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1h38

Structure of a T7 RNA polymerase elongation complex at 2.9A resolution

Method: X-RAY DIFFRACTION Dmax: 200.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-DIRECTED RNA POLYMERASE

BACTERIOPHAGE T7

UniProt P00573

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 A； UniProt 1–883 Not recorded ;5'-D(*GP*GP*GP*AP*AP*TP*CP*GP*AP*CP *AP*TP*CP*GP*CP*CP*GP*C)-3' ; × 1 ;5'-R(*AP*AP*CP*UP*GP*CP*GP*GP*CP*GP *AP*U)-3' ; × 1 5'-D(*GP*TP*CP*GP*AP*TP*TP*CP*CP*CP)-3' × 1 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
2 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 ;5'-D(*GP*GP*GP*AP*AP*TP*CP*GP*AP*CP *AP*TP*CP*GP*CP*CP*GP*C)-3' ; × 1 ;5'-R(*AP*AP*CP*UP*GP*CP*GP*GP*CP*GP *AP*U)-3' ; × 1 5'-D(*GP*TP*CP*GP*AP*TP*TP*CP*CP*CP)-3' × 1 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
3 Other combination Monomer Protein × 1 DNA 2 RNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain C； UniProt 1–883 Not recorded ;5'-D(*GP*GP*GP*AP*AP*TP*CP*GP*AP*CP *AP*TP*CP*GP*CP*CP*GP*C)-3' ; × 1 ;5'-R(*AP*AP*CP*UP*GP*CP*GP*GP*CP*GP *AP*U)-3' ; × 1 5'-D(*GP*TP*CP*GP*AP*TP*TP*CP*CP*CP)-3' × 1 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
4 Other combination Monomer Protein × 1 DNA 2 RNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain D； UniProt 1–883 Not recorded ;5'-D(*GP*GP*GP*AP*AP*TP*CP*GP*AP*CP *AP*TP*CP*GP*CP*CP*GP*C)-3' ; × 1 ;5'-R(*AP*AP*CP*UP*GP*CP*GP*GP*CP*GP *AP*U)-3' ; × 1 5'-D(*GP*TP*CP*GP*AP*TP*TP*CP*CP*CP)-3' × 1 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

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 1H38 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
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 experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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
8DH4 T7 RNA polymerase elongation complex with unnatural base dPa-DsTP pair Deposited 2022-06-24 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric
Chain B 1–883（883 aa）
Not recorded 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
8DH4 T7 RNA polymerase elongation complex with unnatural base dPa-DsTP pair Deposited 2022-06-24 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: tetrameric
Chain E 1–883（883 aa）
Not recorded 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
8DH4 T7 RNA polymerase elongation complex with unnatural base dPa-DsTP pair Deposited 2022-06-24 Different experimental conditions 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 2.80 Å R-free 0.275
8DH4 T7 RNA polymerase elongation complex with unnatural base dPa-DsTP pair Deposited 2022-06-24 Different experimental conditions 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 2.80 Å R-free 0.275
8DH5 T7 RNA polymerase elongation complex with unnatural base dPa-ATP mismatch Deposited 2022-06-24 Different ligand/ion Different experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 A； PDBConstruct 1–883； UniProt 1–883 Author chain B； PDBConstruct 1–883； UniProt 1–883 Author chain C； PDBConstruct 1–883； UniProt 1–883 Author chain D； 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

SAXS profile for 1h38

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1h38
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1h38
Deposition date deposition_date2002-08-24
Structure title titleStructure of a T7 RNA polymerase elongation complex at 2.9A resolution
Keywords keywords;TRANSFERASE, RNA POLYMERASE, T7 RNA POLYMERASE, ELONGATION COMPLEX, PROTEIN/DNA/RNA, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, STRUCTURAL GENOMICS ;; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier64.67 Å
Radius of gyration Rg (electron density) rg_electron65.57 Å
Forward intensity I(0) i02870230000.00
Molecular weight molecular_weight425340.0 kDa
Excluded volume excluded_volume521540 ų
Envelope volume envelope_volume832520 ų
Hydration-shell volume shell_volume108540 ų
Envelope diameter envelope_diameter227.8 Å
Shell Rg shell_rg61.30 Å
Envelope Rg envelope_rg64.56 Å
Shape Rg shape_rg65.56 Å
Total Rg total_rg65.51 Å
Total atoms total_atoms29786
Residues n_residues3565
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax200.6 Å
Rg (real space) rg_real65.25 Å
Rg uncertainty (real space) rg_real_error1.70 Å
I(0) (real space) i0_real2.8700e+09
I(0) uncertainty (real space) i0_real_error6.2600e+07
Rg (reciprocal space) rg_reciprocal64.11 Å
I(0) (reciprocal space) i0_reciprocal2864000000.0000
Solution quality estimate total_estimate0.8305
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary66.8 Å
Skewness Skewness skewness0.462
Kurtosis Kurtosis kurtosis-0.522
Angular range angular_range— – 0.1200 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha171400000.0000
Real-space data points n_real_points25
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.001
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1h38a_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.8 — DNA/RNA polymerases
Superfamily Superfamily superfamilye.8.1 — DNA/RNA polymerases
Family Family familye.8.1.3 — T7 RNA polymerase
Domain ID domain_idd1h38b_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.8 — DNA/RNA polymerases
Superfamily Superfamily superfamilye.8.1 — DNA/RNA polymerases
Family Family familye.8.1.3 — T7 RNA polymerase
Domain ID domain_idd1h38c_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.8 — DNA/RNA polymerases
Superfamily Superfamily superfamilye.8.1 — DNA/RNA polymerases
Family Family familye.8.1.3 — T7 RNA polymerase
Domain ID domain_idd1h38d_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.8 — DNA/RNA polymerases
Superfamily Superfamily superfamilye.8.1 — DNA/RNA polymerases
Family Family familye.8.1.3 — T7 RNA polymerase

CATH v4.4 (20 domains)

Domain ID domain_id1h38A01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1320 — T7 RNA polymerase; domain 1
Homologous superfamily homologous superfamily10 — DNA-directed RNA polymerase, N-terminal domain
Domain ID domain_id1h38A02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily260 —
Domain ID domain_id1h38A03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily370 —
Domain ID domain_id1h38A04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily280 —
Domain ID domain_id1h38A05
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily20 — 5' to 3' exonuclease, C-terminal subdomain
Domain ID domain_id1h38B01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1320 — T7 RNA polymerase; domain 1
Homologous superfamily homologous superfamily10 — DNA-directed RNA polymerase, N-terminal domain
Domain ID domain_id1h38B02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily260 —
Domain ID domain_id1h38B03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily370 —
Domain ID domain_id1h38B04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily280 —
Domain ID domain_id1h38B05
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily20 — 5' to 3' exonuclease, C-terminal subdomain
Domain ID domain_id1h38C01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1320 — T7 RNA polymerase; domain 1
Homologous superfamily homologous superfamily10 — DNA-directed RNA polymerase, N-terminal domain
Domain ID domain_id1h38C02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily260 —
Domain ID domain_id1h38C03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily370 —
Domain ID domain_id1h38C04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily280 —
Domain ID domain_id1h38C05
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily20 — 5' to 3' exonuclease, C-terminal subdomain
Domain ID domain_id1h38D01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1320 — T7 RNA polymerase; domain 1
Homologous superfamily homologous superfamily10 — DNA-directed RNA polymerase, N-terminal domain
Domain ID domain_id1h38D02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily260 —
Domain ID domain_id1h38D03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily370 —
Domain ID domain_id1h38D04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily280 —
Domain ID domain_id1h38D05
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily20 — 5' to 3' exonuclease, C-terminal subdomain
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8. Citations (1)

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9. Files and Curves (10)