLL 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 ligand/ion 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 ligand/ion 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 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 ligand/ion 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 ligand/ion 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
6N4C EM structure of the DNA wrapping in bacterial open transcription initiation complex Deposited 2018-11-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain F 8–613（606 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
Resolution 17.00 Å
6P18 Q21 transcription antitermination complex: loading complex Deposited 2019-05-19 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 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 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: undecameric
Chain F 1–613（613 aa）
Not recorded ZN ZINC ION × 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: decameric
Chain F 1–613（613 aa）
Not recorded ZN ZINC ION × 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 oligomeric state Different ligand/ion 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
6XLM Cryo-EM structure of E.coli RNAP-DNA elongation complex 1 (RDe1) in EcmrR-dependent transcription Deposited 2020-06-28 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain F 1–613（613 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM Tris pH 8, 50 mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 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 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 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 oligomeric state 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 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 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 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 oligomeric state 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 oligomeric state 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion Different experimental conditions 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 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 ligand/ion Different experimental conditions 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 ligand/ion Different experimental conditions 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 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 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 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 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 5
Chains and sequence ranges Author chain F； PDBConstruct 1–613； UniProt 1–613

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

SAXS scattering curve SAXS Profile

SAXS profile for 6xll

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6xll
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6xll
Deposition date deposition_date2020-06-28
Structure title titleCryo-EM structure of E. coli RNAP-promoter initial transcribing complex with 5-nt RNA transcript (RPitc-5nt)
Keywords keywordsTranscriptional factor, TRANSCRIPTION, TRANSFERASE-DNA complex, promoter escape, multidrug recognition; TRANSCRIPTION, TRANSFERASE/DNA
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier51.83 Å
Radius of gyration Rg (electron density) rg_electron51.35 Å
Forward intensity I(0) i03153780000.00
Molecular weight molecular_weight445350.0 kDa
Excluded volume excluded_volume547920 ų
Envelope volume envelope_volume789410 ų
Hydration-shell volume shell_volume122510 ų
Envelope diameter envelope_diameter184.3 Å
Shell Rg shell_rg58.38 Å
Envelope Rg envelope_rg51.49 Å
Shape Rg shape_rg51.35 Å
Total Rg total_rg51.54 Å
Total atoms total_atoms31134
Residues n_residues3785
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax171.2 Å
Rg (real space) rg_real51.70 Å
Rg uncertainty (real space) rg_real_error1.29 Å
I(0) (real space) i0_real3.1540e+09
I(0) uncertainty (real space) i0_real_error5.8830e+07
Rg (reciprocal space) rg_reciprocal51.92 Å
I(0) (reciprocal space) i0_reciprocal3155000000.0000
Solution quality estimate total_estimate0.8680
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary62.8 Å
Skewness Skewness skewness0.295
Kurtosis Kurtosis kurtosis-0.240
Angular range angular_range— – 0.1500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha440200000.0000
Real-space data points n_real_points31
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.832; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.959; Smooth: 0.825
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (11)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id6xllA01
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology120 — RNA Polymerase Alpha Subunit; Chain A, domain 2
Homologous superfamily homologous superfamily12 — DNA-directed RNA polymerase, insert domain
Domain ID domain_id6xllB01
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology120 — RNA Polymerase Alpha Subunit; Chain A, domain 2
Homologous superfamily homologous superfamily12 — DNA-directed RNA polymerase, insert domain
Domain ID domain_id6xllC01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily150 — RNA polymerase II, Rpb2 subunit, wall domain
Domain ID domain_id6xllD01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology132 — Topoisomerase I; Chain A, domain 4
Homologous superfamily homologous superfamily30 — RNA polymerase Rpb1 funnel domain
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8. Citations (1)

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9. Files and Curves (10)