1ynj

Taq RNA polymerase-Sorangicin complex

Method: X-RAY DIFFRACTION D_max: 214.5 Å Quality: REASONABLE

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

DNA-directed RNA polymerase alpha chain

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 1–314 Chain B； UniProt 1–314	Not recorded	DNA-directed RNA polymerase beta chain × 1 （Q9KWU7） ;DNA-directed RNA polymerase beta' chain ; × 2 （Q9KWU6） DNA-directed RNA polymerase omega chain × 1 （Q9EVV4） SRN SORANGICIN A × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；Tris, ammonium formate, magnesium formate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.20 Å R-free 0.346

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 1YNJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1HQM CRYSTAL STRUCTURE OF THERMUS AQUATICUS CORE RNA POLYMERASE-INCLUDES COMPLETE STRUCTURE WITH SIDE-CHAINS (EXCEPT FOR DISORDERED REGIONS)-FURTHER REFINED FROM ORIGINAL DEPOSITION-CONTAINS ADDITIONAL SEQUENCE INFORMATION Deposited 2000-12-18	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–314（314 aa） Chain B 1–314（314 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；ammonium sulfate, magnesium chloride, Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.30 Å R-free 0.360
1I6V THERMUS AQUATICUS CORE RNA POLYMERASE-RIFAMPICIN COMPLEX Deposited 2001-03-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–314（314 aa） Fragment：ALPHA SUBUNIT Chain B 1–314（314 aa） Fragment：ALPHA SUBUNIT	Not recorded	RFP RIFAMPICIN × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；Tris-HCl, Ammonium Sulfate, Magensium Chloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.30 Å R-free 0.359
1L9U THERMUS AQUATICUS RNA POLYMERASE HOLOENZYME AT 4 A RESOLUTION Deposited 2002-03-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–314（314 aa） Chain B 1–314（314 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；HEPES, sodium formate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 4.00 Å
1L9U THERMUS AQUATICUS RNA POLYMERASE HOLOENZYME AT 4 A RESOLUTION Deposited 2002-03-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain J 1–314（314 aa） Chain K 1–314（314 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；HEPES, sodium formate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 4.00 Å
1L9Z Thermus aquaticus RNA Polymerase Holoenzyme/Fork-Junction Promoter DNA Complex at 6.5 A Resolution Deposited 2002-03-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain A 1–314（314 aa） Chain B 1–314（314 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；ammonium sulfate, Tris, Magnesium chloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 6.50 Å
1YNN Taq RNA polymerase-rifampicin complex Deposited 2005-01-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–314（314 aa） Chain B 1–314（314 aa）	Not recorded	RFP RIFAMPICIN × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；Tris, magnesium sulfate, ammonium sulfate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.30 Å R-free 0.331
2GHO Recombinant Thermus aquaticus RNA polymerase for Structural Studies Deposited 2006-03-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–314（314 aa） Chain B 1–314（314 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；0.05 M Na cacodylate 10 mM MgCl2 1.0 M Li2SO4, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 5.00 Å R-free 0.337
4XLN Crystal structure of T. aquaticus transcription initiation complex containing bubble promoter and RNA Deposited 2015-01-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric	Chain A 1–314（314 aa） Chain B 1–314（314 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.00 Å R-free 0.315
4XLN Crystal structure of T. aquaticus transcription initiation complex containing bubble promoter and RNA Deposited 2015-01-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 6 PDB declaration: nonameric	Chain G 1–314（314 aa） Chain H 1–314（314 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.00 Å R-free 0.315
4XLP Crystal structure of T.aquaticus transcription initiation complex containing upstream fork promoter Deposited 2015-01-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain A 1–314（314 aa） Chain B 1–314（314 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.00 Å R-free 0.297
4XLP Crystal structure of T.aquaticus transcription initiation complex containing upstream fork promoter Deposited 2015-01-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain G 1–314（314 aa） Chain H 1–314（314 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.00 Å R-free 0.297
4XLQ Crystal structure of T.aquaticus transcription initiation complex containing upstream fork (-11 base-paired) promoter Deposited 2015-01-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain A 1–314（314 aa） Chain B 1–314（314 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.60 Å R-free 0.281
4XLQ Crystal structure of T.aquaticus transcription initiation complex containing upstream fork (-11 base-paired) promoter Deposited 2015-01-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain G 1–314（314 aa） Chain H 1–314（314 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.60 Å R-free 0.281
4XLR Crystal structure of T.aquaticus transcription initiation complex with CarD containing bubble promoter and RNA Deposited 2015-01-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: decameric	Chain A 1–314（314 aa） Chain B 1–314（314 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.30 Å R-free 0.310
4XLR Crystal structure of T.aquaticus transcription initiation complex with CarD containing bubble promoter and RNA Deposited 2015-01-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 7 PDB declaration: decameric	Chain G 1–314（314 aa） Chain H 1–314（314 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.30 Å R-free 0.310
4XLS Crystal structure of T. aquaticus transcription initiation complex with CarD containing upstream fork promoter. Deposited 2015-01-13	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 1–314（314 aa） Chain B 1–314（314 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.01 Å R-free 0.272
4XLS Crystal structure of T. aquaticus transcription initiation complex with CarD containing upstream fork promoter. Deposited 2015-01-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric	Chain G 1–314（314 aa） Chain H 1–314（314 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.01 Å R-free 0.272
4XLS Crystal structure of T. aquaticus transcription initiation complex with CarD containing upstream fork promoter. Deposited 2015-01-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain A 1–314（314 aa） Chain B 1–314（314 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.01 Å R-free 0.272
4XLS Crystal structure of T. aquaticus transcription initiation complex with CarD containing upstream fork promoter. Deposited 2015-01-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain G 1–314（314 aa） Chain H 1–314（314 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.01 Å R-free 0.272
5TJG Thermus aquaticus delta1.1-sigmaA holoenzyme/downstream-fork promoter complex with an open clamp Deposited 2016-10-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: heptameric	Chain A 1–314（314 aa） Chain B 1–314（314 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；0.1 M MES, pH 6.5, 50 mM MgCl2, 5-8% (w/v) polyethylene glycol, 10% (v/v) isopropanol	Resolution 2.60 Å R-free 0.262

12 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RPOA_THEAQ
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–314； UniProt 1–314 Author chain B； PDBConstruct 1–314； UniProt 1–314

DNA-directed RNA polymerase beta chain

OrganismNot specified

UniProt Q9KWU7

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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain C； UniProt 1–1119	Not recorded	DNA-directed RNA polymerase alpha chain × 2 （Q9KWU8） ;DNA-directed RNA polymerase beta' chain ; × 2 （Q9KWU6） DNA-directed RNA polymerase omega chain × 1 （Q9EVV4） SRN SORANGICIN A × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；Tris, ammonium formate, magnesium formate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.20 Å R-free 0.346

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 1YNJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1HQM CRYSTAL STRUCTURE OF THERMUS AQUATICUS CORE RNA POLYMERASE-INCLUDES COMPLETE STRUCTURE WITH SIDE-CHAINS (EXCEPT FOR DISORDERED REGIONS)-FURTHER REFINED FROM ORIGINAL DEPOSITION-CONTAINS ADDITIONAL SEQUENCE INFORMATION Deposited 2000-12-18	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 1–1119（1119 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；ammonium sulfate, magnesium chloride, Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.30 Å R-free 0.360
1I6V THERMUS AQUATICUS CORE RNA POLYMERASE-RIFAMPICIN COMPLEX Deposited 2001-03-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 1–1119（1119 aa） Fragment：BETA SUBUNIT	Not recorded	RFP RIFAMPICIN × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；Tris-HCl, Ammonium Sulfate, Magensium Chloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.30 Å R-free 0.359
1L9U THERMUS AQUATICUS RNA POLYMERASE HOLOENZYME AT 4 A RESOLUTION Deposited 2002-03-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 1–1119（1119 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；HEPES, sodium formate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 4.00 Å
1L9U THERMUS AQUATICUS RNA POLYMERASE HOLOENZYME AT 4 A RESOLUTION Deposited 2002-03-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain L 1–1119（1119 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；HEPES, sodium formate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 4.00 Å
1L9Z Thermus aquaticus RNA Polymerase Holoenzyme/Fork-Junction Promoter DNA Complex at 6.5 A Resolution Deposited 2002-03-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain C 1–1119（1119 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；ammonium sulfate, Tris, Magnesium chloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 6.50 Å
1YNN Taq RNA polymerase-rifampicin complex Deposited 2005-01-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 1–1119（1119 aa）	Not recorded	RFP RIFAMPICIN × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；Tris, magnesium sulfate, ammonium sulfate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.30 Å R-free 0.331
2GHO Recombinant Thermus aquaticus RNA polymerase for Structural Studies Deposited 2006-03-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–1119（1119 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；0.05 M Na cacodylate 10 mM MgCl2 1.0 M Li2SO4, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 5.00 Å R-free 0.337
3MLQ Crystal structure of the Thermus thermophilus transcription-repair coupling factor RNA polymerase interacting domain with the Thermus aquaticus RNA polymerase beta1 domain Deposited 2010-04-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 17–139（123 aa） Fragment：beta1 domain (UNP residues 17-139 and 334-395) Chain A 334–395（62 aa） Fragment：beta1 domain (UNP residues 17-139 and 334-395)	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；0.1 M Tris-HCl, 1.6 M di-potassium ammonium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.91 Å R-free 0.250
3MLQ Crystal structure of the Thermus thermophilus transcription-repair coupling factor RNA polymerase interacting domain with the Thermus aquaticus RNA polymerase beta1 domain Deposited 2010-04-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 17–139（123 aa） Fragment：beta1 domain (UNP residues 17-139 and 334-395) Chain B 334–395（62 aa） Fragment：beta1 domain (UNP residues 17-139 and 334-395)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；0.1 M Tris-HCl, 1.6 M di-potassium ammonium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.91 Å R-free 0.250
3MLQ Crystal structure of the Thermus thermophilus transcription-repair coupling factor RNA polymerase interacting domain with the Thermus aquaticus RNA polymerase beta1 domain Deposited 2010-04-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 17–139（123 aa） Fragment：beta1 domain (UNP residues 17-139 and 334-395) Chain C 334–395（62 aa） Fragment：beta1 domain (UNP residues 17-139 and 334-395)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；0.1 M Tris-HCl, 1.6 M di-potassium ammonium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.91 Å R-free 0.250
3MLQ Crystal structure of the Thermus thermophilus transcription-repair coupling factor RNA polymerase interacting domain with the Thermus aquaticus RNA polymerase beta1 domain Deposited 2010-04-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 17–139（123 aa） Fragment：beta1 domain (UNP residues 17-139 and 334-395) Chain D 334–395（62 aa） Fragment：beta1 domain (UNP residues 17-139 and 334-395)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；0.1 M Tris-HCl, 1.6 M di-potassium ammonium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.91 Å R-free 0.250
4XAX Crystal structure of Thermus thermophilus CarD in complex with the Thermus aquaticus RNA polymerase beta1 domain Deposited 2014-12-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 17–139（123 aa） Chain A 334–392（59 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；Ammonium sulfate, sodium acetate, ethylene gycol	Resolution 2.40 Å R-free 0.180
4XLN Crystal structure of T. aquaticus transcription initiation complex containing bubble promoter and RNA Deposited 2015-01-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric	Chain C 1–1119（1119 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.00 Å R-free 0.315
4XLN Crystal structure of T. aquaticus transcription initiation complex containing bubble promoter and RNA Deposited 2015-01-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 6 PDB declaration: nonameric	Chain I 1–1119（1119 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.00 Å R-free 0.315
4XLP Crystal structure of T.aquaticus transcription initiation complex containing upstream fork promoter Deposited 2015-01-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain C 1–1119（1119 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.00 Å R-free 0.297
4XLP Crystal structure of T.aquaticus transcription initiation complex containing upstream fork promoter Deposited 2015-01-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain I 1–1119（1119 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.00 Å R-free 0.297
4XLQ Crystal structure of T.aquaticus transcription initiation complex containing upstream fork (-11 base-paired) promoter Deposited 2015-01-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain C 1–1119（1119 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.60 Å R-free 0.281
4XLQ Crystal structure of T.aquaticus transcription initiation complex containing upstream fork (-11 base-paired) promoter Deposited 2015-01-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain I 1–1119（1119 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.60 Å R-free 0.281
4XLR Crystal structure of T.aquaticus transcription initiation complex with CarD containing bubble promoter and RNA Deposited 2015-01-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: decameric	Chain C 1–1119（1119 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.30 Å R-free 0.310
4XLR Crystal structure of T.aquaticus transcription initiation complex with CarD containing bubble promoter and RNA Deposited 2015-01-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 7 PDB declaration: decameric	Chain I 1–1119（1119 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.30 Å R-free 0.310
4XLS Crystal structure of T. aquaticus transcription initiation complex with CarD containing upstream fork promoter. Deposited 2015-01-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric	Chain C 1–1119（1119 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.01 Å R-free 0.272
4XLS Crystal structure of T. aquaticus transcription initiation complex with CarD containing upstream fork promoter. Deposited 2015-01-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric	Chain I 1–1119（1119 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.01 Å R-free 0.272
4XLS Crystal structure of T. aquaticus transcription initiation complex with CarD containing upstream fork promoter. Deposited 2015-01-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain C 1–1119（1119 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.01 Å R-free 0.272
4XLS Crystal structure of T. aquaticus transcription initiation complex with CarD containing upstream fork promoter. Deposited 2015-01-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain I 1–1119（1119 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.01 Å R-free 0.272
5TJG Thermus aquaticus delta1.1-sigmaA holoenzyme/downstream-fork promoter complex with an open clamp Deposited 2016-10-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: heptameric	Chain C 1–1119（1119 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；0.1 M MES, pH 6.5, 50 mM MgCl2, 5-8% (w/v) polyethylene glycol, 10% (v/v) isopropanol	Resolution 2.60 Å R-free 0.262

14 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RPOB_THEAQ
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–1119； UniProt 1–1119

;DNA-directed RNA polymerase beta' chain ;

OrganismNot specified

UniProt Q9KWU6

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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain D； UniProt 1–1524 Chain J； UniProt 1–1524	Not recorded	DNA-directed RNA polymerase alpha chain × 2 （Q9KWU8） DNA-directed RNA polymerase beta chain × 1 （Q9KWU7） DNA-directed RNA polymerase omega chain × 1 （Q9EVV4） SRN SORANGICIN A × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；Tris, ammonium formate, magnesium formate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.20 Å R-free 0.346

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 1YNJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1HQM CRYSTAL STRUCTURE OF THERMUS AQUATICUS CORE RNA POLYMERASE-INCLUDES COMPLETE STRUCTURE WITH SIDE-CHAINS (EXCEPT FOR DISORDERED REGIONS)-FURTHER REFINED FROM ORIGINAL DEPOSITION-CONTAINS ADDITIONAL SEQUENCE INFORMATION Deposited 2000-12-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 1–155（155 aa） Chain D 452–1524（1073 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；ammonium sulfate, magnesium chloride, Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.30 Å R-free 0.360
1I6V THERMUS AQUATICUS CORE RNA POLYMERASE-RIFAMPICIN COMPLEX Deposited 2001-03-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 1–1524（1524 aa） Fragment：BETA-PRIME SUBUNIT	Not recorded	RFP RIFAMPICIN × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；Tris-HCl, Ammonium Sulfate, Magensium Chloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.30 Å R-free 0.359
1L9U THERMUS AQUATICUS RNA POLYMERASE HOLOENZYME AT 4 A RESOLUTION Deposited 2002-03-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 1–1524（1524 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；HEPES, sodium formate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 4.00 Å
1L9U THERMUS AQUATICUS RNA POLYMERASE HOLOENZYME AT 4 A RESOLUTION Deposited 2002-03-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain M 1–1524（1524 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；HEPES, sodium formate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 4.00 Å
1L9Z Thermus aquaticus RNA Polymerase Holoenzyme/Fork-Junction Promoter DNA Complex at 6.5 A Resolution Deposited 2002-03-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain D 1–1524（1524 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；ammonium sulfate, Tris, Magnesium chloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 6.50 Å
1YNN Taq RNA polymerase-rifampicin complex Deposited 2005-01-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 1–1524（1524 aa） Chain J 1–1524（1524 aa）	Not recorded	RFP RIFAMPICIN × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；Tris, magnesium sulfate, ammonium sulfate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.30 Å R-free 0.331
2AUJ Structure of Thermus aquaticus RNA polymerase beta'-subunit insert Deposited 2005-08-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 151–455（305 aa） Fragment：residues 151-455	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；sodium cacodylate/magnesium acetate/polyethylene glycol 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.279
2GHO Recombinant Thermus aquaticus RNA polymerase for Structural Studies Deposited 2006-03-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–158（158 aa） Chain D 452–1524（1073 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；0.05 M Na cacodylate 10 mM MgCl2 1.0 M Li2SO4, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 5.00 Å R-free 0.337
4XLN Crystal structure of T. aquaticus transcription initiation complex containing bubble promoter and RNA Deposited 2015-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric	Chain D 1–1524（1524 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.00 Å R-free 0.315
4XLN Crystal structure of T. aquaticus transcription initiation complex containing bubble promoter and RNA Deposited 2015-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 6 PDB declaration: nonameric	Chain J 1–1524（1524 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.00 Å R-free 0.315
4XLP Crystal structure of T.aquaticus transcription initiation complex containing upstream fork promoter Deposited 2015-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain D 1–1524（1524 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.00 Å R-free 0.297
4XLP Crystal structure of T.aquaticus transcription initiation complex containing upstream fork promoter Deposited 2015-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain J 1–1524（1524 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.00 Å R-free 0.297
4XLQ Crystal structure of T.aquaticus transcription initiation complex containing upstream fork (-11 base-paired) promoter Deposited 2015-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain D 1–1524（1524 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.60 Å R-free 0.281
4XLQ Crystal structure of T.aquaticus transcription initiation complex containing upstream fork (-11 base-paired) promoter Deposited 2015-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain J 1–1524（1524 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.60 Å R-free 0.281
4XLR Crystal structure of T.aquaticus transcription initiation complex with CarD containing bubble promoter and RNA Deposited 2015-01-13	Different construct Different mutation/modification 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 1–1524（1524 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.30 Å R-free 0.310
4XLR Crystal structure of T.aquaticus transcription initiation complex with CarD containing bubble promoter and RNA Deposited 2015-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 7 PDB declaration: decameric	Chain J 1–1524（1524 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.30 Å R-free 0.310
4XLS Crystal structure of T. aquaticus transcription initiation complex with CarD containing upstream fork promoter. Deposited 2015-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric	Chain D 1–1524（1524 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.01 Å R-free 0.272
4XLS Crystal structure of T. aquaticus transcription initiation complex with CarD containing upstream fork promoter. Deposited 2015-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric	Chain J 1–1524（1524 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.01 Å R-free 0.272
4XLS Crystal structure of T. aquaticus transcription initiation complex with CarD containing upstream fork promoter. Deposited 2015-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain D 1–1524（1524 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.01 Å R-free 0.272
4XLS Crystal structure of T. aquaticus transcription initiation complex with CarD containing upstream fork promoter. Deposited 2015-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain J 1–1524（1524 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.01 Å R-free 0.272
5TJG Thermus aquaticus delta1.1-sigmaA holoenzyme/downstream-fork promoter complex with an open clamp Deposited 2016-10-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: heptameric	Chain D 1–1524（1524 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；0.1 M MES, pH 6.5, 50 mM MgCl2, 5-8% (w/v) polyethylene glycol, 10% (v/v) isopropanol	Resolution 2.60 Å R-free 0.262

13 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RPOC_THEAQ
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–1524； UniProt 1–1524 Author chain J； PDBConstruct 1–1524； UniProt 1–1524

DNA-directed RNA polymerase omega chain

OrganismNot specified

UniProt Q9EVV4

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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain K； UniProt 0–98	Not recorded	DNA-directed RNA polymerase alpha chain × 2 （Q9KWU8） DNA-directed RNA polymerase beta chain × 1 （Q9KWU7） ;DNA-directed RNA polymerase beta' chain ; × 2 （Q9KWU6） SRN SORANGICIN A × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；Tris, ammonium formate, magnesium formate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.20 Å R-free 0.346

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 1YNJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1HQM CRYSTAL STRUCTURE OF THERMUS AQUATICUS CORE RNA POLYMERASE-INCLUDES COMPLETE STRUCTURE WITH SIDE-CHAINS (EXCEPT FOR DISORDERED REGIONS)-FURTHER REFINED FROM ORIGINAL DEPOSITION-CONTAINS ADDITIONAL SEQUENCE INFORMATION Deposited 2000-12-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 1–99（99 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；ammonium sulfate, magnesium chloride, Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.30 Å R-free 0.360
1I6V THERMUS AQUATICUS CORE RNA POLYMERASE-RIFAMPICIN COMPLEX Deposited 2001-03-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 1–99（99 aa） Fragment：OMEGA SUBUNIT	Not recorded	RFP RIFAMPICIN × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；Tris-HCl, Ammonium Sulfate, Magensium Chloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.30 Å R-free 0.359
1L9U THERMUS AQUATICUS RNA POLYMERASE HOLOENZYME AT 4 A RESOLUTION Deposited 2002-03-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 0–98（99 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；HEPES, sodium formate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 4.00 Å
1L9U THERMUS AQUATICUS RNA POLYMERASE HOLOENZYME AT 4 A RESOLUTION Deposited 2002-03-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain N 0–98（99 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；HEPES, sodium formate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 4.00 Å
1L9Z Thermus aquaticus RNA Polymerase Holoenzyme/Fork-Junction Promoter DNA Complex at 6.5 A Resolution Deposited 2002-03-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain E 0–98（99 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；ammonium sulfate, Tris, Magnesium chloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 6.50 Å
1YNN Taq RNA polymerase-rifampicin complex Deposited 2005-01-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain K 0–98（99 aa）	Not recorded	RFP RIFAMPICIN × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；Tris, magnesium sulfate, ammonium sulfate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.30 Å R-free 0.331
4XLN Crystal structure of T. aquaticus transcription initiation complex containing bubble promoter and RNA Deposited 2015-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric	Chain E 1–99（99 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.00 Å R-free 0.315
4XLN Crystal structure of T. aquaticus transcription initiation complex containing bubble promoter and RNA Deposited 2015-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 6 PDB declaration: nonameric	Chain K 1–99（99 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.00 Å R-free 0.315
4XLP Crystal structure of T.aquaticus transcription initiation complex containing upstream fork promoter Deposited 2015-01-13	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 E 1–99（99 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.00 Å R-free 0.297
4XLP Crystal structure of T.aquaticus transcription initiation complex containing upstream fork promoter Deposited 2015-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain K 1–99（99 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.00 Å R-free 0.297
4XLQ Crystal structure of T.aquaticus transcription initiation complex containing upstream fork (-11 base-paired) promoter Deposited 2015-01-13	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 E 1–99（99 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.60 Å R-free 0.281
4XLQ Crystal structure of T.aquaticus transcription initiation complex containing upstream fork (-11 base-paired) promoter Deposited 2015-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain K 1–99（99 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.60 Å R-free 0.281
4XLR Crystal structure of T.aquaticus transcription initiation complex with CarD containing bubble promoter and RNA Deposited 2015-01-13	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 E 1–99（99 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.30 Å R-free 0.310
4XLR Crystal structure of T.aquaticus transcription initiation complex with CarD containing bubble promoter and RNA Deposited 2015-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 7 PDB declaration: decameric	Chain K 1–99（99 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.30 Å R-free 0.310
4XLS Crystal structure of T. aquaticus transcription initiation complex with CarD containing upstream fork promoter. Deposited 2015-01-13	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 E 1–99（99 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.01 Å R-free 0.272
4XLS Crystal structure of T. aquaticus transcription initiation complex with CarD containing upstream fork promoter. Deposited 2015-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric	Chain K 1–99（99 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.01 Å R-free 0.272
4XLS Crystal structure of T. aquaticus transcription initiation complex with CarD containing upstream fork promoter. Deposited 2015-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain E 1–99（99 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.01 Å R-free 0.272
4XLS Crystal structure of T. aquaticus transcription initiation complex with CarD containing upstream fork promoter. Deposited 2015-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain K 1–99（99 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, magnesium chloride, Tris-HCl	Resolution 4.01 Å R-free 0.272
5TJG Thermus aquaticus delta1.1-sigmaA holoenzyme/downstream-fork promoter complex with an open clamp Deposited 2016-10-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: heptameric	Chain E 1–99（99 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；0.1 M MES, pH 6.5, 50 mM MgCl2, 5-8% (w/v) polyethylene glycol, 10% (v/v) isopropanol	Resolution 2.60 Å R-free 0.262

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

View Construct and Data Evidence

UniProt name	RPOZ_THEAQ
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain K； PDBConstruct 1–99； UniProt 0–98

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1ynj
Deposition date deposition_date	2005-01-24
Structure title title	Taq RNA polymerase-Sorangicin complex
Keywords keywords	TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	53.49 Å
Radius of gyration Rg (electron density) rg_electron	54.20 Å
Forward intensity I(0) i0	1686970000.00
Molecular weight molecular_weight	345750.0 kDa
Excluded volume excluded_volume	434650 Å³
Envelope volume envelope_volume	638940 Å³
Hydration-shell volume shell_volume	102170 Å³
Envelope diameter envelope_diameter	230.8 Å
Shell Rg shell_rg	55.49 Å
Envelope Rg envelope_rg	55.13 Å
Shape Rg shape_rg	54.23 Å
Total Rg total_rg	54.13 Å
Total atoms total_atoms	24369
Residues n_residues	3151
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	214.5 Å
Rg (real space) rg_real	54.16 Å
Rg uncertainty (real space) rg_real_error	2.70 Å
I(0) (real space) i0_real	1.6870e+09
I(0) uncertainty (real space) i0_real_error	3.3100e+07
Rg (reciprocal space) rg_reciprocal	52.98 Å
I(0) (reciprocal space) i0_reciprocal	1684000000.0000
Solution quality estimate total_estimate	0.7452
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	59.2 Å
Skewness Skewness skewness	0.982
Kurtosis Kurtosis kurtosis	1.271
Angular range angular_range	— – 0.1450 Å⁻¹
Current regularization parameter α current_alpha	0.0003
Highest regularization parameter α highest_alpha	168600000.0000
Real-space data points n_real_points	30
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.272; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.944; Smooth: 0.924

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	DNA-directed RNA polymerase alpha chain
Molecular weight formula_weight	34830.9 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	24369

MLESKLKAPVFTATTQGDHYGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLKELVVRFLDPKMASTTLILRAEGPKEVRAGDFTPSADVEIMNPDLHIATLEEGGKLYMEVRVDRGVGYVPAERHGIKDRINAIPVDAIFSPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSVTPLEALNQAVAILKEHLNYFANPEASLLPTPEVSKGEKRESAEEDLDLPLEELGLSTRVLHSLKEEGIESVRALLALNLKDLRNIPGIGERSLEEIRQALAKKGFTLKE

Entity 2 Entity 2 polymer

Description description	DNA-directed RNA polymerase beta chain
Molecular weight formula_weight	124930.0 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MEIKRFGRIREVIPLPPLTEIQVESYKKALQADVPPEKRENVGIQAAFKETFPIEEGDKGKGGLVLDFLEYRIGDPPFSQDECREKDLTYQAPLYARLQLIHKDTGLIKEDEVFLGHLPLMTEDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGRYIASIIPLPKRGPWIDLEVEASGVVTMKVNKRKFPLVLLLRVLGYDQETLVRELSAYGDLVQGLLDEAVLAMRPEEAMVRLFTLLRPGDPPKKDKALAYLFGLLADPKRYDLGEAGRYKAEEKLGVGLSGRTLVRFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMADQFRVGLARLARGVRERMVMGSPDTLTPAKLVNSRPLEAALREFFSRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARVDALGFIRTPYRRVKNGVVTEEVVYMTASEEDRYTIAQANTPLEGDRIATDRVVARRRGEPVIVAPEEVEFMDVSPKQVFSLNTNLIPFLEHDDANRALMGSNMQTQAVPLIRAQAPVVMTGLEERVVRDSLAALYAEEDGEVVKVDGTRIAVRYEDGRLVEHPLRRYARSNQGTAFDQRPRVRVGQRVKKGDLLADGPASEEGFLALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPERITRDIPHLSEAALRDLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVGRLRLRRGDPGVELKPGVREVVRVFVAQKRKLQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQRYISPVFDGATEPEIKELLAEAFNLYFGKRQGEGFGVDKREKEVLARAEKLGLVSPGKSPEEQLKELFDLGKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTIKSDDIEGRNAAYQAIIKGEDVPEPSVPESFRVLVKELQALALDVQTLDEKDNPVDIFEGLASKR

Entity 3 Entity 3 polymer

Description description	;DNA-directed RNA polymerase beta' chain ;
Molecular weight formula_weight	171187.5 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,J

MKKEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKYKRQRFEGKVCERCGVEVTRSIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLSATELEQVLYFNKYIVLDPKGAVLDGVPVEKRQLLTDEEYRELRYGKQETYPLPAGVDALVKDGEEVVKGQELAPGVVSRMDGVALYRFPRRVRVDYLRKERAALRIPLSAWVEKEAYRPGEVLAELSEPYLFRAEESGVVELKDLAEGHLIYLRQEEEVVARYFLPAGMTPLVVEGEIVEVGQPLAEGKGLLRLPRHMTAKEVEAEEEGDSVHLTLFLEWTEPKDYKVAPHMNVIVPEGAKVQAGEKIVAAIDPEEEVIAEAEGVVHLHEPASILVVKARVYPFEDDVEVTTGDRVAPGDVLADGGKVKSEIYGRVEVDLVRNVVRVVESYDIDARMGAEAIQELLKELDLEKLERELLEEMKHPSRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDAVIDNGRRGSPVTNPGSERPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKAFAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGMAFATPEEALAAYERGEVALNAPIVVAGRETSVGRLKFVFANPDEALLAVAHGLLDLQDVVTVRYLGRRLETSPGRILFARIVGEAVGDEKVAQELIQMDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTLSTTSGITIGIDDAVIPEEKQRYLEEADRKLRQIEQAYEMGFLTDRERYDQVIQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGMRGLMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVAHEIVVREADCGTTNYISVPLFQMDEVTRTLRLRKRSDIESGLYGRVLAREVEALGRRLEEGRYLSLEDVHFLIKAAEAGEVREVPVRSPLTCQTRYGVCQKCYGYDLSMARPVSIGEAVGVVAAESIGEPGTQLTMRTFHTGGVAVGTDITQGLPRVIELFEARRPKAKAVISEIDGVVRIEEGEDRLSVFVESEGFSKEYKLPKDARLLVKDGDYVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVDEIQKVYRAQGVKLHDKHIEIVVRQMLKYVEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKVPVAWKPLLMGVTKSALSTKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVVDQRTLKAIEEARKEAVEAKEKEAPRRPVRREQPGKGL

Entity 4 Entity 4 polymer

Description description	DNA-directed RNA polymerase omega chain
Molecular weight formula_weight	11642.4 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

MAEPGIDKLFGMVDSKYRLTVVVAKRAQQLLRHRFKNTVLEPEERPKMRTLEGLYDDPNAVTWAMKELLTGRLFFGENLVPEDRLQKEMERLYPTEEEA

Entity 5 Entity 5 non-polymer

Description description	SORANGICIN A
Molecular weight formula_weight	807.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

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7. Fold Classification (SCOP + CATH) 25 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d1ynja1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.74 — DCoH-like
Superfamily Superfamily superfamily	d.74.3 — RBP11-like subunits of RNA polymerase
Family Family family	d.74.3.1 — RNA polymerase alpha subunit dimerisation domain

Domain ID domain_id	d1ynja2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.181 — Insert subdomain of RNA polymerase alpha subunit
Superfamily Superfamily superfamily	d.181.1 — Insert subdomain of RNA polymerase alpha subunit
Family Family family	d.181.1.1 — Insert subdomain of RNA polymerase alpha subunit

Domain ID domain_id	d1ynjb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.74 — DCoH-like
Superfamily Superfamily superfamily	d.74.3 — RBP11-like subunits of RNA polymerase
Family Family family	d.74.3.1 — RNA polymerase alpha subunit dimerisation domain

Domain ID domain_id	d1ynjb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.181 — Insert subdomain of RNA polymerase alpha subunit
Superfamily Superfamily superfamily	d.181.1 — Insert subdomain of RNA polymerase alpha subunit
Family Family family	d.181.1.1 — Insert subdomain of RNA polymerase alpha subunit

Domain ID domain_id	d1ynjc1
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.29 — beta and beta-prime subunits of DNA dependent RNA-polymerase
Superfamily Superfamily superfamily	e.29.1 — beta and beta-prime subunits of DNA dependent RNA-polymerase
Family Family family	e.29.1.1 — RNA-polymerase beta

Domain ID domain_id	d1ynjd1
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.29 — beta and beta-prime subunits of DNA dependent RNA-polymerase
Superfamily Superfamily superfamily	e.29.1 — beta and beta-prime subunits of DNA dependent RNA-polymerase
Family Family family	e.29.1.2 — RNA-polymerase beta-prime

Domain ID domain_id	d1ynjk1
Class class	a — All alpha proteins
Fold Fold fold	a.143 — RPB6/omega subunit-like
Superfamily Superfamily superfamily	a.143.1 — RPB6/omega subunit-like
Family Family family	a.143.1.1 — RNA polymerase omega subunit

CATH v4.4 (18 domains)

Domain ID domain_id	1ynjA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	10 — RNA polymerase, RBP11-like subunit

Domain ID domain_id	1ynjA02
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	120 — RNA Polymerase Alpha Subunit; Chain A, domain 2
Homologous superfamily homologous superfamily	12 — DNA-directed RNA polymerase, insert domain

Domain ID domain_id	1ynjB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	10 — RNA polymerase, RBP11-like subunit

Domain ID domain_id	1ynjB02
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	120 — RNA Polymerase Alpha Subunit; Chain A, domain 2
Homologous superfamily homologous superfamily	12 — DNA-directed RNA polymerase, insert domain

Domain ID domain_id	1ynjC01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	270 — Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6
Homologous superfamily homologous superfamily	10 — DNA-directed RNA polymerase, subunit 2, domain 6

Domain ID domain_id	1ynjC02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1100 — Rna Polymerase Beta Subunit; Chain: C,domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1ynjC03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1110 — Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3
Homologous superfamily homologous superfamily	10 — RNA polymerase Rpb2, domain 2

Domain ID domain_id	1ynjC04
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	150 — Rna Polymerase Beta Subunit; Chain: C, domain 4
Homologous superfamily homologous superfamily	10 — DNA-directed RNA polymerase, beta subunit, external 1 domain

Domain ID domain_id	1ynjC05
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

Domain ID domain_id	1ynjC06
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	150 — RNA polymerase II, Rpb2 subunit, wall domain

Domain ID domain_id	1ynjD03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

Domain ID domain_id	1ynjD04
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1ynjD05
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	274 — Enzyme I; Chain A, domain 2
Homologous superfamily homologous superfamily	100 — RNA polymerase Rpb1, domain 3

Domain ID domain_id	1ynjD06
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	132 — Topoisomerase I; Chain A, domain 4
Homologous superfamily homologous superfamily	30 — RNA polymerase Rpb1 funnel domain

Domain ID domain_id	1ynjJ01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1790 — PTS-regulatory domain, PRD
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1ynjJ02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

Domain ID domain_id	1ynjJ03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	390 —

Domain ID domain_id	1ynjK00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	940 — Eukaryotic RPB6 RNA polymerase subunit
Homologous superfamily homologous superfamily	10 — RNA polymerase subunit, RPB6/omega

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8. Citations (1)

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Unit-cell length a length_a	199.190 Å
Unit-cell length b length_b	199.190 Å
Unit-cell length c length_c	289.306 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2844
R_work r_work	0.2812
R_free r_free	0.3461

fit	/app/data/saxs_computation/yn/1ynj/1ynj.fit
pddf	/app/data/pr_computation/yn/1ynj/1ynj.pr.out
profile	/app/data/saxs_computation/yn/1ynj/1ynj.dat

Taq RNA polymerase-Sorangicin complex

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

DNA-directed RNA polymerase alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerase beta chain

State in the Current Structure

Other States of the Same Protein in the Database

;DNA-directed RNA polymerase beta' chain ;

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerase omega chain

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

7. Fold Classification (SCOP + CATH) 25 domains

SCOP 2.08 (7 domains)

CATH v4.4 (18 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)