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Protein Structures and Oligomeric States

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

Current Protein Identity：P20433 New Search
104PDB entries
108Biological assembly
110chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics

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

Related-Structure Differences

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

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
1NT9 Complete 12-subunit RNA polymerase II Deposited 2003-01-29 Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric（12） Consistent with protein count
Chain D 1–221（221 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 Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric（13） Consistent with protein count
Chain D 1–221（221 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
1Y14 Crystal structure of yeast subcomplex of Rpb4 and Rpb7 Deposited 2004-11-17 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain A 35–221（187 aa） Fragment：residues 35-221
Chain C 35–221（187 aa） Fragment：residues 35-221
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å R-free 0.274
1Y14 Crystal structure of yeast subcomplex of Rpb4 and Rpb7 Deposited 2004-11-17 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 35–221（187 aa） Fragment：residues 35-221
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å R-free 0.274
1Y14 Crystal structure of yeast subcomplex of Rpb4 and Rpb7 Deposited 2004-11-17 Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain C 35–221（187 aa） Fragment：residues 35-221
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å R-free 0.274
1Y1V Refined RNA Polymerase II-TFIIS complex Deposited 2004-11-19 Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric（13） Consistent with protein count
Chain D 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: tridecameric（13） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric（12） Consistent with protein count
Chain D 1–221（221 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
2JA5 CPD lesion containing RNA Polymerase II elongation complex A Deposited 2006-11-23 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Review required
Chain D 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain D 1–221（221 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 Assembly 2 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain P 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain D 1–221（221 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
2R7Z Cisplatin lesion containing RNA polymerase II elongation complex Deposited 2007-09-10 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: tridecameric（13） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric（16） Consistent with all polymers
Chain D 1–221（221 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
3FKI 12-Subunit RNA Polymerase II Refined with Zn-SAD data Deposited 2008-12-16 Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric（12） Consistent with protein count
Chain D 1–221（221 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
3H3V Yeast RNAP II containing poly(A)-signal sequence in the active site Deposited 2009-04-17 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain E 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain D 1–221（221 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 Assembly 2 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain P 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric（12） Consistent with protein count
Chain D 4–221（218 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 Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric（13） Consistent with protein count
Chain D 1–221（221 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
3PO2 Arrested RNA Polymerase II elongation complex Deposited 2010-11-21 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric（16） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric（12） Consistent with protein count
Chain D 3–221（219 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
4A3B RNA Polymerase II initial transcribing complex with a 4nt DNA-RNA hybrid Deposited 2011-09-30 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain D 1–221（221 aa）
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 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain D 1–221（221 aa）
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 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain D 1–221（221 aa）
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 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain D 1–221（221 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；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 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain D 1–221（221 aa）
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 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain D 1–221（221 aa）
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 Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers
Chain D 1–221（221 aa）
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 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain D 1–221（221 aa）
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 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain D 1–221（221 aa）
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 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain D 1–221（221 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；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 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain D 1–221（221 aa）
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 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain D 1–221（221 aa）
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric（13） Consistent with protein count
Chain D 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric（16） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric（16） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric（13） Consistent with protein count
Chain D 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric（16） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric（16） Consistent with all polymers
Chain D 1–221（221 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
4V1N Architecture of the RNA polymerase II-Mediator core transcription initiation complex Deposited 2014-09-29 Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: nonadecameric（19） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric（26） Consistent with all polymers
Chain D 1–221（221 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
5C3E Crystal structure of a transcribing RNA Polymerase II complex reveals a complete transcription bubble Deposited 2015-06-17 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain D 1–221（221 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
5C4X Crystal structure of a transcribing RNA Polymerase II complex reveals a complete transcription bubble Deposited 2015-06-18 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain D 1–221（221 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
5FYW Transcription initiation complex structures elucidate DNA opening (OC) Deposited 2016-03-10 Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric（22） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric（22） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric（13） Consistent with protein count
Chain D 1–221（221 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 Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric（13） Consistent with protein count
Chain D 1–221（221 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 Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric（31） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Insufficient information Heteromer；Protein × 44 PDB declaration: 46-meric（46） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric（40） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric（12） Consistent with protein count
Chain D 1–221（221 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
5VVR Ternary complex of RNA Pol II, transcription scaffold and Rad26 Deposited 2017-05-19 Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric（16） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain D 1–221（221 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
6GYK Structure of a yeast closed complex (core CC1) Deposited 2018-06-30 Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric（20） Consistent with all polymers
Chain D 2–221（220 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 Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric（22） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric（31） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric（23） Consistent with all polymers
Chain D 1–221（221 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
7NKX RNA polymerase II-Spt4/5-nucleosome-Chd1 structure Deposited 2021-02-19 Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric（26） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 24 PDB declaration: 27-meric（27） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric（30） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric（30） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric（17） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric（17） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric（30） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric（30） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric（30） Consistent with all polymers
Chain D 1–221（221 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
7UI9 Core Mediator-PICearly (Copy A) Deposited 2022-03-28 Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric（33） Consistent with protein count
Chain D 1–221（221 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 Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric（33） Consistent with protein count
Chain D 1–221（221 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
7UIO Mediator-PIC Early (Composite Model) Deposited 2022-03-29 Assembly 1 Protein–DNA Heteromer；Protein × 78 PDB declaration: 80-meric（80） Consistent with all polymers
Chain AD 1–221（221 aa）
Chain BD 1–221（221 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 Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric（38） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric（38） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric（38） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Protein–DNA Heteromer；Protein × 44 PDB declaration: 46-meric（46） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Protein–DNA Heteromer；Protein × 52 PDB declaration: 54-meric（54） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: 18-meric（18） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: 18-meric（18） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: 19-meric（19） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: 19-meric（19） Consistent with all polymers
Chain D 1–221（221 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
8UOQ Composite map of PIC_delta_TFIIK form2 Deposited 2023-10-20 Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric（30） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric（30） Consistent with all polymers
Chain D 1–221（221 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
9JA1 The RNA polymerase II elongation complex from Saccharomyces cerevisiae Deposited 2024-08-23 Assembly 1 Other combination Heteromer；Protein × 11 PDB declaration: tetradecameric（14） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric（16） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric（16） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric（16） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric（16） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric（17） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: octadecameric（18） Consistent with all polymers
Chain D 1–221（221 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
9QEB CryoEM structure of transcribing RNA polymerase II elongation complex Deposited 2025-03-08 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric（15） Consistent with all polymers
Chain D 1–221（221 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 Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain D 1–221（221 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

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