DNA-directed RNA polymerase II subunit RPB1
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 Heteromer Protein × 10 DNA 1 RNA 1 PDB declaration: dodecameric（12） Consistent with all polymer counts | Chain A； UniProt 1–1733 | Not recorded | DNA-directed RNA polymerase II subunit RPB2 × 1 （P08518） DNA-directed RNA polymerase II subunit RPB3 × 1 （P16370） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （P20434） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （P20435） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （P20436） DNA-directed RNA polymerase II subunit RPB9 × 1 （P27999） DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 （P22139） DNA-directed RNA polymerase II subunit RPB11 × 1 （P38902） DNA-directed RNA polymerases I, II, and III subunit RPABC4 × 1 （P40422） ;RNA (5'-R(*AP*GP*AP*CP*G)-3') ; × 1 ;DNA (5'-D(*CP*TP*AP*CP*CP*GP*AP*TP*AP*AP*GP*CP*AP*GP*AP*CP*GP*AP*TP*CP*GP*TP*CP*TP*CP*GP*AP*TP*G)-3') ; × 1 ZN ZINC ION × 8 MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；293 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.0, 50mM dioxane, 9-11% PEG 6.000, 15mM DTT, vapor diffusion, temperature 293K | Resolution 3.13 Å R-free 0.233 |
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 3S1M | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1I3Q RNA POLYMERASE II CRYSTAL FORM I AT 3.1 A RESOLUTION Deposited 2001-02-15 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 6000, Ammoniumhydrogenphosphate, Sodiumdihydrogenphosphate, dioxane, DTT, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.10 Å R-free 0.283 |
| 1I50 RNA POLYMERASE II CRYSTAL FORM II AT 2.8 A RESOLUTION Deposited 2001-02-23 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MN MANGANESE (II) ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；PEG 6000, AMMONIUMHYDROGENPHOSPHATE, SODIUMDIHYDROGENPHOSPHATE, DIOXANE, DTT, pH 6.00, VAPOR DIFFUSION, HANGING DROP,
temperature 100K
|
Resolution 2.80 Å R-free 0.282 |
| 1I50 RNA POLYMERASE II CRYSTAL FORM II AT 2.8 A RESOLUTION Deposited 2001-02-23 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 16 MN MANGANESE (II) ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；PEG 6000, AMMONIUMHYDROGENPHOSPHATE, SODIUMDIHYDROGENPHOSPHATE, DIOXANE, DTT, pH 6.00, VAPOR DIFFUSION, HANGING DROP,
temperature 100K
|
Resolution 2.80 Å R-free 0.282 |
| 1I6H RNA POLYMERASE II ELONGATION COMPLEX Deposited 2001-03-02 | Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；PEG 6000, AMMONIUM HYDROGEN PHOSPHATE, SODIUM DIHYDROGEN PHOSPHATE, DIOXANE, DTT, pH 6.00, VAPOR DIFFUSION, SITTING
DROP, temperature 100K
|
Resolution 3.30 Å R-free 0.298 |
| 1K83 Crystal Structure of Yeast RNA Polymerase II Complexed with the Inhibitor Alpha Amanitin Deposited 2001-10-22 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MN MANGANESE (II) ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6；PH 6.00
|
Resolution 2.80 Å R-free 0.280 |
| 1NIK Wild Type RNA Polymerase II Deposited 2002-12-24 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 7 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.3；291 K；peg400, peg 6K, NaCl, Dioaxne, ZnCl2, Ammonium phosphate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 6.30
|
Resolution 4.10 Å R-free 0.360 |
| 1NT9 Complete 12-subunit RNA polymerase II Deposited 2003-01-29 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG 20000, ammonium sodium phosphate, sodium chloride, dioxane, DTT, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 4.20 Å |
| 1PQV RNA polymerase II-TFIIS complex Deposited 2003-06-19 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 9 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；sodium-ammonium tartrate, Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 3.80 Å |
| 1R5U RNA POLYMERASE II TFIIB COMPLEX Deposited 2003-10-13 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium sulfate, MES, NaCl, CdCl2, DTT, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 4.50 Å R-free 0.373 |
| 1R9S RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX, MATCHED NUCLEOTIDE Deposited 2003-10-30 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | MG MAGNESIUM ION × 2 UTP URIDINE 5'-TRIPHOSPHATE × 1 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 6000, Ammonium hydrogen phosphate, sodium dihydrogen phosphate, dioxane, DTT, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 4.25 Å R-free 0.398 |
| 1R9T RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX, MISMATCHED NUCLEOTIDE Deposited 2003-10-30 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 6000, Ammonium hydrogen phosphate, sodium dihydrogen phosphate, dioxane, DTT, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.50 Å R-free 0.317 |
| 1SFO RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX Deposited 2004-02-20 | Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 6000, ammonium sodium phosphate, DTT, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.61 Å R-free 0.343 |
| 1TWA RNA polymerase II complexed with ATP Deposited 2004-06-30 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric |
Chain A
1–1733（1733 aa）
|
Not recorded | MN MANGANESE (II) ION × 2 ZN ZINC ION × 8 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 6000, AMMONIUM HYDROGEN PHOSPHATE, SODIUM DIHYDROGEN PHOSPHATE, DIOXANE, DTT, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.20 Å R-free 0.246 |
| 1TWC RNA polymerase II complexed with GTP Deposited 2004-06-30 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MN MANGANESE (II) ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6；PEG 6000, AMMONIUM HYDROGEN PHOSPHATE, SODIUM DIHYDROGEN PHOSPHATE, DIOXANE, DTT, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.00 Å R-free 0.255 |
| 1TWF RNA polymerase II complexed with UTP at 2.3 A resolution Deposited 2004-06-30 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MN MANGANESE (II) ION × 2 UTP URIDINE 5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；PEG 6000, AMMONIUM HYDROGEN PHOSPHATE, SODIUM DIHYDROGEN PHOSPHATE, DIOXANE, DTT, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.30 Å R-free 0.294 |
| 1TWF RNA polymerase II complexed with UTP at 2.3 A resolution Deposited 2004-06-30 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 16 MN MANGANESE (II) ION × 4 UTP URIDINE 5'-TRIPHOSPHATE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；PEG 6000, AMMONIUM HYDROGEN PHOSPHATE, SODIUM DIHYDROGEN PHOSPHATE, DIOXANE, DTT, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.30 Å R-free 0.294 |
| 1TWG RNA polymerase II complexed with CTP Deposited 2004-06-30 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric |
Chain A
1–1733（1733 aa）
|
Not recorded | MN MANGANESE (II) ION × 2 ZN ZINC ION × 8 CTP CYTIDINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；PEG 6000, AMMONIUM HYDROGEN PHOSPHATE, SODIUM DIHYDROGEN PHOSPHATE, DIOXANE, DTT, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.30 Å R-free 0.281 |
| 1TWG RNA polymerase II complexed with CTP Deposited 2004-06-30 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 40 PDB declaration: 40-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | MN MANGANESE (II) ION × 8 ZN ZINC ION × 32 CTP CYTIDINE-5'-TRIPHOSPHATE × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；PEG 6000, AMMONIUM HYDROGEN PHOSPHATE, SODIUM DIHYDROGEN PHOSPHATE, DIOXANE, DTT, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.30 Å R-free 0.281 |
| 1TWG RNA polymerase II complexed with CTP Deposited 2004-06-30 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric |
Chain A
1–1733（1733 aa）
|
Not recorded | MN MANGANESE (II) ION × 4 ZN ZINC ION × 16 CTP CYTIDINE-5'-TRIPHOSPHATE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；PEG 6000, AMMONIUM HYDROGEN PHOSPHATE, SODIUM DIHYDROGEN PHOSPHATE, DIOXANE, DTT, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.30 Å R-free 0.281 |
| 1TWH RNA polymerase II complexed with 2'dATP Deposited 2004-06-30 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric |
Chain A
1–1733（1733 aa）
|
Not recorded | MN MANGANESE (II) ION × 2 ZN ZINC ION × 8 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 6000, AMMONIUM HYDROGEN PHOSPHATE, SODIUM DIHYDROGEN PHOSPHATE, DIOXANE, DTT, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.40 Å R-free 0.262 |
| 1WCM Complete 12-Subunit RNA Polymerase II at 3.8 Angstrom Deposited 2004-11-17 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 3.80 Å R-free 0.285 |
| 1Y1V Refined RNA Polymerase II-TFIIS complex Deposited 2004-11-19 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 3.80 Å R-free 0.294 |
| 1Y1W Complete RNA Polymerase II elongation complex Deposited 2004-11-19 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 4.00 Å R-free 0.276 |
| 1Y1Y RNA Polymerase II-TFIIS-DNA/RNA complex Deposited 2004-11-19 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: pentadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 4.00 Å |
| 1Y77 Complete RNA Polymerase II elongation complex with substrate analogue GMPCPP Deposited 2004-12-08 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 4.50 Å |
| 2B63 Complete RNA Polymerase II-RNA inhibitor complex Deposited 2005-09-30 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
200 mM ammonium acetate, 150 mM magnesium acetate, 50 mM Hepes (pH 7.0), 5% PEG 6000, and 5 mM TCEP
|
Resolution 3.80 Å R-free 0.273 |
| 2B8K 12-subunit RNA Polymerase II Deposited 2005-10-07 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
|
Resolution 4.15 Å |
| 2E2H RNA polymerase II elongation complex at 5 mM Mg2+ with GTP Deposited 2006-11-14 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 8 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 50mM dioxane, 10mM DTT, 9-11% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.95 Å R-free 0.368 |
| 2E2I RNA polymerase II elongation complex in 5 mM Mg+2 with 2'-dGTP Deposited 2006-11-14 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 50mM dioxane, 10mM DTT, 9-11% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.41 Å R-free 0.316 |
| 2E2J RNA polymerase II elongation complex in 5 mM Mg+2 with GMPCPP Deposited 2006-11-14 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ZN ZINC ION × 8 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 50mM dioxane, 10mM DTT, 9-11% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.50 Å R-free 0.306 |
| 2JA5 CPD lesion containing RNA Polymerase II elongation complex A Deposited 2006-11-23 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；pH 7.00
|
Resolution 3.80 Å R-free 0.280 |
| 2JA6 CPD lesion containing RNA Polymerase II elongation complex B Deposited 2006-11-23 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；pH 7.0
|
Resolution 4.00 Å R-free 0.301 |
| 2JA7 CPD lesion containing RNA Polymerase II elongation complex C Deposited 2006-11-23 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；pH 7.0
|
Resolution 3.80 Å R-free 0.275 |
| 2JA7 CPD lesion containing RNA Polymerase II elongation complex C Deposited 2006-11-23 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain M
1–1733（1733 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；pH 7.0
|
Resolution 3.80 Å R-free 0.275 |
| 2JA8 CPD lesion containing RNA Polymerase II elongation complex D Deposited 2006-11-23 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；pH 7.0
|
Resolution 3.80 Å R-free 0.288 |
| 2LO6 Structure of Nrd1 CID bound to phosphorylated RNAP II CTD Deposited 2012-01-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1556–1569（14 aa）
Fragment：UNP residues 1556-1569
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 8；293 K；Ionic strength (raw mmCIF value) 100；Pressure ambient
NMR sample composition
2 mM [U-100% 13C; U-100% 15N] Nrd1 polypeptide, 2.3 mM phosphopeptide, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2NVQ RNA Polymerase II Elongation Complex in 150 mM Mg+2 with 2'dUTP Deposited 2006-11-13 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | DUT DEOXYURIDINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 8 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；200mM NH4OAc, 150mM Mg(OAc)2, 50mM Hepes, pH 7.0, 5% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.90 Å R-free 0.283 |
| 2NVT RNA Polymerase II Elongation Complex in 150 mM Mg+2 with GMPCPP Deposited 2006-11-13 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ZN ZINC ION × 8 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；200mM NH4OAc, 150mM Mg(OAc)2, 50mM Hepes, pH 7.0, 5% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.36 Å R-free 0.283 |
| 2NVX RNA polymerase II elongation complex in 5 mM Mg+2 with 2'-dUTP Deposited 2006-11-13 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 DUT DEOXYURIDINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 50mM dioxane, 10mM DTT, 9-11% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.60 Å R-free 0.304 |
| 2NVY RNA Polymerase II form II in 150 mM Mn+2 Deposited 2006-11-13 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MN MANGANESE (II) ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 50mM dioxane, 10mM DTT, 12% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.40 Å R-free 0.323 |
| 2NVY RNA Polymerase II form II in 150 mM Mn+2 Deposited 2006-11-13 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 16 MN MANGANESE (II) ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 50mM dioxane, 10mM DTT, 12% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.40 Å R-free 0.323 |
| 2NVZ RNA Polymerase II elongation complex with UTP, updated 11/2006 Deposited 2006-11-14 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 2 UTP URIDINE 5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 50mM dioxane, 10mM DTT, 9-12% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 4.30 Å R-free 0.332 |
| 2R7Z Cisplatin lesion containing RNA polymerase II elongation complex Deposited 2007-09-10 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | CPT Cisplatin × 1 ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；200 mM ammonium acetate, 150 mM magnesium acetate, 50 mM Hepes pH 7.0, 5% (v/v) PEG 6000, 5 mM TCEP, VAPOR DIFFUSION, HANGING DROP
|
Resolution 3.80 Å R-free 0.240 |
| 2R92 Elongation complex of RNA polymerase II with artificial RdRP scaffold Deposited 2007-09-12 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；295 K；5% (w/v) PEG 6000, 200 mM ammonium acetate, 150 mM magnesium acetate, 50 mM Hepes pH 7.0, 5 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K, pH 7.00
|
Resolution 3.80 Å R-free 0.246 |
| 2R93 Elongation complex of RNA polymerase II with a hepatitis delta virus-derived RNA stem loop Deposited 2007-09-12 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；5% (w/v) PEG 6000, 200 mM ammonium acetate, 150 mM magnesium acetate, 50 mM Hepes pH 7.0, 5 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
|
Resolution 4.00 Å R-free 0.241 |
| 2VUM Alpha-amanitin inhibited complete RNA polymerase II elongation complex Deposited 2008-05-27 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；200 MM AMMONIUM ACETATE, 300 MM SODIUM ACETATE, 50 MM HEPES PH 7.0, 4-7% PEG 6000, 5 MM TCEP
|
Resolution 3.40 Å R-free 0.288 |
| 2YU9 RNA polymerase II elongation complex in 150 mm MG+2 with UTP Deposited 2007-04-06 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 2 UTP URIDINE 5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；200MM NH4OAC, 150MM MG(OAC)2, 50MM HEPES, PH 7.0, 5% PEG6000, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.40 Å R-free 0.344 |
| 3CQZ Crystal structure of 10 subunit RNA polymerase II in complex with the inhibitor alpha-amanitin Deposited 2008-04-03 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.80 Å R-free 0.273 |
| 3FKI 12-Subunit RNA Polymerase II Refined with Zn-SAD data Deposited 2008-12-16 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；5-7% PEG 4000, 50 mM HEPES pH 7.0, 10 mM DTT, 70 mM glucosamine, 50 mM dioxane, VAPOR DIFFUSION, HANGING DROP
|
Resolution 3.88 Å R-free 0.301 |
| 3GTG Backtracked RNA polymerase II complex with 12mer RNA Deposited 2009-03-27 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
Fragment：DNA-directed RNA polymerase II largest subunit
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.0, 50mM Dioxane, 10mM DTT, 9-11% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.78 Å R-free 0.300 |
| 3GTJ Backtracked RNA polymerase II complex with 13mer RNA Deposited 2009-03-27 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
Fragment：DNA-directed RNA polymerase II largest subunit
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.0, 50mM Dioxane, 10mM DTT, 9-11% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.42 Å R-free 0.292 |
| 3GTK Backtracked RNA polymerase II complex with 18mer RNA Deposited 2009-03-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
Fragment：DNA-directed RNA polymerase II largest subunit
|
Not recorded | ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.0, 50mM Dioxane, 10mM DTT, 9-11% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.80 Å R-free 0.278 |
| 3GTL Backtracked RNA polymerase II complex with 13mer with G<>U mismatch Deposited 2009-03-27 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
Fragment：DNA-directed RNA polymerase II largest subunit
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.0, 50mM Dioxane, 10mM DTT, 9-11% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.38 Å R-free 0.322 |
| 3GTM Co-complex of Backtracked RNA polymerase II with TFIIS Deposited 2009-03-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 11 PDB declaration: tetradecameric |
Chain A
1–1733（1733 aa）
Fragment：DNA-directed RNA polymerase II largest subunit
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 9 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.0, 50mM Dioxane, 10mM DTT, 9-11% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.80 Å R-free 0.289 |
| 3GTO Backtracked RNA polymerase II complex with 15mer RNA Deposited 2009-03-27 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
Fragment：DNA-directed RNA polymerase II largest subunit
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.0, 50mM Dioxane, 10mM DTT, 9-11% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 4.00 Å R-free 0.290 |
| 3GTP Backtracked RNA polymerase II complex with 24mer RNA Deposited 2009-03-27 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
Fragment：DNA-directed RNA polymerase II largest subunit
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.0, 50mM Dioxane, 10mM DTT, 9-11% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.90 Å R-free 0.299 |
| 3GTQ Backtracked RNA polymerase II complex induced by damage Deposited 2009-03-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–1733（1733 aa）
Fragment：DNA-directed RNA polymerase II largest subunit
|
Not recorded | ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.0, 50mM Dioxane, 10mM DTT, 9-11% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.80 Å R-free 0.335 |
| 3H3V Yeast RNAP II containing poly(A)-signal sequence in the active site Deposited 2009-04-17 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain B
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；295 K；200 mM ammonium acetate, 50mM HEPES pH 7.0, 4% polyethylene glycol 6000, 5mM TCEP (tris (2-carboxyethyl) phosphine hydrochloride), VAPOR DIFFUSION, HANGING DROP, temperature 295.0 K
|
Resolution 4.00 Å R-free 0.241 |
| 3HOU Complete RNA polymerase II elongation complex I with a T-U mismatch Deposited 2009-06-03 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；200mM ammonium acetate, 300mM SODIUM ACETATE, 50mM Hepes pH 7.0, 4-6% PEG 6000, 5mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 3.20 Å R-free 0.252 |
| 3HOU Complete RNA polymerase II elongation complex I with a T-U mismatch Deposited 2009-06-03 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain M
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；200mM ammonium acetate, 300mM SODIUM ACETATE, 50mM Hepes pH 7.0, 4-6% PEG 6000, 5mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 3.20 Å R-free 0.252 |
| 3HOV Complete RNA polymerase II elongation complex II Deposited 2009-06-03 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；200mM ammonium acetate, 300mM SODIUM ACETATE,, 50mM Hepes pH 7.0, 4-6% PEG 6000, 5mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 3.50 Å R-free 0.226 |
| 3HOW Complete RNA polymerase II elongation complex III with a T-U mismatch and a frayed RNA 3'-uridine Deposited 2009-06-03 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；200mM ammonium acetate, 300mM SODIUM ACETATE, 50mM Hepes pH 7.0, 4-6% PEG 6000, 5mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 3.60 Å R-free 0.254 |
| 3HOX Complete RNA polymerase II elongation complex V Deposited 2009-06-03 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；200mM ammonium acetate, 300mM SODIUM ACETATE, 50mM Hepes pH 7.0, 4-6% PEG 6000, 5mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 3.65 Å R-free 0.250 |
| 3HOY Complete RNA polymerase II elongation complex VI Deposited 2009-06-03 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 3.40 Å R-free 0.254 |
| 3HOZ Complete RNA polymerase II elongation complex IV with a T-U mismatch and a frayed RNA 3'-guanine Deposited 2009-06-03 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；20mM ammonium acetate, 300mM SODIUM ACETATE, 50mM Hepes pH 7.0, 4-6% PEG 6000, 5mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 3.65 Å R-free 0.253 |
| 3I4M 8-oxoguanine containing RNA polymerase II elongation complex D Deposited 2009-07-02 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；200mM ammonium acetate, 300mM sodium acetate, 50mM Hepes, 4%(w/v) PEG 6000, 5mM TCEP, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 3.70 Å R-free 0.258 |
| 3I4N 8-oxoguanine containing RNA polymerase II elongation complex E Deposited 2009-07-02 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；5%(w/v) PEG 6000, 200mM ammonium acetate, 300mM sodium acetate, 50mM Hepes, 5mM TCEP , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 3.90 Å R-free 0.266 |
| 3J1N Cryo-EM map of a yeast minimal preinitiation complex interacting with the Mediator Head module Deposited 2012-03-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain A
1–1455（1455 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
25 mM KCl, 25 mM Tris-HCl, 10 mM DTT；pH 8；25 mM KCl, 25 mM Tris-HCl, 10 mM DTT
cryo-EM vitrification conditions
Blot for ~2 sec before plunging；77 K；Cryogen ETHANE；Blot for approximately 2 seconds before plunging into liquid ethane.
|
Resolution 16.00 Å |
| 3K1F Crystal structure of RNA Polymerase II in complex with TFIIB Deposited 2009-09-27 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 9 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；800 mM sodium ammonium tartrate, 100 mM HEPES pH 7.5, 5 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 4.30 Å R-free 0.255 |
| 3K7A Crystal Structure of an RNA polymerase II-TFIIB complex Deposited 2009-10-12 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 9 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.9；295 K；1.2 M sodium/potassium phosphate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 3.80 Å R-free 0.313 |
| 3M3Y RNA polymerase II elongation complex C Deposited 2010-03-10 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 C7P cis-diammine(pyridine)chloroplatinum(II) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；390mM (NH4)2HPO4/NaH2PO4, 50mM dioxane, 10mM DTT, 9-11% PEG6,000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.18 Å R-free 0.255 |
| 3M4O RNA polymerase II elongation complex B Deposited 2010-03-11 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 C7P cis-diammine(pyridine)chloroplatinum(II) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；390mM (NH4)2HPO4/NaH2PO4, 50mM dioxane, 10mM DTT, 9-11% PEG6,000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.57 Å R-free 0.292 |
| 3PO2 Arrested RNA Polymerase II elongation complex Deposited 2010-11-21 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ACT ACETATE ION × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；4-7% PEG6000, 50mM HEPES pH 7.0, 200mM ammonium acetate, 300mM sodium acetate, 5mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 3.30 Å R-free 0.178 |
| 3PO3 Arrested RNA Polymerase II reactivation intermediate Deposited 2010-11-21 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ACT ACETATE ION × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 PGE TRIETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；4-7% PEG6000, 50mM HEPES pH 7.0, 200mM AMMONIUM ACETATE, 300mM SODIUM ACETATE, 5mM TCEP
, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 3.30 Å R-free 0.189 |
| 3QT1 RNA polymerase II variant containing A Chimeric RPB9-C11 subunit Deposited 2011-02-22 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 7 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；200mM ammonium acetate, 300mM SODIUM ACETATE, 50mM Hepes pH 7.0, 5-6% PEG 6000, 5mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 4.30 Å R-free 0.281 |
| 3RZD RNA Polymerase II Initiation Complex with a 5-nt RNA Deposited 2011-05-11 | Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；293 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.0, 50mM dioxane, 9-11% PEG 6,000, 15mM DTT, vapor diffusion, temperature 293K, VAPOR DIFFUSION
|
Resolution 3.30 Å R-free 0.230 |
| 3RZO RNA Polymerase II Initiation Complex with a 4-nt RNA Deposited 2011-05-12 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；293 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.0, 50mM dioxane, 9-11% PEG 6.000, 15mM DTT, vapor diffusion, temperature 293K, VAPOR DIFFUSION
|
Resolution 3.00 Å R-free 0.236 |
| 3S14 RNA Polymerase II Initiation Complex with a 6-nt RNA Deposited 2011-05-14 | Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；293 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.0, 50mM dioxane, 9-11% PEG 6,000, 15mM DTT, vapor diffusion, temperature 293K, VAPOR DIFFUSION
|
Resolution 2.85 Å R-free 0.227 |
| 3S15 RNA Polymerase II Initiation Complex with a 7-nt RNA Deposited 2011-05-14 | Different ligand/ion Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；293 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.0, 50mM dioxane, 9-11% PEG 6.000, 15mM DTT, vapor diffusion, temperature 293K
|
Resolution 3.30 Å R-free 0.228 |
| 3S16 RNA Polymerase II Initiation Complex with an 8-nt RNA Deposited 2011-05-14 | Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；293 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.0, 50mM dioxane, 9-11% PEG 6.000, 15mM DTT, vapor diffusion, temperature 293K
|
Resolution 3.24 Å R-free 0.227 |
| 3S17 RNA Polymerase II Initiation Complex with a 9-nt RNA Deposited 2011-05-14 | Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；293 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.9, 50mM dioxane, 9-11% PEG 6,000, 15mM DTT, vapor diffusion, temperature 293K, VAPOR DIFFUSION
|
Resolution 3.20 Å R-free 0.236 |
| 3S1N RNA Polymerase II Initiation Complex with a 5-nt RNA (variant 2) Deposited 2011-05-15 | Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；293 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.0, 50mM dioxane, 9-11% PEG 6.000, 15mM DTT, vapor diffusion, temperature 293K
|
Resolution 3.10 Å R-free 0.232 |
| 3S1Q RNA Polymerase II Initiation Complex with a 5-nt 3'-deoxy RNA soaked with ATP Deposited 2011-05-16 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | MG MAGNESIUM ION × 2 ZN ZINC ION × 8 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；293 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.0, 50mM dioxane, 9-11% PEG 6,000, 15mM DTT, vapor diffusion, temperature 293K, VAPOR DIFFUSION
|
Resolution 3.30 Å R-free 0.229 |
| 3S1R RNA Polymerase II Initiation Complex with a 5-nt 3'-deoxy RNA soaked with GTP Deposited 2011-05-16 | Different ligand/ion Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；293 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.0, 50mM dioxane, 9-11% PEG 6.000, 15mM DTT, vapor diffusion, temperature 293K
|
Resolution 3.20 Å R-free 0.226 |
| 3S2D RNA Polymerase II Initiation Complex with a 5-nt RNA containing a 5Br-U Deposited 2011-05-16 | Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；293 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.0, 50mM dioxane, 9-11% PEG 6,000, 15mM DTT, vapor diffusion, temperature 293K
|
Resolution 3.20 Å R-free 0.231 |
| 3S2H RNA Polymerase II Initiation Complex with a 6-nt RNA containing a 2[prime]-iodo ATP Deposited 2011-05-16 | Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；293 K；390mM (NH4)2HPO4/NaH2PO4, pH 5.9-6.1, 50mM dioxane, 9-11% PEG 6,000, 15mM DTT, vapor diffusion, temperature 293K
|
Resolution 3.30 Å R-free 0.240 |
| 4A3B RNA Polymerase II initial transcribing complex with a 4nt DNA-RNA hybrid Deposited 2011-09-30 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain A
1–1732（1732 aa）
Fragment：RESIDUES 1-1732
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；pH 7
|
Resolution 3.50 Å R-free 0.197 |
| 4A3C RNA Polymerase II initial transcribing complex with a 5nt DNA-RNA hybrid Deposited 2011-09-30 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain A
1–1732（1732 aa）
Fragment：RESIDUES 1-1732
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；pH 7
|
Resolution 3.50 Å R-free 0.184 |
| 4A3D RNA Polymerase II initial transcribing complex with a 6nt DNA-RNA hybrid Deposited 2011-09-30 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain A
1–1732（1732 aa）
Fragment：RESIDUES 1-1732
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；pH 7
|
Resolution 3.40 Å R-free 0.186 |
| 4A3E RNA Polymerase II initial transcribing complex with a 5nt DNA-RNA hybrid and soaked with AMPCPP Deposited 2011-09-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain A
1–1732（1732 aa）
Fragment：RESIDUES 1-1732
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；pH 7
|
Resolution 3.40 Å R-free 0.188 |
| 4A3F RNA Polymerase II initial transcribing complex with a 6nt DNA-RNA hybrid and soaked with AMPCPP Deposited 2011-09-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain A
1–1732（1732 aa）
Fragment：RESIDUES 1-1732
|
Not recorded | APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；pH 7
|
Resolution 3.50 Å R-free 0.185 |
| 4A3G RNA Polymerase II initial transcribing complex with a 2nt DNA-RNA hybrid Deposited 2011-09-30 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain A
1–1732（1732 aa）
Fragment：RESIDUES 1-1732
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；pH 7
|
Resolution 3.50 Å R-free 0.194 |
| 4A3I RNA Polymerase II binary complex with DNA Deposited 2011-09-30 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain A
1–1732（1732 aa）
Fragment：RESIDUES 1-1732
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；pH 7
|
Resolution 3.80 Å R-free 0.191 |
| 4A3J RNA Polymerase II initial transcribing complex with a 2nt DNA-RNA hybrid and soaked with GMPCPP Deposited 2011-09-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain A
1–1732（1732 aa）
Fragment：RESIDUES 1-1732
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；pH 7
|
Resolution 3.70 Å R-free 0.194 |
| 4A3K RNA Polymerase II initial transcribing complex with a 7nt DNA-RNA hybrid Deposited 2011-09-30 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain A
1–1732（1732 aa）
Fragment：RESIDUES 1-1732
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 3.50 Å R-free 0.185 |
| 4A3L RNA Polymerase II initial transcribing complex with a 7nt DNA-RNA hybrid and soaked with AMPCPP Deposited 2011-09-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain A
1–1732（1732 aa）
Fragment：RESIDUES 1-1732
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；pH 7
|
Resolution 3.50 Å R-free 0.187 |
| 4A3M RNA Polymerase II initial transcribing complex with a 4nt DNA-RNA hybrid and soaked with AMPCPP Deposited 2011-09-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain A
1–1732（1732 aa）
Fragment：RESIDUES 1-1732
|
Not recorded | APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；pH 7
|
Resolution 3.90 Å R-free 0.190 |
| 4A93 RNA Polymerase II elongation complex containing a CPD Lesion Deposited 2011-11-23 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain A
1–1732（1732 aa）
Fragment：RESIDUES 1-1732
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；4-7% PEG 6000, 50 MM HEPES PH 7.0, 200 MM AMMONIUM ACETATE, 300MM SODIUM ACETATE, 5 MM TCEP, VAPOR DIFFUSION, HANGING DROP.
|
Resolution 3.40 Å R-free 0.199 |
| 4BBR Structure of RNA polymerase II-TFIIB complex Deposited 2012-09-27 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 3.40 Å R-free 0.211 |
| 4BBS Structure of an initially transcribing RNA polymerase II-TFIIB complex Deposited 2012-09-27 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 3.60 Å R-free 0.225 |
| 4BXX Arrested RNA polymerase II-Bye1 complex Deposited 2013-07-16 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；5-7% PEG6000, 50 MM HEPES PH 7.0, 300 MM SODIUM ACETATE, 5 MM TCEP, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293 K
|
Resolution 3.28 Å R-free 0.208 |
| 4BXZ RNA Polymerase II-Bye1 complex Deposited 2013-07-16 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；750 MM TRI-SODIUM CITRATE, 100 MM HEPES PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
|
Resolution 4.80 Å R-free 0.253 |
| 4BY1 elongating RNA Polymerase II-Bye1 TLD complex soaked with AMPCPP Deposited 2013-07-17 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；5-7% PEG6000, 50 MM HEPES PH 7.0, 200 MM AMMONIUM ACETATE, 300 MM SODIUM ACETATE, 5 MM TCEP, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293 K
|
Resolution 3.60 Å R-free 0.206 |
| 4BY7 elongating RNA Polymerase II-Bye1 TLD complex Deposited 2013-07-18 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；5-7% PEG6000, 50 MM HEPES PH 7.0, 200 MM AMMONIUM ACETATE, 300 MM SODIUM ACETATE, 5 MM TCEP, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293 K
|
Resolution 3.15 Å R-free 0.212 |
| 4GWQ Structure of the Mediator Head Module from S. cerevisiae in complex with the carboxy-terminal domain (CTD) of RNA Polymerase II Rpb1 subunit Deposited 2012-09-03 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain H
1556–1590（35 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；291.2 K；275mM ammonium citrate tribasic pH 7.0, 10% w/v PEG 3350, 2mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 291.2K
|
Resolution 4.50 Å R-free 0.345 |
| 4V1M Architecture of the RNA polymerase II-Mediator core transcription initiation complex Deposited 2014-09-29 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
25 MM HEPES-KOH PH 7.5, 180 MM POTASSIUM ACETATE, 5 % GLYCEROL, 5 MM DTT；pH 7.5；25 MM HEPES-KOH PH 7.5, 180 MM POTASSIUM ACETATE, 5 % GLYCEROL, 5 MM DTT
cryo-EM vitrification conditions
Cryogen ETHANE；GRIDS WERE GLOW- DISCHARGED FOR 20 S BEFORE DEPOSITION OF 4 MICROLITERS SAMPLE AND INCUBATED FOR 30 S. GRIDS WERE WASHED TWICE WITH 4 MICROLITERS DISTILLED WATER, BLOTTED, AND VITRIFIED BY PLUNGING INTO LIQUID ETHANE WITH A MANUAL PLUNGER.
|
Resolution 6.60 Å |
| 4V1N Architecture of the RNA polymerase II-Mediator core transcription initiation complex Deposited 2014-09-29 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: nonadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
25 MM HEPES-KOH PH 7.5, 180 MM POTASSIUM ACETATE, 5 % GLYCEROL, 5 MM DTT；pH 7.5；25 MM HEPES-KOH PH 7.5, 180 MM POTASSIUM ACETATE, 5 % GLYCEROL, 5 MM DTT
cryo-EM vitrification conditions
Cryogen ETHANE；GRIDS WERE GLOW- DISCHARGED FOR 20 S BEFORE DEPOSITION OF 4 MICROLITERS SAMPLE AND INCUBATED FOR 30 S. GRIDS WERE WASHED TWICE WITH 4 MICROLITERS DISTILLED WATER, BLOTTED, AND VITRIFIED BY PLUNGING INTO LIQUID ETHANE WITH A MANUAL PLUNGER.
|
Resolution 7.80 Å |
| 4V1O Architecture of the RNA polymerase II-Mediator core transcription initiation complex Deposited 2014-09-29 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
25 MM HEPES-KOH PH 7.5, 180 MM POTASSIUM ACETATE, 5 % GLYCEROL, 5 MM DTT；pH 7.5；25 MM HEPES-KOH PH 7.5, 180 MM POTASSIUM ACETATE, 5 % GLYCEROL, 5 MM DTT
cryo-EM vitrification conditions
Cryogen ETHANE；GRIDS WERE GLOW- DISCHARGED FOR 20 S BEFORE DEPOSITION OF 4 MICROLITERS SAMPLE AND INCUBATED FOR 30 S. GRIDS WERE WASHED TWICE WITH 4 MICROLITERS DISTILLED WATER, BLOTTED, AND VITRIFIED BY PLUNGING INTO LIQUID ETHANE WITH A MANUAL PLUNGER.
|
Resolution 9.70 Å |
| 4X67 Crystal structure of elongating yeast RNA polymerase II stalled at oxidative Cyclopurine DNA lesions. Deposited 2014-12-07 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；390 mM (NH4)2HPO4/NaH2PO4, PH 5.9-6.3, 50 mM dioxane, 10 mM DTT, and 10.7% - 11.6% PEG6000
|
Resolution 4.10 Å R-free 0.289 |
| 4X6A Crystal structure of yeast RNA polymerase II encountering oxidative Cyclopurine DNA lesions Deposited 2014-12-07 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；390 mM (NH4)2HPO4/NaH2PO4, PH 5.9-6.3, 50 mM dioxane, 10 mM DTT, and 10.7% - 11.6% PEG6000
|
Resolution 3.96 Å R-free 0.296 |
| 4Y52 Crystal structure of 5-Carboxycytosine Recognition by RNA Polymerase II during Transcription Elongation. Deposited 2015-02-11 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293.15 K；390 mM (NH4)2HPO4/NaH2PO4, 50 mM dioxane, 10 mM DTT, and 10.7-11.6%(w/v) PEG6000
|
Resolution 3.50 Å R-free 0.232 |
| 4Y7N The Structure Insight into 5-Carboxycytosine Recognition by RNA Polymerase II during Transcription Elongation. Deposited 2015-02-15 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 2 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293.15 K；390 mM (NH4)2HPO4/NaH2PO4, pH 6.0, 50 mM dioxane, 10 mM DTT, and 10.7-11.6%(w/v) PEG6000
|
Resolution 3.30 Å R-free 0.250 |
| 5C3E Crystal structure of a transcribing RNA Polymerase II complex reveals a complete transcription bubble Deposited 2015-06-17 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；PEG 6000, Ammonium Acetate, Sodium Acetate, DTT
|
Resolution 3.70 Å R-free 0.220 |
| 5C44 Crystal structure of a transcribing RNA Polymerase II complex reveals a complete transcription bubble Deposited 2015-06-17 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；PEG 6000, Ammonium Acetate, Sodium Acetate, DTT
|
Resolution 3.95 Å R-free 0.236 |
| 5C4A Crystal structure of a transcribing RNA Polymerase II complex reveals a complete transcription bubble Deposited 2015-06-17 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；PEG 4000, POTASSIUM THIOCYANATE, MES, DTT
|
Resolution 4.20 Å R-free 0.242 |
| 5C4J Crystal structure of a transcribing RNA Polymerase II complex reveals a complete transcription bubble Deposited 2015-06-18 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；PEG 4000, SODIUM MALONATE, HEPES, DTT
|
Resolution 4.00 Å R-free 0.271 |
| 5C4X Crystal structure of a transcribing RNA Polymerase II complex reveals a complete transcription bubble Deposited 2015-06-18 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；PEG 4000, SODIUM CITRATE, MES, DTT
|
Resolution 4.00 Å R-free 0.227 |
| 5FMF the P-lobe of RNA polymerase II pre-initiation complex Deposited 2015-11-03 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | MG MAGNESIUM ION × 2 ZN ZINC ION × 9 |
ELECTRON MICROSCOPY
cryo-EM buffer
20 MM HEPES (PH7.6), 5 MM DTT, 2 MM MG(OAC)2,AND 40 MM KOAC；pH 7.6；20 MM HEPES (PH7.6), 5 MM DTT, 2 MM MG(OAC)2,AND 40 MM KOAC
cryo-EM vitrification conditions
Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 120, INSTRUMENT- FEI VITROBOT MARK III,
|
Resolution 6.00 Å |
| 5FYW Transcription initiation complex structures elucidate DNA opening (OC) Deposited 2016-03-10 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
25 MM HEPES-KOH PH 7.5, 150 MM POTASSIUM ACETATE, 2 MM MGCL2, 5 MM DTT；pH 7.5；25 MM HEPES-KOH PH 7.5, 150 MM POTASSIUM ACETATE, 2 MM MGCL2, 5 MM DTT
cryo-EM vitrification conditions
Cryogen ETHANE；CRYOGEN - ETHANE. INSTRUMENT - FEI VITROBOT MARK IV. QUANTIFOIL R 3.5- 1 HOLEY CARBON GRIDS WERE GLOW-DISCHARGED BEFORE DEPOSITION OF 4.5 MICROLITERS OF SAMPLE. GRIDS WERE THEN BLOTTED FOR 8.5 S AND PLUNGE- FROZEN IN LIQUID ETHANE.
|
Resolution 4.35 Å |
| 5FZ5 Transcription initiation complex structures elucidate DNA opening (CC) Deposited 2016-03-10 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
25 MM HEPES-KOH PH 7.5, 150 MM POTASSIUM ACETATE, 2 MM MGCL2, 5 MM DTT；pH 7.5；25 MM HEPES-KOH PH 7.5, 150 MM POTASSIUM ACETATE, 2 MM MGCL2, 5 MM DTT
cryo-EM vitrification conditions
Cryogen ETHANE；LIQUID ETHANE
|
Resolution 8.80 Å |
| 5IP7 Structure of RNA Polymerase II-Tfg1 peptide complex Deposited 2016-03-09 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
2–1733（1732 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；295 K；PEG 6000, sodium acetate, ammonium acetate, hepes, tcep
|
Resolution 3.52 Å R-free 0.180 |
| 5IP9 Structure of RNA Polymerase II-TFIIF complex Deposited 2016-03-09 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
2–1733（1732 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；295 K；peg 6000, sodium acetate, ammonium acetate, hepes, tcep
|
Resolution 3.90 Å R-free 0.194 |
| 5OQJ STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH Deposited 2017-08-11 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；GRIDS WERE BLOTTED FOR 8 S AND PLUNGE-FROZEN IN LIQUID ETHANE.
|
Resolution 4.70 Å |
| 5OQM STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH AND CORE MEDIATOR Deposited 2017-08-13 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 44 PDB declaration: 46-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；Grids were blotted for 8 s and plunge-frozen in liquid ethane.
|
Resolution 5.80 Å |
| 5OT2 RNA polymerase II elongation complex in the presence of 3d-Napht-A Deposited 2017-08-19 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 AHW 2-ethyl-7-methoxy-naphthalene × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；4-7% PEG 6000, 200 mM ammonium acetate, 300 mM sodium acetate, 50 mM HEPES pH 7.0, 5 mM TCEP
|
Resolution 3.20 Å R-free 0.222 |
| 5SVA Mediator-RNA Polymerase II Pre-Initiation Complex Deposited 2016-08-05 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric |
Chain A
1–1733（1733 aa）
Chain k
1561–1585（25 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 15.30 Å |
| 5U5Q 12 Subunit RNA Polymerase II at Room Temperature collected using SFX Deposited 2016-12-07 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICRODIALYSIS；pH 6.3；289.65 K；21-22% PEG 400, 5% PEG 5%, 100 mM Ammonium Phosphate pH 6.3, 100 mM NaCl, 1 mM ZnCl2 and 10 mM DTT
|
Resolution 3.80 Å R-free 0.271 |
| 5VKL SPT6 tSH2-RPB1 1476-1500 pS1493 Deposited 2017-04-21 | 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 B
1476–1498（23 aa）
Fragment：UNP residues 1476-1498
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；40% ethanol, 100 mM Tris pH 7.0
|
Resolution 2.20 Å R-free 0.243 |
| 5VKO SPT6 tSH2-RPB1 1468-1500 pT1471, pS1493 Deposited 2017-04-21 | 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 B
1468–1500（33 aa）
Fragment：UNP residues 1468-1500
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | IPA ISOPROPYL ALCOHOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；10% iso-Propanol, 0.1 M Na Hepes pH 7.5, 20% PEG 4000
|
Resolution 1.80 Å R-free 0.198 |
| 5VVR Ternary complex of RNA Pol II, transcription scaffold and Rad26 Deposited 2017-05-19 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.80 Å |
| 5VVS RNA pol II elongation complex Deposited 2017-05-20 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.40 Å |
| 5W4U Pol II elongation complex with an N6-methyladenine-containing template Deposited 2017-06-13 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 50mM dioxane, 10mM DTT, 10-12.5% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.60 Å R-free 0.259 |
| 5W51 Pol II elongation complex with an N6-methyladenine-containing template and a matched UMPNPP Deposited 2017-06-13 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 2 2KH 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 50mM dioxane, 10mM DTT, 10-12.5% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.40 Å R-free 0.254 |
| 6BLO Pol II elongation complex with an abasic lesion at i+1 position Deposited 2017-11-10 | Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 50mM dioxane, 10mM DTT, 9-12% PEG6000
|
Resolution 3.40 Å R-free 0.227 |
| 6BLP Pol II elongation complex with an abasic lesion at i+1 position, soaking AMPCPP Deposited 2017-11-11 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 2 APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 50mM dioxane, 10mM DTT, 9-12% PEG6000
|
Resolution 3.20 Å R-free 0.257 |
| 6BM2 Pol II elongation complex with an abasic lesion at i-1 position Deposited 2017-11-13 | Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 50mM dioxane, 10mM DTT, 9-12% PEG6000
|
Resolution 3.40 Å R-free 0.244 |
| 6BM4 Pol II elongation complex with an abasic lesion at i-1 position,soaking UMPNPP Deposited 2017-11-13 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 2 2KH 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 50mM dioxane, 10mM DTT, 9-12% PEG6000
|
Resolution 2.95 Å R-free 0.260 |
| 6BQF Pol II elongation complex with 'dT-AP' at i+1, i-1 position Deposited 2017-11-27 | Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 50mM dioxane, 10mM DTT, 9-12% PEG6000
|
Resolution 3.35 Å R-free 0.245 |
| 6GYK Structure of a yeast closed complex (core CC1) Deposited 2018-06-30 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.10 Å |
| 6GYL Structure of a yeast closed complex with distorted DNA (core CCdist) Deposited 2018-06-30 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.80 Å |
| 6GYM Structure of a yeast closed complex with distorted DNA (CCdist) Deposited 2018-06-30 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 16 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.70 Å |
| 6I84 Structure of transcribing RNA polymerase II-nucleosome complex Deposited 2018-11-19 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.40 Å |
| 6O6C RNA polymerase II elongation complex arrested at a CPD lesion Deposited 2019-03-05 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；The sample was manually wicked from the grid. 1.2 uL sample buffer was then applied to the streptavidin side. The grid was then blotted.
|
Resolution 3.10 Å |
| 6UPX RNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 1 Deposited 2019-10-18 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 5mM dioxane, 5mM DTT, 10-12% PEG6000
|
Resolution 3.40 Å R-free 0.266 |
| 6UPY RNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 2E Deposited 2019-10-18 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 5mM dioxane, 5mM DTT, 10-12% PEG6000
|
Resolution 3.40 Å R-free 0.282 |
| 6UPZ RNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 3 Deposited 2019-10-18 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 PPV PYROPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 5mM dioxane, 5mM DTT, 10-12% PEG6000
|
Resolution 3.10 Å R-free 0.269 |
| 6UQ0 RNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 4 Deposited 2019-10-18 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 5mM dioxane, 5mM DTT, 10-12% PEG6000
|
Resolution 3.56 Å R-free 0.278 |
| 6UQ1 RNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 6 Deposited 2019-10-18 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 5mM dioxane, 5mM DTT, 10-12% PEG6000
|
Resolution 3.60 Å R-free 0.287 |
| 6UQ2 RNA polymerase II elongation complex with dG in state 1 Deposited 2019-10-18 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 5mM dioxane, 5mM DTT, 10-12% PEG6000
|
Resolution 3.20 Å R-free 0.280 |
| 6UQ3 RNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 5 Deposited 2019-10-18 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 8 PPV PYROPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 5mM dioxane, 5mM DTT, 10-12% PEG6000
|
Resolution 3.47 Å R-free 0.286 |
| 7KED RNA polymerase II elongation complex with unnatural base dTPT3 Deposited 2020-10-10 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 5mM dioxane, 5mM DTT, 10-12% PEG6000
|
Resolution 3.60 Å R-free 0.305 |
| 7KEE RNA polymerase II elongation complex with unnatural base dTPT3, rNaMTP bound to E-site Deposited 2020-10-10 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 WCG (1S)-1,4-anhydro-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-1-(3-methoxynaphthalen-2-yl)-D-ribitol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 5mM dioxane, 5mM DTT, 10-12% PEG6000
|
Resolution 3.45 Å R-free 0.302 |
| 7KEF RNA polymerase II elongation complex with unnatural base dTPT3, rNaM in swing state Deposited 2020-10-10 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 WC4 (1S)-1,4-anhydro-1-(3-methoxynaphthalen-2-yl)-5-O-phosphono-D-ribitol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 5mM dioxane, 5mM DTT, 10-12% PEG6000
|
Resolution 3.89 Å R-free 0.326 |
| 7NKX RNA polymerase II-Spt4/5-nucleosome-Chd1 structure Deposited 2021-02-19 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 7NKY RNA Polymerase II-Spt4/5-nucleosome-FACT structure Deposited 2021-02-19 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 24 PDB declaration: 27-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7O4I Yeast RNA polymerase II transcription pre-initiation complex with initial transcription bubble Deposited 2021-04-06 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7O4J Yeast RNA polymerase II transcription pre-initiation complex (consensus) Deposited 2021-04-06 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 7O4K Yeast TFIIH in the contracted state within the pre-initiation complex Deposited 2021-04-06 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 10 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7O4L Yeast TFIIH in the expanded state within the pre-initiation complex Deposited 2021-04-06 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 11 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7O72 Yeast RNA polymerase II transcription pre-initiation complex with closed promoter DNA Deposited 2021-04-12 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7O73 Yeast RNA polymerase II transcription pre-initiation complex with closed distorted promoter DNA Deposited 2021-04-12 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7O75 Yeast RNA polymerase II transcription pre-initiation complex with open promoter DNA Deposited 2021-04-13 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7RIM RNA polymerase II elongation complex with hairpin polyamide Py-Im 1, scaffold 1 Deposited 2021-07-20 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | 5N0 3-({3-[(3-{[4-({4-[(4-{[4-({(2R)-2-amino-4-[(1-methyl-4-{[1-methyl-4-({1-methyl-4-[(1-methyl-1H-imidazole-2-carbonyl)amino]-1H-imidazole-2-carbonyl}amino)-1H-pyrrole-2-carbonyl]amino}-1H-pyrrole-2-carbonyl)amino]butanoyl}amino)-1-methyl-1H-imidazole-2-carbonyl]amino}-1-methyl-1H-pyrrole-2-carbonyl)amino]-1-methyl-1H-pyrrole-2-carbonyl}amino)-1-methyl-1H-pyrrole-2-carbonyl]amino}propyl)(methyl)amino]propyl}carbamoyl)benzoic acid × 1 ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 5mM dioxane, 5mM DTT, 10-12% PEG6000
|
Resolution 2.90 Å R-free 0.251 |
| 7RIP RNA polymerase II elongation complex with hairpin polyamide Py-Im 1, scaffold 1 soaked with CTP Deposited 2021-07-20 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | MG MAGNESIUM ION × 1 5N0 3-({3-[(3-{[4-({4-[(4-{[4-({(2R)-2-amino-4-[(1-methyl-4-{[1-methyl-4-({1-methyl-4-[(1-methyl-1H-imidazole-2-carbonyl)amino]-1H-imidazole-2-carbonyl}amino)-1H-pyrrole-2-carbonyl]amino}-1H-pyrrole-2-carbonyl)amino]butanoyl}amino)-1-methyl-1H-imidazole-2-carbonyl]amino}-1-methyl-1H-pyrrole-2-carbonyl)amino]-1-methyl-1H-pyrrole-2-carbonyl}amino)-1-methyl-1H-pyrrole-2-carbonyl]amino}propyl)(methyl)amino]propyl}carbamoyl)benzoic acid × 1 ZN ZINC ION × 8 PPV PYROPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 5mM dioxane, 5mM DTT, 10-12% PEG6000
|
Resolution 3.30 Å R-free 0.261 |
| 7RIQ RNA polymerase II elongation complex scaffold 1 without polyamide Deposited 2021-07-20 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 5mM dioxane, 5mM DTT, 10-12% PEG6000
|
Resolution 3.00 Å R-free 0.264 |
| 7RIW RNA polymerase II elongation complex scaffold 2, without polyamide Deposited 2021-07-20 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 5mM dioxane, 5mM DTT, 10-12% PEG6000
|
Resolution 3.20 Å R-free 0.265 |
| 7RIX RNA polymerase II elongation complex with hairpin polyamide Py-Im 1, scaffold 2 Deposited 2021-07-20 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | MG MAGNESIUM ION × 1 5N0 3-({3-[(3-{[4-({4-[(4-{[4-({(2R)-2-amino-4-[(1-methyl-4-{[1-methyl-4-({1-methyl-4-[(1-methyl-1H-imidazole-2-carbonyl)amino]-1H-imidazole-2-carbonyl}amino)-1H-pyrrole-2-carbonyl]amino}-1H-pyrrole-2-carbonyl)amino]butanoyl}amino)-1-methyl-1H-imidazole-2-carbonyl]amino}-1-methyl-1H-pyrrole-2-carbonyl)amino]-1-methyl-1H-pyrrole-2-carbonyl}amino)-1-methyl-1H-pyrrole-2-carbonyl]amino}propyl)(methyl)amino]propyl}carbamoyl)benzoic acid × 1 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 5mM dioxane, 5mM DTT, 10-12% PEG6000
|
Resolution 3.40 Å R-free 0.268 |
| 7RIY RNA polymerase II elongation complex with hairpin polyamide Py-Im 1, scaffold 2 soaked with UTP Deposited 2021-07-20 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | MG MAGNESIUM ION × 1 5N0 3-({3-[(3-{[4-({4-[(4-{[4-({(2R)-2-amino-4-[(1-methyl-4-{[1-methyl-4-({1-methyl-4-[(1-methyl-1H-imidazole-2-carbonyl)amino]-1H-imidazole-2-carbonyl}amino)-1H-pyrrole-2-carbonyl]amino}-1H-pyrrole-2-carbonyl)amino]butanoyl}amino)-1-methyl-1H-imidazole-2-carbonyl]amino}-1-methyl-1H-pyrrole-2-carbonyl)amino]-1-methyl-1H-pyrrole-2-carbonyl}amino)-1-methyl-1H-pyrrole-2-carbonyl]amino}propyl)(methyl)amino]propyl}carbamoyl)benzoic acid × 1 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 5mM dioxane, 5mM DTT, 10-12% PEG6000
|
Resolution 3.70 Å R-free 0.281 |
| 7UI9 Core Mediator-PICearly (Copy A) Deposited 2022-03-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric |
Chain A
1–1453（1453 aa）
Chain z
1561–1585（25 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7UIF Mediator-PIC Early (Core B) Deposited 2022-03-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric |
Chain A
1–1733（1733 aa）
Chain z
1–1733（1733 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.60 Å |
| 7UIG Mediator-PIC Early (Mediator A) Deposited 2022-03-29 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric |
Chain z
1–1733（1733 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å |
| 7UIO Mediator-PIC Early (Composite Model) Deposited 2022-03-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 78 PDB declaration: 80-meric |
Chain AA
1–1453（1453 aa）
Chain Az
1561–1585（25 aa）
Chain BA
1–1453（1453 aa）
Chain Bz
1561–1585（25 aa）
|
Not recorded | ZN ZINC ION × 4 THR THREONINE × 1 ALA ALANINE × 1 ASP ASPARTIC ACID × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7ZS9 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome (complex A) Deposited 2022-05-06 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7ZSA Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP (complex B) Deposited 2022-05-06 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 7ZSB Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP, complex C Deposited 2022-05-06 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.60 Å |
| 8CEN Yeast RNA polymerase II transcription pre-initiation complex with core Mediator Deposited 2023-02-02 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 44 PDB declaration: 46-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 8CEO Yeast RNA polymerase II transcription pre-initiation complex with core Mediator and the +1 nucleosome Deposited 2023-02-02 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 52 PDB declaration: 54-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 8JCH Cryo-EM structure of yeast Rat1-bound Pol II pre-termination transcription complex 1 (Pol II Rat1-PTTC1) Deposited 2023-05-11 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: 18-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 8K5P Cryo-EM structure of yeast Rat1-bound Pol II pre-termination transcription complex 2 (Pol II Rat1-PTTC2) Deposited 2023-07-23 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: 18-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 8RAM Structure of Sen1 bound RNA Polymerase II pre-termination complex Deposited 2023-12-01 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: 19-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 8RAP Structure of Sen1-ADP.BeF3 bound RNA Polymerase II pre-termination complex Deposited 2023-12-01 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: 19-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å |
| 8TUG Cryo-EM structure of CPD-stalled Pol II in complex with Rad26 (engaged state) Deposited 2023-08-16 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 8TVP Cryo-EM structure of CPD-stalled Pol II in complex with Rad26 (open state) Deposited 2023-08-18 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 8TVQ Cryo-EM structure of CPD stalled 10-subunit Pol II in complex with Rad26 Deposited 2023-08-18 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 11 PDB declaration: 14-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.60 Å |
| 8TVV Cryo-EM structure of backtracked Pol II Deposited 2023-08-18 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 8TVW Cryo-EM structure of CPD-stalled Pol II (conformation 1) Deposited 2023-08-18 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 8TVX Cryo-EM structure of CPD-stalled Pol II (Conformation 2) Deposited 2023-08-18 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 8TVY Cryo-EM structure of CPD lesion containing RNA Polymerase II elongation complex with Rad26 and Elf1 (closed state) Deposited 2023-08-18 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: 17-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8U9R STRUCTURAL BASIS OF TRANSCRIPTION: RNA POLYMERASE II SUBSTRATE BINDING AND METAL COORDINATION USING A FREE-ELECTRON LASER Deposited 2023-09-20 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 GOL GLYCEROL × 1 MG MAGNESIUM ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；10-15 % tacsimate
100mM Hepes
pH 7.5
|
Resolution 3.34 Å R-free 0.261 |
| 8U9X STRUCTURAL BASIS OF TRANSCRIPTION: RNA POLYMERASE II SUBSTRATE BINDING AND METAL COORDINATION AT 3.0 A OF T834P MUTANT USING A FREE-ELECTRON LASER Deposited 2023-09-20 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MN MANGANESE (II) ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；289 K；10-15 % tacsimate
100mM Hepes
|
Resolution 3.05 Å R-free 0.307 |
| 8UKQ RNA polymerase II elongation complex with Fapy-dG lesion in apo state Deposited 2023-10-15 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: 13-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；295 K；390 mM ammonium phosphate (pH 6.0), 5 mM DTT, 5 mM dioxane, and 9-13 % (w/v) PEG 6,000
|
Resolution 3.50 Å R-free 0.302 |
| 8UKR RNA polymerase II elongation complex with Fapy-dG lesion soaking with ATP before chemistry Deposited 2023-10-15 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；295 K；390 mM ammonium phosphate (pH 6.0), 5 mM DTT, 5 mM dioxane, and 9-13% (w/v) PEG 6,000
|
Resolution 3.78 Å R-free 0.310 |
| 8UKS RNA polymerase II elongation complex with Fapy-dG lesion soaking with CTP before chemistry Deposited 2023-10-15 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | MG MAGNESIUM ION × 2 ZN ZINC ION × 8 CTP CYTIDINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；295 K；390 mM ammonium phosphate (pH 6.0), 5 mM DTT, 5 mM dioxane, and 9-13% (w/v) PEG 6,000
|
Resolution 3.40 Å R-free 0.301 |
| 8UKT RNA polymerase II elongation complex with Fapy-dG lesion with AMP added Deposited 2023-10-15 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: 13-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 8 POP PYROPHOSPHATE 2- × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；295 K；390 mM ammonium phosphate (pH 6.0), 5 mM DTT, 5 mM dioxane, and 9-13% (w/v) PEG 6,000
|
Resolution 3.60 Å R-free 0.289 |
| 8UKU RNA polymerase II elongation complex with Fapy-dG lesion with CMP added Deposited 2023-10-15 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 POP PYROPHOSPHATE 2- × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；295 K；390 mM ammonium phosphate (pH 6.0), 5 mM DTT, 5 mM dioxane, and 9-13% (w/v) PEG 6,000
|
Resolution 3.60 Å R-free 0.301 |
| 8UOQ Composite map of PIC_delta_TFIIK form2 Deposited 2023-10-20 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 15 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 8UOT Composite map of PICdeltaTFIIK form1 Deposited 2023-10-20 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 MG MAGNESIUM ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6；20 mM HEPES PH 7.6
50 mM KOAc
5 mM DTT
2 mM MgOAc
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 9BVT RNA Pol II - High Mn(+2) concentration Deposited 2024-05-20 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MN MANGANESE (II) ION × 2 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；Tacsimate Hepes
|
Resolution 3.40 Å R-free 0.249 |
| 9BW0 RNA Polymerase II - No ATP Deposited 2024-05-20 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；Tacsimate, Hepes pH 7.0
|
Resolution 3.51 Å R-free 0.246 |
| 9JA1 The RNA polymerase II elongation complex from Saccharomyces cerevisiae Deposited 2024-08-23 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 11 PDB declaration: tetradecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 6 MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.98 Å |
| 9K7F RNA polymerase II elongation complex apo structure. Deposited 2024-10-23 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.50 Å |
| 9KD7 The structure of RNA polymerase II elongation complex paused at N-1 state by actinomycin D. Deposited 2024-11-03 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.09 Å |
| 9KD8 The structure of RNA polymerase II elongation complex paused at N-2 state by actinomycin D. Deposited 2024-11-03 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.46 Å |
| 9KD9 The structure of RNA polymerase II elongation complex paused at N-5 state by actinomycin D. Deposited 2024-11-03 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.88 Å |
| 9KDN The structure of 1 ACTD bound to RNA polymerase II elongation complex with 2 CTG repeats. Deposited 2024-11-03 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.96 Å |
| 9KDO The structure of 2 ACTD bound to RNA polymerase II elongation complex with 3 CTG repeats Deposited 2024-11-03 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.92 Å |
| 9KDQ The structure of 3 ACTD bound to RNA polymerase II elongation complex with 4 CTG repeats. Deposited 2024-11-03 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: octadecameric |
Chain A
1–1454（1454 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.63 Å |
| 9N5B RNA polymerase II elongation complex containing 8-oxoG at +1 site, apo form Deposited 2025-02-04 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 5mM dioxane, 5mM DTT, 10-12% PEG6000
|
Resolution 3.10 Å R-free 0.256 |
| 9N5C RNA polymerase II elongation complex with 8-oxoG at +1 site, CMPCPP-bound Deposited 2025-02-04 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 2TM 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 5mM dioxane, 5mM DTT, 10-12% PEG6000
|
Resolution 3.60 Å R-free 0.297 |
| 9N5D RNA polymerase II elongation complex with 8-oxoG at +1 site, CMP added Deposited 2025-02-04 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 PPV PYROPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 5mM dioxane, 5mM DTT, 10-12% PEG6000
|
Resolution 3.35 Å R-free 0.300 |
| 9N5E RNA polymerase II elongation complex with 8-oxoG at +1 site, AMPCPP in E-site Deposited 2025-02-04 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 5mM dioxane, 5mM DTT, 10-12% PEG6000
|
Resolution 3.75 Å R-free 0.291 |
| 9N5F RNA polymerase II elongation complex with 8-oxoG in syn-conformation with added AMP Deposited 2025-02-04 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 5mM dioxane, 5mM DTT, 10-12% PEG6000
|
Resolution 3.60 Å R-free 0.281 |
| 9N5G RNA polymerase II elongation complex with 8-oxoG at +1 site, ATP in both A- and E-site Deposited 2025-02-04 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 5mM dioxane, 5mM DTT, 10-12% PEG6000
|
Resolution 3.15 Å R-free 0.254 |
| 9PVV RNA polymerase II elongation complex with dC at +1 site, 8-oxo-GTP bound in A-site. Deposited 2025-08-03 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 3.48 Å R-free 0.258 |
| 9PVW RNA polymerase II elongation complex with dA at +1 site, 8-oxo-GMP added in Syn-conformation Deposited 2025-08-03 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 3.56 Å R-free 0.288 |
| 9PVX RNA polymerase II elongation complex with dA at +1 site, 8-oxo-GTP bound in E-site. Deposited 2025-08-03 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 3.39 Å R-free 0.236 |
| 9QEB CryoEM structure of transcribing RNA polymerase II elongation complex Deposited 2025-03-08 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric |
Chain A
1–1733（1733 aa）
|
Not recorded | ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 K POTASSIUM ION × 1 ZN ZINC ION × 8 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.26 Å |
| 9RYB CryoEM structure of transcribing RNA polymerase II elongation complex in post-catalysis state Deposited 2025-07-15 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric |
Chain A
1–1733（1733 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 8 K POTASSIUM ION × 1 DPO DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.33 Å |
211 other PDB entries and 218 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | RPB1_YEAST |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–1733； UniProt 1–1733 |
