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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：A7ZUK2 New Search
13PDB entries
25Biological assembly
25chain/assembly records
Main Difference Dimensions in This Set
Different construct Different assembly state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
4XSX Crystal structure of CBR 703 bound to Escherichia coli RNA polymerase holoenzyme Deposited 2015-01-22 Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
Chain D 1–1407（1407 aa）
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 Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
Chain J 1–1407（1407 aa）
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
Chain D 1–1407（1407 aa）
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 Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
Chain J 1–1407（1407 aa）
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
Chain D 1–1407（1407 aa）
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 Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
Chain J 1–1407（1407 aa）
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
Chain D 1–1407（1407 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 Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
Chain J 1–1407（1407 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 Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
Chain D 1–1407（1407 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 Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
Chain J 1–1407（1407 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 Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
Chain D 1–1407（1407 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 Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
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；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 Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric（9） Consistent with all polymers
Chain D 1–1407（1407 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 Assembly 2 Other combination Heteromer；Protein × 6 PDB declaration: nonameric（9） Consistent with all polymers
Chain J 1–1407（1407 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 Assembly 3 Other combination Heteromer；Protein × 6 PDB declaration: nonameric（9） Consistent with all polymers
Chain P 1–1407（1407 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 Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric（9） Consistent with all polymers
Chain D 1–1407（1407 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 Assembly 2 Other combination Heteromer；Protein × 6 PDB declaration: nonameric（9） Consistent with all polymers
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, 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 Assembly 3 Other combination Heteromer；Protein × 6 PDB declaration: nonameric（9） Consistent with all polymers
Chain P 1–1407（1407 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 Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric（9） Consistent with all polymers
Chain D 1–1407（1407 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 Assembly 2 Other combination Heteromer；Protein × 6 PDB declaration: nonameric（9） Consistent with all polymers
Chain J 1–1407（1407 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 Assembly 3 Other combination Heteromer；Protein × 6 PDB declaration: nonameric（9） Consistent with all polymers
Chain P 1–1407（1407 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
8G1S Cryo-EM structure of 3DVA component 1 of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase minus preQ1 ligand Deposited 2023-02-02 Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric（8） Consistent with all polymers
Chain J 1–1373（1373 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM TRIS-HCl, pH 7.5; 100 mM potassium chloride, 1mM
cryo-EM vitrification conditions Cryogen ETHANE；Vitrification was carried out in a chamber with the temperature set to 4 C.
Resolution 3.70 Å
8G7E Cryo-EM structure of 3DVA component 0 of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase plus preQ1 ligand Deposited 2023-02-16 Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: octameric（8） Consistent with all polymers
Chain J 1–1407（1407 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 3.90 Å
8SZW Reconstituted E. coli RNA polymerase post-termination complex on negatively-supercoiled DNA: open duplex DNA (rPTCo) Deposited 2023-05-30 Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric（7） Consistent with all polymers
Chain J 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 3.63 Å
8T02 Reconstituted E. coli RNA polymerase post-termination complex on negatively-supercoiled DNA: unwinding duplex DNA (rPTCi) Deposited 2023-05-31 Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric（7） Consistent with all polymers
Chain J 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 3.79 Å

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.