← Back to search
8t0l

E. coli Sw2/Snf2 ATPase RapA bound to both ADP-AlF3 and reconstituted E. coli RNA polymerase post-termination complex on negatively-supercoiled DNA

Method: ELECTRON MICROSCOPY Dmax: 180.4 Å Quality: GOOD
▼

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

DNA-directed RNA polymerase subunit alpha

Escherichia coli

UniProt C3SR67

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 6 DNA 2 PDB declaration: octameric（8） Consistent with all polymer counts Chain G； UniProt 4–234 Chain H； UniProt 4–234 Not recorded DNA-directed RNA polymerase subunit beta × 1 （C3SIA7） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A0A369F490） DNA-directed RNA polymerase subunit omega × 1 （A7ZTK1） RNA polymerase-associated protein RapA × 1 （B7MAI2） DNA (29-MER) × 1 ;DNA (5'-D(P*TP*CP*TP*GP*AP*AP*TP*TP*TP*AP*AP*AP*TP*TP*CP*AP*GP*A)-3') ; × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.62 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 8T0L Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9M7Y Cryo-EM structure of gp79-dependent RNAP promoter open complex Deposited 2025-03-11 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain C 1–329（329 aa）
Chain D 1–329（329 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9M7Z Cryo-EM structure of gp79 bound RNAP core enzyme Deposited 2025-03-11 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–329（329 aa）
Chain D 1–329（329 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.50 Å
9W3D Cryo-EM structure of E. coli RNA polymerase in complex with EP1 Deposited 2025-07-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–329（329 aa）
Chain B 1–329（329 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
9W3E Cryo-EM structure of E. coli RNA polymerase in complex with PP1 Deposited 2025-07-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–329（329 aa）
Chain B 1–329（329 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9W3G Cryo-EM structure of E. coli RNA polymerase in complex with VP1 Deposited 2025-07-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain A 1–329（329 aa）
Chain B 1–329（329 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

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name C3SR67_ECOLX
Isoform —
PDB entities 1
Chains and sequence ranges Author chain G； PDBConstruct 1–231； UniProt 4–234 Author chain H； PDBConstruct 1–231； UniProt 4–234

DNA-directed RNA polymerase subunit beta

Escherichia coli

UniProt C3SIA7

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 6 DNA 2 PDB declaration: octameric（8） Consistent with all polymer counts Chain I； UniProt 2–1341 Not recorded DNA-directed RNA polymerase subunit alpha × 2 （C3SR67） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A0A369F490） DNA-directed RNA polymerase subunit omega × 1 （A7ZTK1） RNA polymerase-associated protein RapA × 1 （B7MAI2） DNA (29-MER) × 1 ;DNA (5'-D(P*TP*CP*TP*GP*AP*AP*TP*TP*TP*AP*AP*AP*TP*TP*CP*AP*GP*A)-3') ; × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.62 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 8T0L Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8G2W Cryo-EM structure of 3DVA component 2 of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase minus preQ1 ligand Deposited 2023-02-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain I 2–1341（1340 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION WAS CARRIED OUT IN A CHAMBER WITH THE TEMPERATURE SET TO 4 DEGREES CELSIUS.
Resolution 3.70 Å
8G4W Cryo-EM consensus structure of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase plus preQ1 ligand Deposited 2023-02-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain I 2–1341（1340 aa）
Not recorded PRF 7-DEAZA-7-AMINOMETHYL-GUANINE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION WAS CARRIED OUT IN A CHAMBER WITH THE TEMPERATURE SET TO 4 DEGREES CELSIUS.
Resolution 3.80 Å
8G8Z Cryo-EM structure of 3DVA component 1 of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase plus preQ1 ligand Deposited 2023-02-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain I 2–1341（1340 aa）
Not recorded PRF 7-DEAZA-7-AMINOMETHYL-GUANINE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Vitrification was carried out in a chamber with the temperature set to 4 C.
Resolution 4.30 Å
8T00 Reconstituted E. coli RNA polymerase post-termination complex on negatively-supercoiled DNA: closed duplex DNA (rPTCc) Deposited 2023-05-31 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain I 2–1341（1340 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 4.69 Å
9DR1 E. coli RNA polymerase consensus volume with a bound fluoride riboswitch in the ligand-bound state Deposited 2024-09-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain I 2–1341（1340 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
9M7Y Cryo-EM structure of gp79-dependent RNAP promoter open complex Deposited 2025-03-11 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain A 1–1342（1342 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9M7Z Cryo-EM structure of gp79 bound RNAP core enzyme Deposited 2025-03-11 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–1342（1342 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.50 Å
9N07 Mfd-bound E.coli RNA polymerase elongation complex + ADP-BeF3 - L1 state Deposited 2025-01-23 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain I 2–1341（1340 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.48 Å
9N11 Mfd-bound E.coli RNA polymerase elongation complex + ADP-BeF3 - L1.5 state Deposited 2025-01-24 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain I 2–1341（1340 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 4.29 Å
9W3D Cryo-EM structure of E. coli RNA polymerase in complex with EP1 Deposited 2025-07-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–1342（1342 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
9W3E Cryo-EM structure of E. coli RNA polymerase in complex with PP1 Deposited 2025-07-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–1342（1342 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9W3G Cryo-EM structure of E. coli RNA polymerase in complex with VP1 Deposited 2025-07-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain C 1–1342（1342 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å

12 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name C3SIA7_ECOLX
Isoform —
PDB entities 2
Chains and sequence ranges Author chain I； PDBConstruct 1–1340； UniProt 2–1341

;DNA-directed RNA polymerase subunit beta' ;

Escherichia coli

UniProt A0A369F490

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 6 DNA 2 PDB declaration: octameric（8） Consistent with all polymer counts Chain J； UniProt 16–1373 Not recorded DNA-directed RNA polymerase subunit alpha × 2 （C3SR67） DNA-directed RNA polymerase subunit beta × 1 （C3SIA7） DNA-directed RNA polymerase subunit omega × 1 （A7ZTK1） RNA polymerase-associated protein RapA × 1 （B7MAI2） DNA (29-MER) × 1 ;DNA (5'-D(P*TP*CP*TP*GP*AP*AP*TP*TP*TP*AP*AP*AP*TP*TP*CP*AP*GP*A)-3') ; × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.62 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 8T0L Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6N4C EM structure of the DNA wrapping in bacterial open transcription initiation complex Deposited 2018-11-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain D 15–1376（1362 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
Resolution 17.00 Å
8G8Z Cryo-EM structure of 3DVA component 1 of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase plus preQ1 ligand Deposited 2023-02-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain J 16–1373（1358 aa）
Not recorded PRF 7-DEAZA-7-AMINOMETHYL-GUANINE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Vitrification was carried out in a chamber with the temperature set to 4 C.
Resolution 4.30 Å
8T00 Reconstituted E. coli RNA polymerase post-termination complex on negatively-supercoiled DNA: closed duplex DNA (rPTCc) Deposited 2023-05-31 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain J 16–1373（1358 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 4.69 Å
9DR1 E. coli RNA polymerase consensus volume with a bound fluoride riboswitch in the ligand-bound state Deposited 2024-09-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric
Chain J 16–1373（1358 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
9N11 Mfd-bound E.coli RNA polymerase elongation complex + ADP-BeF3 - L1.5 state Deposited 2025-01-24 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain J 16–1373（1358 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 4.29 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A369F490_ECOLX
Isoform —
PDB entities 3
Chains and sequence ranges Author chain J； PDBConstruct 1–1358； UniProt 16–1373

DNA-directed RNA polymerase subunit omega

Escherichia coli

UniProt A7ZTK1

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 6 DNA 2 PDB declaration: octameric（8） Consistent with all polymer counts Chain K； UniProt 3–74 Not recorded DNA-directed RNA polymerase subunit alpha × 2 （C3SR67） DNA-directed RNA polymerase subunit beta × 1 （C3SIA7） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A0A369F490） RNA polymerase-associated protein RapA × 1 （B7MAI2） DNA (29-MER) × 1 ;DNA (5'-D(P*TP*CP*TP*GP*AP*AP*TP*TP*TP*AP*AP*AP*TP*TP*CP*AP*GP*A)-3') ; × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.62 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 8T0L Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4YFK Escherichia coli RNA polymerase in complex with squaramide compound 8. Deposited 2015-02-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 1–91（91 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 2 4C6 3,5-dimethyl-N-{2-[4-(4-methylbenzyl)piperidin-1-yl]-3,4-dioxocyclobut-1-en-1-yl}-1,2-oxazole-4-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；300 K；0.1M HEPES-HCL, 0.2M CaACETATE, 15% PEG400
Resolution 3.57 Å R-free 0.252
4YFK Escherichia coli RNA polymerase in complex with squaramide compound 8. Deposited 2015-02-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain K 1–91（91 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 2 4C6 3,5-dimethyl-N-{2-[4-(4-methylbenzyl)piperidin-1-yl]-3,4-dioxocyclobut-1-en-1-yl}-1,2-oxazole-4-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；300 K；0.1M HEPES-HCL, 0.2M CaACETATE, 15% PEG400
Resolution 3.57 Å R-free 0.252
4YFN Escherichia coli RNA polymerase in complex with squaramide compound 14 (N-[3,4-dioxo-2-(4-{[4-(trifluoromethyl)benzyl]amino}piperidin-1-yl)cyclobut-1-en-1-yl]-3,5-dimethyl-1,2-oxazole-4-sulfonamide) Deposited 2015-02-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 1–91（91 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 4C2 N-[3,4-dioxo-2-(4-{[4-(trifluoromethyl)benzyl]amino}piperidin-1-yl)cyclobut-1-en-1-yl]-3,5-dimethyl-1,2-oxazole-4-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；300 K；0.1M HEPES-HCL (PH7), 0.2M CaACETATE, 15% PEG400
Resolution 3.82 Å R-free 0.270
4YFN Escherichia coli RNA polymerase in complex with squaramide compound 14 (N-[3,4-dioxo-2-(4-{[4-(trifluoromethyl)benzyl]amino}piperidin-1-yl)cyclobut-1-en-1-yl]-3,5-dimethyl-1,2-oxazole-4-sulfonamide) Deposited 2015-02-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain K 1–91（91 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 4C2 N-[3,4-dioxo-2-(4-{[4-(trifluoromethyl)benzyl]amino}piperidin-1-yl)cyclobut-1-en-1-yl]-3,5-dimethyl-1,2-oxazole-4-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；300 K；0.1M HEPES-HCL (PH7), 0.2M CaACETATE, 15% PEG400
Resolution 3.82 Å R-free 0.270
4YFX Escherichia coli RNA polymerase in complex with Myxopyronin B Deposited 2015-02-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 1–91（91 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 4C4 Myxopyronin B × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；300 K；0.1M HEPES-HCL , 0.2M CaACETATE, 15% PEG400
Resolution 3.84 Å R-free 0.300
4YFX Escherichia coli RNA polymerase in complex with Myxopyronin B Deposited 2015-02-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain K 1–91（91 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
4YLN E. coli Transcription Initiation Complex - 17-bp spacer and 4-nt RNA Deposited 2015-03-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain E 2–91（90 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；7% PEG3350, 150 mM magnesium chloride, 100 mM HEPES sodium, pH 7.0
Resolution 5.50 Å R-free 0.328
4YLN E. coli Transcription Initiation Complex - 17-bp spacer and 4-nt RNA Deposited 2015-03-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain K 2–91（90 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；7% PEG3350, 150 mM magnesium chloride, 100 mM HEPES sodium, pH 7.0
Resolution 5.50 Å R-free 0.328
4YLN E. coli Transcription Initiation Complex - 17-bp spacer and 4-nt RNA Deposited 2015-03-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain Q 2–91（90 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；7% PEG3350, 150 mM magnesium chloride, 100 mM HEPES sodium, pH 7.0
Resolution 5.50 Å R-free 0.328
4YLO E. coli Transcription Initiation Complex - 16-bp spacer and 4-nt RNA Deposited 2015-03-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain E 2–91（90 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；7% PEG3350, 150 mM magnesium chloride, 100 mM HEPES sodium, pH 7.0
Resolution 6.00 Å R-free 0.314
4YLO E. coli Transcription Initiation Complex - 16-bp spacer and 4-nt RNA Deposited 2015-03-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain K 2–91（90 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；7% PEG3350, 150 mM magnesium chloride, 100 mM HEPES sodium, pH 7.0
Resolution 6.00 Å R-free 0.314
4YLO E. coli Transcription Initiation Complex - 16-bp spacer and 4-nt RNA Deposited 2015-03-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain Q 2–91（90 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；7% PEG3350, 150 mM magnesium chloride, 100 mM HEPES sodium, pH 7.0
Resolution 6.00 Å R-free 0.314
4YLP E. coli Transcription Initiation Complex - 16-bp spacer and 5-nt RNA Deposited 2015-03-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain E 2–91（90 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；7% PEG3350, 150 mM magnesium chloride, 100 mM HEPES sodium, pH 7.0
Resolution 5.50 Å R-free 0.313
4YLP E. coli Transcription Initiation Complex - 16-bp spacer and 5-nt RNA Deposited 2015-03-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain K 2–91（90 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；7% PEG3350, 150 mM magnesium chloride, 100 mM HEPES sodium, pH 7.0
Resolution 5.50 Å R-free 0.313
4YLP E. coli Transcription Initiation Complex - 16-bp spacer and 5-nt RNA Deposited 2015-03-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Heteromer；Protein × 6 PDB declaration: nonameric
Chain Q 2–91（90 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

6 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPOZ_ECO24
Isoform —
PDB entities 4
Chains and sequence ranges Author chain K； PDBConstruct 1–72； UniProt 3–74

RNA polymerase-associated protein RapA

Escherichia coli

UniProt B7MAI2

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 6 DNA 2 PDB declaration: octameric（8） Consistent with all polymer counts Chain F； UniProt 2–967 Not recorded DNA-directed RNA polymerase subunit alpha × 2 （C3SR67） DNA-directed RNA polymerase subunit beta × 1 （C3SIA7） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A0A369F490） DNA-directed RNA polymerase subunit omega × 1 （A7ZTK1） DNA (29-MER) × 1 ;DNA (5'-D(P*TP*CP*TP*GP*AP*AP*TP*TP*TP*AP*AP*AP*TP*TP*CP*AP*GP*A)-3') ; × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.62 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 8T0L Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6BOG Crystal structure of RapA, a Swi2/Snf2 protein that recycles RNA polymerase during transcription Deposited 2017-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–968（968 aa） Fragment：Full-length
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；292 K；Ammonium sulfate, 1,4-Dioxane, Ethylene glycol, MES
Resolution 3.21 Å R-free 0.279
6BOG Crystal structure of RapA, a Swi2/Snf2 protein that recycles RNA polymerase during transcription Deposited 2017-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–968（968 aa） Fragment：Full-length
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；292 K；Ammonium sulfate, 1,4-Dioxane, Ethylene glycol, MES
Resolution 3.21 Å R-free 0.279

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RAPA_ECO45
Isoform —
PDB entities 5
Chains and sequence ranges Author chain F； PDBConstruct 1–966； UniProt 2–967

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 8t0l

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8t0l
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id8t0l
Deposition date deposition_date2023-06-01
Structure title titleE. coli Sw2/Snf2 ATPase RapA bound to both ADP-AlF3 and reconstituted E. coli RNA polymerase post-termination complex on negatively-supercoiled DNA
Keywords keywords;RNA polymerase, Negatively supercoiled DNA, Sigma-independent transcription, RapA, RNAP recycling, Sw2/Snf2 ATPase, TRANSCRIPTION-DNA complex ;; TRANSCRIPTION/DNA
Experimental Method methodELECTRON MICROSCOPY
▼

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

Radius of gyration Rg (Guinier) rg_guinier55.72 Å
Radius of gyration Rg (electron density) rg_electron55.42 Å
Forward intensity I(0) i03442470000.00
Molecular weight molecular_weight478060.0 kDa
Excluded volume excluded_volume593180 ų
Envelope volume envelope_volume873780 ų
Hydration-shell volume shell_volume128370 ų
Envelope diameter envelope_diameter195.5 Å
Shell Rg shell_rg60.15 Å
Envelope Rg envelope_rg54.70 Å
Shape Rg shape_rg55.45 Å
Total Rg total_rg55.45 Å
Total atoms total_atoms33530
Residues n_residues4198
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

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

Maximum dimension Dmax dmax180.4 Å
Rg (real space) rg_real55.55 Å
Rg uncertainty (real space) rg_real_error1.29 Å
I(0) (real space) i0_real3.4420e+09
I(0) uncertainty (real space) i0_real_error7.1570e+07
Rg (reciprocal space) rg_reciprocal55.84 Å
I(0) (reciprocal space) i0_reciprocal3444000000.0000
Solution quality estimate total_estimate0.8715
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary70.9 Å
Skewness Skewness skewness0.250
Kurtosis Kurtosis kurtosis-0.358
Angular range angular_range— – 0.1400 Å−1
Current regularization parameter α current_alpha0.0002
Highest regularization parameter α highest_alpha392400000.0000
Real-space data points n_real_points29
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.682
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (11)

▶

8. Citations (1)

▶

9. Files and Curves (10)