8dh4

T7 RNA polymerase elongation complex with unnatural base dPa-DsTP pair

Method: X-RAY DIFFRACTION D_max: 197.4 Å Quality: REASONABLE

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

T7 RNA polymerase

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	Other combination Monomer Protein × 1 DNA 2 RNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain B； UniProt 1–883	Not recorded	Template strand DNA × 1 RNA × 1 Non-template strand DNA × 1 S96 (7P)-3-{5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-ribofuranosyl}-7-(thiophen-2-yl)-3H-imidazo[4,5-b]pyridine × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.1；298 K；10% PEG 8000, 8% glycerol, 5 mM B-mercaptoethanol, 100 mM Tris pH 8.1	Resolution 2.80 Å R-free 0.275
2	Other combination Monomer Protein × 1 DNA 2 RNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain E； UniProt 1–883	Not recorded	Template strand DNA × 1 RNA × 1 Non-template strand DNA × 1 S96 (7P)-3-{5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-ribofuranosyl}-7-(thiophen-2-yl)-3H-imidazo[4,5-b]pyridine × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.1；298 K；10% PEG 8000, 8% glycerol, 5 mM B-mercaptoethanol, 100 mM Tris pH 8.1	Resolution 2.80 Å R-free 0.275
3	Other combination Monomer Protein × 1 DNA 2 RNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain I； UniProt 1–883	Not recorded	Template strand DNA × 1 RNA × 1 Non-template strand DNA × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.1；298 K；10% PEG 8000, 8% glycerol, 5 mM B-mercaptoethanol, 100 mM Tris pH 8.1	Resolution 2.80 Å R-free 0.275
4	Other combination Monomer Protein × 1 DNA 2 RNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain M； UniProt 1–883	Not recorded	Template strand DNA × 1 RNA × 1 Non-template strand DNA × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.1；298 K；10% PEG 8000, 8% glycerol, 5 mM B-mercaptoethanol, 100 mM Tris pH 8.1	Resolution 2.80 Å R-free 0.275

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 8DH4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ARO T7 RNA POLYMERASE COMPLEXED WITH T7 LYSOZYME Deposited 1997-08-08	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 P 1–883（883 aa）	Mutation：C347S, C723S, C839S	HG MERCURY (II) ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 2.80 Å R-free 0.309
1CEZ CRYSTAL STRUCTURE OF A T7 RNA POLYMERASE-T7 PROMOTER COMPLEX Deposited 1999-03-11	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–883（883 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.7；pH 8.7	Resolution 2.40 Å R-free 0.270
1H38 Structure of a T7 RNA polymerase elongation complex at 2.9A resolution Deposited 2002-08-24	Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric	Chain A 1–883（883 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.1；10% PEG 8000, 8% GLYCEROL, 5MM BETA-MERCAPTOETHANOL,100 MM TRIS BUFFER, PH8.1, pH 8.10	Resolution 2.90 Å R-free 0.284
1H38 Structure of a T7 RNA polymerase elongation complex at 2.9A resolution Deposited 2002-08-24	Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: tetrameric	Chain B 1–883（883 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.1；10% PEG 8000, 8% GLYCEROL, 5MM BETA-MERCAPTOETHANOL,100 MM TRIS BUFFER, PH8.1, pH 8.10	Resolution 2.90 Å R-free 0.284
1H38 Structure of a T7 RNA polymerase elongation complex at 2.9A resolution Deposited 2002-08-24	Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Monomer；Protein × 1 PDB declaration: tetrameric	Chain C 1–883（883 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.1；10% PEG 8000, 8% GLYCEROL, 5MM BETA-MERCAPTOETHANOL,100 MM TRIS BUFFER, PH8.1, pH 8.10	Resolution 2.90 Å R-free 0.284
1H38 Structure of a T7 RNA polymerase elongation complex at 2.9A resolution Deposited 2002-08-24	Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Monomer；Protein × 1 PDB declaration: tetrameric	Chain D 1–883（883 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.1；10% PEG 8000, 8% GLYCEROL, 5MM BETA-MERCAPTOETHANOL,100 MM TRIS BUFFER, PH8.1, pH 8.10	Resolution 2.90 Å R-free 0.284
1MSW Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase Deposited 2002-09-19	Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric	Chain D 1–883（883 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；PEG 8000, LiSO4, Mg(OAc)2, Tris-HCL, pH 7.0, VAPOR DIFFUSION, HANGING DROP at 294K	Resolution 2.10 Å R-free 0.275
1S0V Structural basis for substrate selection by T7 RNA polymerase Deposited 2004-01-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric	Chain A 1–882（882 aa）	Not recorded	MG MAGNESIUM ION × 2 APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.20 Å R-free 0.307
1S0V Structural basis for substrate selection by T7 RNA polymerase Deposited 2004-01-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: tetrameric	Chain B 1–882（882 aa）	Not recorded	MG MAGNESIUM ION × 2 APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.20 Å R-free 0.307
1S0V Structural basis for substrate selection by T7 RNA polymerase Deposited 2004-01-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Monomer；Protein × 1 PDB declaration: tetrameric	Chain C 1–882（882 aa）	Not recorded	MG MAGNESIUM ION × 2 APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.20 Å R-free 0.307
1S0V Structural basis for substrate selection by T7 RNA polymerase Deposited 2004-01-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Monomer；Protein × 1 PDB declaration: tetrameric	Chain D 1–882（882 aa）	Not recorded	MG MAGNESIUM ION × 2 APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.20 Å R-free 0.307
1S76 T7 RNA polymerase alpha beta methylene ATP elongation complex Deposited 2004-01-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric	Chain D 1–883（883 aa）	Not recorded	APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；T7 RNAP, DNA, RNA, alpha-beta methylene ATP, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.88 Å R-free 0.290
1S77 T7 RNAP product pyrophosphate elongation complex Deposited 2004-01-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric	Chain D 1–883（883 aa）	Not recorded	MG MAGNESIUM ION × 2 POP PYROPHOSPHATE 2- × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；T7RNAP, DNA,RNA, 3'deoxyATP, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.69 Å R-free 0.285
2PI4 T7RNAP complexed with a phi10 protein and initiating GTPs. Deposited 2007-04-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 6–883（878 aa）	Not recorded	MG MAGNESIUM ION × 2 GH3 3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；300 K；50 mM Tris-HCl, 200 mM Li2SO4, 20% PEG 8000, 5% Glycerol, 15 mM magnesium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 2.50 Å R-free 0.297
2PI5 T7 RNA polymerase complexed with a phi10 promoter Deposited 2007-04-12	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 6–883（878 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；300 K；50 mM Tris-HCl, 200 mM Li2SO4, 20% PEG 8000, 5% Glycerol, 15 mM magnesium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 2.90 Å R-free 0.268
3E2E Crystal Structure of an Intermediate Complex of T7 RNAP and 7nt of RNA Deposited 2008-08-05	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric	Chain A 1–883（883 aa）	Mutation：P266L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；285 K；PEG 6000, MgCl2, Tris ph8.0 at 285K, VAPOR DIFFUSION, SITTING DROP	Resolution 3.00 Å R-free 0.292
3E3J Crystal Structure of an Intermediate Complex of T7 RNAP and 8nt of RNA Deposited 2008-08-07	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric	Chain B 1–883（883 aa）	Mutation：P266L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；285 K；PEG 6000, MgCl2, Tris ph8.5 at 285K, VAPOR DIFFUSION, SITTING DROP	Resolution 6.70 Å R-free 0.454
3E3J Crystal Structure of an Intermediate Complex of T7 RNAP and 8nt of RNA Deposited 2008-08-07	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: tetrameric	Chain C 1–883（883 aa）	Mutation：P266L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；285 K；PEG 6000, MgCl2, Tris ph8.5 at 285K, VAPOR DIFFUSION, SITTING DROP	Resolution 6.70 Å R-free 0.454
4RNP BACTERIOPHAGE T7 RNA POLYMERASE, HIGH SALT CRYSTAL FORM, LOW TEMPERATURE DATA, ALPHA-CARBONS ONLY Deposited 1997-09-11	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–883（883 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å
4RNP BACTERIOPHAGE T7 RNA POLYMERASE, HIGH SALT CRYSTAL FORM, LOW TEMPERATURE DATA, ALPHA-CARBONS ONLY Deposited 1997-09-11	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–883（883 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å
4RNP BACTERIOPHAGE T7 RNA POLYMERASE, HIGH SALT CRYSTAL FORM, LOW TEMPERATURE DATA, ALPHA-CARBONS ONLY Deposited 1997-09-11	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–883（883 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å
8DH0 T7 RNA polymerase elongation complex with unnatural base dDs Deposited 2022-06-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetradecameric	Chain B 1–883（883 aa） Chain F 1–883（883 aa） Chain J 1–883（883 aa） Chain N 1–883（883 aa）	Not recorded	GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；298 K；10% PEG 8000, 8% glycerol, 5 mM B-mercaptoethanol, 100 mM Tris pH 8.1	Resolution 2.90 Å R-free 0.261
8DH1 T7 RNA polymerase elongation complex with unnatural base dDs-PaTP pair Deposited 2022-06-24	Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric	Chain B 1–883（883 aa）	Not recorded	GOL GLYCEROL × 2 S8L 1-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-ribofuranosyl}-1H-pyrrole-2-carbaldehyde × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；298 K；10% PEG 8000, 8% glycerol, 5 mM B-mercaptoethanol, 100 mM Tris pH 8.1	Resolution 2.65 Å R-free 0.272
8DH1 T7 RNA polymerase elongation complex with unnatural base dDs-PaTP pair Deposited 2022-06-24	Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: tetrameric	Chain E 1–883（883 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；298 K；10% PEG 8000, 8% glycerol, 5 mM B-mercaptoethanol, 100 mM Tris pH 8.1	Resolution 2.65 Å R-free 0.272
8DH1 T7 RNA polymerase elongation complex with unnatural base dDs-PaTP pair Deposited 2022-06-24	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 3 Other combination Monomer；Protein × 1 PDB declaration: trimeric	Chain I 1–883（883 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；298 K；10% PEG 8000, 8% glycerol, 5 mM B-mercaptoethanol, 100 mM Tris pH 8.1	Resolution 2.65 Å R-free 0.272
8DH1 T7 RNA polymerase elongation complex with unnatural base dDs-PaTP pair Deposited 2022-06-24	Different structure-quality metrics	Assembly 4 Other combination Monomer；Protein × 1 PDB declaration: tetrameric	Chain L 1–883（883 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；298 K；10% PEG 8000, 8% glycerol, 5 mM B-mercaptoethanol, 100 mM Tris pH 8.1	Resolution 2.65 Å R-free 0.272
8DH2 T7 RNA polymerase elongation complex with unnatural base dDs-ATP mismatch Deposited 2022-06-24	Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric	Chain B 1–883（883 aa）	Not recorded	GOL GLYCEROL × 2 3PO TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；298 K；10% PEG 8000, 8% glycerol, 5 mM B-mercaptoethanol, 100 mM Tris pH 8.1	Resolution 2.90 Å R-free 0.307
8DH2 T7 RNA polymerase elongation complex with unnatural base dDs-ATP mismatch Deposited 2022-06-24	Different ligand/ion Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: tetrameric	Chain E 1–883（883 aa）	Not recorded	3PO TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；298 K；10% PEG 8000, 8% glycerol, 5 mM B-mercaptoethanol, 100 mM Tris pH 8.1	Resolution 2.90 Å R-free 0.307
8DH2 T7 RNA polymerase elongation complex with unnatural base dDs-ATP mismatch Deposited 2022-06-24	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 3 Other combination Monomer；Protein × 1 PDB declaration: trimeric	Chain I 1–883（883 aa）	Not recorded	GOL GLYCEROL × 1 3PO TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；298 K；10% PEG 8000, 8% glycerol, 5 mM B-mercaptoethanol, 100 mM Tris pH 8.1	Resolution 2.90 Å R-free 0.307
8DH2 T7 RNA polymerase elongation complex with unnatural base dDs-ATP mismatch Deposited 2022-06-24	Different ligand/ion Different structure-quality metrics	Assembly 4 Other combination Monomer；Protein × 1 PDB declaration: tetrameric	Chain L 1–883（883 aa）	Not recorded	3PO TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；298 K；10% PEG 8000, 8% glycerol, 5 mM B-mercaptoethanol, 100 mM Tris pH 8.1	Resolution 2.90 Å R-free 0.307
8DH3 T7 RNA polymerase elongation complex with unnatural base dPa Deposited 2022-06-24	Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric	Chain B 1–883（883 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；298 K；10% PEG 8000, 8% glycerol, 5 mM B-mercaptoethanol, 100 mM Tris pH 8.1	Resolution 3.00 Å R-free 0.276
8DH3 T7 RNA polymerase elongation complex with unnatural base dPa Deposited 2022-06-24	Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: tetrameric	Chain E 1–883（883 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；298 K；10% PEG 8000, 8% glycerol, 5 mM B-mercaptoethanol, 100 mM Tris pH 8.1	Resolution 3.00 Å R-free 0.276
8DH3 T7 RNA polymerase elongation complex with unnatural base dPa Deposited 2022-06-24	Different structure-quality metrics	Assembly 3 Other combination Monomer；Protein × 1 PDB declaration: tetrameric	Chain I 1–883（883 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；298 K；10% PEG 8000, 8% glycerol, 5 mM B-mercaptoethanol, 100 mM Tris pH 8.1	Resolution 3.00 Å R-free 0.276
8DH3 T7 RNA polymerase elongation complex with unnatural base dPa Deposited 2022-06-24	Different structure-quality metrics	Assembly 4 Other combination Monomer；Protein × 1 PDB declaration: tetrameric	Chain M 1–883（883 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；298 K；10% PEG 8000, 8% glycerol, 5 mM B-mercaptoethanol, 100 mM Tris pH 8.1	Resolution 3.00 Å R-free 0.276
8DH5 T7 RNA polymerase elongation complex with unnatural base dPa-ATP mismatch Deposited 2022-06-24	Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric	Chain B 1–883（883 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；298 K；10% PEG 8000, 8% glycerol, 5 mM B-mercaptoethanol, 100 mM Tris pH 8.1	Resolution 2.85 Å R-free 0.267
8DH5 T7 RNA polymerase elongation complex with unnatural base dPa-ATP mismatch Deposited 2022-06-24	Different ligand/ion Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: tetrameric	Chain E 1–883（883 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；298 K；10% PEG 8000, 8% glycerol, 5 mM B-mercaptoethanol, 100 mM Tris pH 8.1	Resolution 2.85 Å R-free 0.267
8DH5 T7 RNA polymerase elongation complex with unnatural base dPa-ATP mismatch Deposited 2022-06-24	Different ligand/ion Different structure-quality metrics	Assembly 3 Other combination Monomer；Protein × 1 PDB declaration: tetrameric	Chain I 1–883（883 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；298 K；10% PEG 8000, 8% glycerol, 5 mM B-mercaptoethanol, 100 mM Tris pH 8.1	Resolution 2.85 Å R-free 0.267
8DH5 T7 RNA polymerase elongation complex with unnatural base dPa-ATP mismatch Deposited 2022-06-24	Different ligand/ion Different structure-quality metrics	Assembly 4 Other combination Monomer；Protein × 1 PDB declaration: tetrameric	Chain M 1–883（883 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；298 K；10% PEG 8000, 8% glycerol, 5 mM B-mercaptoethanol, 100 mM Tris pH 8.1	Resolution 2.85 Å R-free 0.267
9YXM 10-23 DNAzyme in complex with T7 RNA Polymerase Deposited 2025-10-27	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–883（883 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 4.62 Å

18 other PDB entries and 39 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RPOL_BPT7
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 1–883； UniProt 1–883 Author chain E； PDBConstruct 1–883； UniProt 1–883 Author chain I； PDBConstruct 1–883； UniProt 1–883 Author chain M； PDBConstruct 1–883； UniProt 1–883

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	8dh4
Deposition date deposition_date	2022-06-24
Structure title title	T7 RNA polymerase elongation complex with unnatural base dPa-DsTP pair
Keywords keywords	T7 RNA polymerase, elongation complex, unnatural base, Ds-Pa, synthetic DNA, transcription, Transferase-DNA-RNA complex; Transferase/DNA/RNA
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	65.79 Å
Radius of gyration Rg (electron density) rg_electron	66.57 Å
Forward intensity I(0) i0	2593960000.00
Molecular weight molecular_weight	406230.0 kDa
Excluded volume excluded_volume	499000 Å³
Envelope volume envelope_volume	837320 Å³
Hydration-shell volume shell_volume	109870 Å³
Envelope diameter envelope_diameter	220.0 Å
Shell Rg shell_rg	61.47 Å
Envelope Rg envelope_rg	65.03 Å
Shape Rg shape_rg	66.57 Å
Total Rg total_rg	66.44 Å
Total atoms total_atoms	28446
Residues n_residues	3428
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	197.4 Å
Rg (real space) rg_real	66.19 Å
Rg uncertainty (real space) rg_real_error	1.47 Å
I(0) (real space) i0_real	2.5940e+09
I(0) uncertainty (real space) i0_real_error	4.8380e+07
Rg (reciprocal space) rg_reciprocal	65.34 Å
I(0) (reciprocal space) i0_reciprocal	2590000000.0000
Solution quality estimate total_estimate	0.6118
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	65.8 Å
Skewness Skewness skewness	0.338
Kurtosis Kurtosis kurtosis	-0.690
Angular range angular_range	— – 0.1200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	113600000.0000
Real-space data points n_real_points	25
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.979; Stabil: 1.000; Sysdev: 0.013; Positv: 1.000; Valcen: 0.974; Smooth: 0.000

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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	T7 RNA polymerase
Molecular weight formula_weight	98984.2 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E,I,M
Atom count atom_count	28446

MNTINIAKNDFSDIELAAIPFNTLADHYGERLAREQLALEHESYEMGEARFRKMFERQLKAGEVADNAAAKPLITTLLPKMIARINDWFEEVKAKRGKRPTAFQFLQEIKPEAVAYITIKTTLACLTSADNTTVQAVASAIGRAIEDEARFGRIRDLEAKHFKKNVEEQLNKRVGHVYKKAFMQVVEADMLSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGMVSLHRQNAGVVGQDSETIELAPEYAEAIATRAGALAGISPMFQPCVVPPKPWTGITGGGYWANGRRPLALVRTHSKKALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVITKWKHCPVEDIPAIEREELPMKPEDIDMNPEALTAWKRAAAAVYRKDKARKSRRISLEFMLEQANKFANHKAIWFPYNMDWRGRVYAVSMFNPQGNDMTKGLLTLAKGKPIGKEGYYWLKIHGANCAGVDKVPFPERIKFIEENHENIMACAKSPLENTWWAEQDSPFCFLAFCFEYAGVQHHGLSYNCSLPLAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQDIYGIVAKKVNEILQADAINGTDNEVVTVTDENTGEISEKVKLGTKALAGQWLAYGVTRSVTKRSVMTLAYGSKEFGFRQQVLEDTIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVAAVEAMNWLKSAAKLLAAEVKDKKTGEILRKRCAVHWVTPDGFPVWQEYKKPIQTRLNLMFLGQFRLQPTINTNKDSEIDAHKQESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESFALIHDSFGTIPADAANLFKAVRETMVDTYESCDVLADFYDQFADQLHESQLDKMPALPAKGNLNLRDILESDFAFA

Entity 2 Entity 2 polymer

Description description	Template strand DNA
Molecular weight formula_weight	5510.6 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	A,F,J,N

GGGAATCGAXATCGCCGC

Entity 3 Entity 3 polymer

Description description	RNA
Molecular weight formula_weight	3851.4 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	C,G,K,O

AACUGCGGCGAU

Entity 4 Entity 4 polymer

Description description	Non-template strand DNA
Molecular weight formula_weight	2666.8 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D,H,L,P

TCGATTCCC

Entity 5 Entity 5 non-polymer

Description description	;(7P)-3-{5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-ribofuranosyl}-7-(thiophen-2-yl)-3H-imidazo[4,5-b]pyridine ;
Molecular weight formula_weight	573.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	8dh4M01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1320 — T7 RNA polymerase; domain 1
Homologous superfamily homologous superfamily	10 — DNA-directed RNA polymerase, N-terminal domain

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8. Citations (1)

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Unit-cell length a length_a	78.779 Å
Unit-cell length b length_b	86.230 Å
Unit-cell length c length_c	201.463 Å
Unit-cell angle α angle_alpha	89.85 °
Unit-cell angle β angle_beta	85.39 °
Unit-cell angle γ angle_gamma	69.59 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	43.200 Å
R factor r_factor	0.2334
R_work r_work	0.2328
R_free r_free	0.2745

fit	/app/data/saxs_computation/dh/8dh4/8dh4.fit
pddf	/app/data/pr_computation/dh/8dh4/8dh4.pr.out
profile	/app/data/saxs_computation/dh/8dh4/8dh4.dat

T7 RNA polymerase elongation complex with unnatural base dPa-DsTP pair

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

T7 RNA polymerase

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) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)