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7o4k

Yeast TFIIH in the contracted state within the pre-initiation complex

Method: ELECTRON MICROSCOPY Dmax: 197.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

General transcription and DNA repair factor IIH helicase subunit XPD

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P06839

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 15 DNA 2 PDB declaration: heptadecameric（17） Consistent with all polymer counts Chain 0； UniProt 1–778 Not recorded General transcription and DNA repair factor IIH subunit TFB1 × 1 （P32776） General transcription and DNA repair factor IIH subunit TFB2 × 1 （Q02939） RNA polymerase II transcription factor B subunit 3 × 1 （Q03290） General transcription and DNA repair factor IIH subunit TFB4 × 1 （Q12004） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH subunit SSL1 × 1 （Q04673） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） DNA-directed RNA polymerase II subunit RPB1 × 1 （P04050） DNA-directed RNA polymerase II subunit RPB2 × 1 （P08518） DNA-directed RNA polymerase II subunit RPB4 × 1 （P20433） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （P20435） DNA-directed RNA polymerase II subunit RPB7 × 1 （P34087） Non-template DNA × 1 Template DNA × 1 Transcription initiation factor IIE subunit alpha × 1 （P36100） Transcription initiation factor IIE subunit beta × 1 （P36145） 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

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 7O4K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5FMF the P-lobe of RNA polymerase II pre-initiation complex Deposited 2015-11-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain Y 1–778（778 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
5OQJ STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH Deposited 2017-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 0 1–293（293 aa）
Chain 0 327–778（452 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 44 PDB declaration: 46-meric
Chain 0 1–293（293 aa）
Chain 0 328–778（451 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
5SVA Mediator-RNA Polymerase II Pre-Initiation Complex Deposited 2016-08-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric
Chain Y 1–778（778 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
6GYM Structure of a yeast closed complex with distorted DNA (CCdist) Deposited 2018-06-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 0 1–293（293 aa）
Chain 0 327–778（452 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) 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
7K01 Structure of TFIIH in TFIIH/Rad4-Rad23-Rad33 DNA opening complex Deposited 2020-09-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain 0 1–778（778 aa）
Not recorded ZN ZINC ION × 5 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；Sample dialyzed for 30 minutes into above buffer prior to grid making
cryo-EM vitrification conditions Cryogen ETHANE；Grids were manually blotted for 2-3 seconds prior to plunge freezing
Resolution 3.90 Å
7K04 Structure of TFIIH/Rad4-Rad23-Rad33/DNA in DNA opening Deposited 2020-09-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain 0 1–778（778 aa）
Not recorded CA CALCIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Manually blotted by Leica EM CPC
Resolution 9.25 Å
7M2U Nucleotide Excision Repair complex TFIIH Rad4-33 Deposited 2021-03-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain 0 1–778（778 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 5 CA CALCIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.20 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 0 1–778（778 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 0 1–778（778 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
7O4L Yeast TFIIH in the expanded state within the pre-initiation complex Deposited 2021-04-06 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain 0 1–778（778 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 0 1–778（778 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 0 1–778（778 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 0 1–778（778 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
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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain 0 1–778（778 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain 0 1–778（778 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain 0 1–778（778 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 44 PDB declaration: 46-meric
Chain 0 1–778（778 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 conditions Assembly 1 Protein–DNA Heteromer；Protein × 52 PDB declaration: 54-meric
Chain 0 1–778（778 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
8UOQ Composite map of PIC_delta_TFIIK form2 Deposited 2023-10-20 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 0 1–778（778 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 0 1–778（778 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

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

View Construct and Data Evidence
UniProt name RAD3_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain 0； PDBConstruct 1–778； UniProt 1–778

General transcription and DNA repair factor IIH subunit TFB1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P32776

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 15 DNA 2 PDB declaration: heptadecameric（17） Consistent with all polymer counts Chain 1； UniProt 1–642 Not recorded General transcription and DNA repair factor IIH helicase subunit XPD × 1 （P06839） General transcription and DNA repair factor IIH subunit TFB2 × 1 （Q02939） RNA polymerase II transcription factor B subunit 3 × 1 （Q03290） General transcription and DNA repair factor IIH subunit TFB4 × 1 （Q12004） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH subunit SSL1 × 1 （Q04673） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） DNA-directed RNA polymerase II subunit RPB1 × 1 （P04050） DNA-directed RNA polymerase II subunit RPB2 × 1 （P08518） DNA-directed RNA polymerase II subunit RPB4 × 1 （P20433） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （P20435） DNA-directed RNA polymerase II subunit RPB7 × 1 （P34087） Non-template DNA × 1 Template DNA × 1 Transcription initiation factor IIE subunit alpha × 1 （P36100） Transcription initiation factor IIE subunit beta × 1 （P36145） 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

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 7O4K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1Y5O NMR structure of the amino-terminal domain from the Tfb1 subunit of yeast TFIIH Deposited 2004-12-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–115（115 aa） Fragment：sequence database residues 1-115
Mutation：M1P No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 20 mM SODIUM PHOSPHATE；Pressure AMBIENT
NMR sample composition 1.2 MM TFB1 [UNLABELED], 20 MM PHOSPHATE BUFFER, 1MM EDTA, 100% D2O; 1.2 MM TFB1 [U-15N], 20 MM PHOSPHATE BUFFER, 1MM EDTA, 90% H2O, 10% D2O; 1.2 MM TFB1 [U-15N,13C], 20 MM PHOSPHATE BUFFER, 1MM EDTA, 100% D2O
Resolution not provided
2GS0 NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and the activation domain of p53 Deposited 2006-04-25 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 A 1–115（115 aa）
Mutation：M1P No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 20 mM sodium phosphate；Pressure ambient
NMR sample composition 1.0 mM Tfb1 U-15N, 1.0 mM p53 unlabeled, 1.00 mM EDTA, 20 mM phosphate buffer; 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 1.0 mM Tfb1 U-15N,13C, 1.0 mM p53 unlabeled, 1.00 mM EDTA, 20 mM phosphate buffer; 100% D20 | 100% D20
NMR sample composition 1.0 mM p53 U-15N, 1.0 mM Tfb1 unlabeled, 1.00 mM EDTA, 20 mM phosphate buffer; 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 1.0 mM p53 U-15N, 1.0 mM Tfb1 unlabeled, 1.00 mM EDTA, 20 mM phosphate buffer; 100% D20 | 100% D20
Resolution not provided
2K2U NMR Structure of the complex between Tfb1 subunit of TFIIH and the activation domain of VP16 Deposited 2008-04-11 Different construct 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 A 1–115（115 aa） Fragment：PH domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 20mM Sodium Phosphate；Pressure Ambient
NMR sample composition 1.0 mM [U-99% 15N] Tfb1, 1.0 mM VP16, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 1.0 mM [U-99% 13C; U-99% 15N] Tfb1, 1.0 mM VP16, 100% D2O | 100% D2O
NMR sample composition 1.0 mM [U-99% 15N] VP16, 1.0 mM Tfb1, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 1.0 mM [U-99% 13C; U-99% 15N] VP16, 1.0 mM Tfb1, 100% D2O | 100% D2O
Resolution not provided
2L2I NMR Structure of the complex between the Tfb1 subunit of TFIIH and the activation domain of EKLF Deposited 2010-08-18 Different construct 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 A 2–115（114 aa） Fragment：PH domain (UNP residues 2-115)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 20mM Sodium Phosphate；Pressure ambient
NMR sample composition 1 mM [U-100% 15N] Tfb1, 2 mM EKLF, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Tfb1, 2 mM EKLF, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.6 mM [U-100% 15N] EKLF, 1.2 mM Tfb1, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.6 mM [U-100% 13C; U-100% 15N] EKLF, 1.2 mM Tfb1, 100% D2O | 100% D2O
NMR sample composition 0.6 mM [U-100% 13C; U-100% 15N] EKLF, 1.2 mM Tfb1, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Tfb1, 2 mM EKLF, 100% D2O | 100% D2O
Resolution not provided
2LOX NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and Rad2 Deposited 2012-01-27 Different construct 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 A 2–115（114 aa） Fragment：UNP residues 2-115
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；300 K；Pressure ambient
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Tfb1, 1.25 mM Rad2, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Tfb1, 1.25 mM Rad2, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 100% D2O | 100% D2O
NMR sample composition 1 mM [U-100% 15N] Tfb1, 1.25 mM Rad2, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1.25 mM Tfb1, 1 mM [U-100% 13C; U-100% 15N] Rad2, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1.25 mM Tfb1, 1 mM [U-100% 13C; U-100% 15N] Rad2, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 100% D2O | 100% D2O
NMR sample composition 1.25 mM Tfb1, 1 mM [U-100% 15N] Rad2, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2M14 NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and Rad4 Deposited 2012-11-16 Different construct 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 A 2–115（114 aa） Fragment：UNP residues 2-115
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 20；Pressure ambient
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Tfb1, 1.25 mM Rad4, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Tfb1, 1.25 mM Rad4, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 100% D2O | 100% D2O
NMR sample composition 1 mM [U-100% 15N] Tfb1, 1.25 mM Rad4, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1.25 mM Tfb1, 1 mM [U-100% 13C; U-100% 15N] Rad4, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1.25 mM Tfb1, 1 mM [U-100% 13C; U-100% 15N] Rad4, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 100% D2O | 100% D2O
NMR sample composition 1.25 mM Tfb1, 1 mM [U-100% 15N] Rad4, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2MKR Structural Characterization of a Complex Between the Acidic Transactivation Domain of EBNA2 and the Tfb1/p62 subunit of TFIIH. Deposited 2014-02-12 Different construct 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 A 1–115（115 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 20；Pressure ambient
NMR sample composition 0.7 mM [U-13C; U-15N] Tfb1, 2.1 mM EBNA2, 20 mM sodium phosphate, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.7 mM [U-15N] Tfb1, 2.1 mM EBNA2, 20 mM sodium phosphate, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.7 mM [U-13C; U-15N] Tfb1, 2.1 mM EBNA2, 20 mM sodium phosphate, 1 mM DTT, 100% D2O | 100% D2O
NMR sample composition 0.5 mM [U-13C; U-15N] EBNA2, 1.5 mM Tfb1, 20 mM sodium phosphate, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.5 mM [U-100% 15N] EBNA2, 1.5 mM Tfb1, 20 mM sodium phosphate, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.5 mM [U-13C; U-15N] EBNA2, 1.5 mM Tfb1, 20 mM sodium phosphate, 1 mM DTT-24, 100% D2O | 100% D2O
Resolution not provided
2N0Y NMR structure of the complex between the C-terminal domain of the Rift Valley fever virus protein NSs and the PH domain of the Tfb1 subunit of TFIIH Deposited 2015-03-18 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 A 1–115（115 aa） Fragment：Pleckstrin homology domain residues 1-115
Mutation：M1P No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 0；Pressure ambient
NMR sample composition 1 mM [U-13C; U-15N] RNA polymerase II transcription factor B subunit 1, 2 mM Non-structural protein NS-S, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-13C; U-15N] RNA polymerase II transcription factor B subunit 1, 2 mM Non-structural protein NS-S, 100% D2O | 100% D2O
NMR sample composition 0.5 mM [U-15N] RNA polymerase II transcription factor B subunit 1, 1 mM Non-structural protein NS-S, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM RNA polymerase II transcription factor B subunit 1, 0.5 mM [U-13C; U-15N] Non-structural protein NS-S, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.5 mM RNA polymerase II transcription factor B subunit 1, 1 mM [U-13C; U-15N] Non-structural protein NS-S, 100% D2O | 100% D2O
NMR sample composition 0.4 mM RNA polymerase II transcription factor B subunit 1, 0.2 mM [U-15N] Non-structural protein NS-S, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2N23 NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and the N-terminal activation domain of EKLF (TAD1) Deposited 2015-04-27 Different construct 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 A 2–115（114 aa） Fragment：Pleckstrin homology domain, UNP residues 2-115
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 0；Pressure ambient
NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N] RNA polymerase II transcription factor B subunit 1, 2 mM N-terminal transactivation domain of Krueppel-like factor 1, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N] RNA polymerase II transcription factor B subunit 1, 2 mM N-terminal transactivation domain of Krueppel-like factor 1, 100% D2O | 100% D2O
NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N] N-terminal transactivation domain of Krueppel-like factor 1, 2 mM RNA polymerase II transcription factor B subunit 1, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N] N-terminal transactivation domain of Krueppel-like factor 1, 2 mM RNA polymerase II transcription factor B subunit 1, 100% D2O | 100% D2O
Resolution not provided
5OQJ STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH Deposited 2017-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 1 1–218（218 aa）
Chain 1 250–295（46 aa）
Chain 1 537–642（106 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 44 PDB declaration: 46-meric
Chain 1 1–121（121 aa）
Chain 1 176–218（43 aa）
Chain 1 250–295（46 aa）
Chain 1 522–642（121 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
5URN NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and the transactivation domain 1 of p65 Deposited 2017-02-11 Different construct 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 A 2–115（114 aa） Fragment：PLECKSTRIN HOMOLOGY DOMAIN, UNP RESIDUES 2-115
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0；Pressure AMBIENT
NMR sample composition 0.8 mM [U-99% 13C; U-99% 15N] RNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT 1, 1.6 mM TRANSCRIPTION FACTOR P65, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.8 mM [U-99% 13C; U-99% 15N] TRANSCRIPTION FACTOR P65, 1.6 mM RNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT 1, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.8 mM [U-99% 13C; U-99% 15N] RNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT 1, 1.6 mM TRANSCRIPTION FACTOR P65, 100% D2O | 100% D2O
NMR sample composition 0.8 mM [U-99% 13C; U-99% 15N] TRANSCRIPTION FACTOR P65, 1.6 mM RNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT 1, 100% D2O | 100% D2O
Resolution not provided
6GYM Structure of a yeast closed complex with distorted DNA (CCdist) Deposited 2018-06-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 1 1–218（218 aa）
Chain 1 250–295（46 aa）
Chain 1 537–642（106 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
7K01 Structure of TFIIH in TFIIH/Rad4-Rad23-Rad33 DNA opening complex Deposited 2020-09-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain 1 1–642（642 aa）
Not recorded ZN ZINC ION × 5 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；Sample dialyzed for 30 minutes into above buffer prior to grid making
cryo-EM vitrification conditions Cryogen ETHANE；Grids were manually blotted for 2-3 seconds prior to plunge freezing
Resolution 3.90 Å
7K04 Structure of TFIIH/Rad4-Rad23-Rad33/DNA in DNA opening Deposited 2020-09-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain 1 2–642（641 aa）
Not recorded CA CALCIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Manually blotted by Leica EM CPC
Resolution 9.25 Å
7M2U Nucleotide Excision Repair complex TFIIH Rad4-33 Deposited 2021-03-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain 1 1–642（642 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 5 CA CALCIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.20 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 1 1–642（642 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 1 1–642（642 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
7O4L Yeast TFIIH in the expanded state within the pre-initiation complex Deposited 2021-04-06 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain 1 1–642（642 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 1 1–642（642 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 1 1–642（642 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 1 1–642（642 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
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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain 1 1–642（642 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain 1 1–642（642 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain 1 1–642（642 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
8UOQ Composite map of PIC_delta_TFIIK form2 Deposited 2023-10-20 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 1 1–642（642 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 1 1–642（642 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

27 other PDB entries and 27 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TFB1_YEAST
Isoform —
PDB entities 2
Chains and sequence ranges Author chain 1； PDBConstruct 4–645； UniProt 1–642

General transcription and DNA repair factor IIH subunit TFB2

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q02939

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 15 DNA 2 PDB declaration: heptadecameric（17） Consistent with all polymer counts Chain 2； UniProt 1–513 Not recorded General transcription and DNA repair factor IIH helicase subunit XPD × 1 （P06839） General transcription and DNA repair factor IIH subunit TFB1 × 1 （P32776） RNA polymerase II transcription factor B subunit 3 × 1 （Q03290） General transcription and DNA repair factor IIH subunit TFB4 × 1 （Q12004） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH subunit SSL1 × 1 （Q04673） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） DNA-directed RNA polymerase II subunit RPB1 × 1 （P04050） DNA-directed RNA polymerase II subunit RPB2 × 1 （P08518） DNA-directed RNA polymerase II subunit RPB4 × 1 （P20433） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （P20435） DNA-directed RNA polymerase II subunit RPB7 × 1 （P34087） Non-template DNA × 1 Template DNA × 1 Transcription initiation factor IIE subunit alpha × 1 （P36100） Transcription initiation factor IIE subunit beta × 1 （P36145） 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

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 7O4K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3DGP Crystal Structure of the complex between Tfb5 and the C-terminal domain of Tfb2 Deposited 2008-06-14 Different construct 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 A 435–513（79 aa） Fragment：C-terminal Domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8.9；277 K；Tris 20 mM, NaCl 50 mM, pH 8.9, EVAPORATION, temperature 277K
Resolution 1.80 Å R-free 0.237
3DOM Crystal Structure of the complex between Tfb5 and the C-terminal domain of Tfb2 Deposited 2008-07-04 Different construct 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 A 412–513（102 aa） Fragment：C-terminal domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PEG3350 MME, NaCl, Hepes, pH 7.5, vapor diffusion, sitting drop, temperature 293K
Resolution 2.60 Å R-free 0.261
3DOM Crystal Structure of the complex between Tfb5 and the C-terminal domain of Tfb2 Deposited 2008-07-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 412–513（102 aa） Fragment：C-terminal domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PEG3350 MME, NaCl, Hepes, pH 7.5, vapor diffusion, sitting drop, temperature 293K
Resolution 2.60 Å R-free 0.261
5FMF the P-lobe of RNA polymerase II pre-initiation complex Deposited 2015-11-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain W 447–508（62 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
5OQJ STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH Deposited 2017-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 2 1–112（112 aa）
Chain 2 160–194（35 aa）
Chain 2 215–281（67 aa）
Chain 2 433–513（81 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 44 PDB declaration: 46-meric
Chain 2 1–112（112 aa）
Chain 2 160–194（35 aa）
Chain 2 215–281（67 aa）
Chain 2 282–513（232 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
5SVA Mediator-RNA Polymerase II Pre-Initiation Complex Deposited 2016-08-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric
Chain a 1–513（513 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
6GYM Structure of a yeast closed complex with distorted DNA (CCdist) Deposited 2018-06-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 2 1–112（112 aa）
Chain 2 160–194（35 aa）
Chain 2 215–281（67 aa）
Chain 2 433–513（81 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
7K01 Structure of TFIIH in TFIIH/Rad4-Rad23-Rad33 DNA opening complex Deposited 2020-09-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain 2 1–513（513 aa）
Not recorded ZN ZINC ION × 5 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；Sample dialyzed for 30 minutes into above buffer prior to grid making
cryo-EM vitrification conditions Cryogen ETHANE；Grids were manually blotted for 2-3 seconds prior to plunge freezing
Resolution 3.90 Å
7K04 Structure of TFIIH/Rad4-Rad23-Rad33/DNA in DNA opening Deposited 2020-09-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain 2 1–513（513 aa）
Not recorded CA CALCIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Manually blotted by Leica EM CPC
Resolution 9.25 Å
7M2U Nucleotide Excision Repair complex TFIIH Rad4-33 Deposited 2021-03-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain 2 1–513（513 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 5 CA CALCIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.20 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 2 1–513（513 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 2 1–513（513 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
7O4L Yeast TFIIH in the expanded state within the pre-initiation complex Deposited 2021-04-06 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain 2 1–513（513 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 2 1–513（513 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 2 1–513（513 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 2 1–513（513 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
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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain 2 1–513（513 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain 2 1–513（513 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain 2 1–513（513 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
8UOQ Composite map of PIC_delta_TFIIK form2 Deposited 2023-10-20 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 2 1–513（513 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 2 1–513（513 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

21 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TFB2_YEAST
Isoform —
PDB entities 3
Chains and sequence ranges Author chain 2； PDBConstruct 5–517； UniProt 1–513

RNA polymerase II transcription factor B subunit 3

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q03290

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 15 DNA 2 PDB declaration: heptadecameric（17） Consistent with all polymer counts Chain 3； UniProt 1–321 Not recorded General transcription and DNA repair factor IIH helicase subunit XPD × 1 （P06839） General transcription and DNA repair factor IIH subunit TFB1 × 1 （P32776） General transcription and DNA repair factor IIH subunit TFB2 × 1 （Q02939） General transcription and DNA repair factor IIH subunit TFB4 × 1 （Q12004） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH subunit SSL1 × 1 （Q04673） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） DNA-directed RNA polymerase II subunit RPB1 × 1 （P04050） DNA-directed RNA polymerase II subunit RPB2 × 1 （P08518） DNA-directed RNA polymerase II subunit RPB4 × 1 （P20433） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （P20435） DNA-directed RNA polymerase II subunit RPB7 × 1 （P34087） Non-template DNA × 1 Template DNA × 1 Transcription initiation factor IIE subunit alpha × 1 （P36100） Transcription initiation factor IIE subunit beta × 1 （P36145） 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

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 7O4K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5OQJ STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH Deposited 2017-08-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 3 1–321（321 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 conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 44 PDB declaration: 46-meric
Chain 3 1–321（321 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
6GYM Structure of a yeast closed complex with distorted DNA (CCdist) Deposited 2018-06-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 3 1–321（321 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
6XI8 Yeast TFIIK (Kin28/Ccl1/Tfb3) Complex Deposited 2020-06-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 259–321（63 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；blotted for 2 seconds with Whatman 41 ashless filter paper
Resolution 3.64 Å
7KUE CryoEM structure of Yeast TFIIK (Kin28/Ccl1/Tfb3) Complex Deposited 2020-11-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–321（321 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；blotted for 2 seconds with Whatman 41 ashless filter paper
Resolution 3.50 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 3 1–321（321 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 3 1–321（321 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
7O4L Yeast TFIIH in the expanded state within the pre-initiation complex Deposited 2021-04-06 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain 3 1–321（321 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 3 1–321（321 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 3 1–321（321 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 3 1–321（321 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
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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain 3 1–321（321 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain 3 1–321（321 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain 3 1–321（321 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

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

View Construct and Data Evidence
UniProt name TFB3_YEAST
Isoform —
PDB entities 4
Chains and sequence ranges Author chain 3； PDBConstruct 4–324； UniProt 1–321

General transcription and DNA repair factor IIH subunit TFB4

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q12004

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 15 DNA 2 PDB declaration: heptadecameric（17） Consistent with all polymer counts Chain 4； UniProt 1–338 Not recorded General transcription and DNA repair factor IIH helicase subunit XPD × 1 （P06839） General transcription and DNA repair factor IIH subunit TFB1 × 1 （P32776） General transcription and DNA repair factor IIH subunit TFB2 × 1 （Q02939） RNA polymerase II transcription factor B subunit 3 × 1 （Q03290） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH subunit SSL1 × 1 （Q04673） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） DNA-directed RNA polymerase II subunit RPB1 × 1 （P04050） DNA-directed RNA polymerase II subunit RPB2 × 1 （P08518） DNA-directed RNA polymerase II subunit RPB4 × 1 （P20433） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （P20435） DNA-directed RNA polymerase II subunit RPB7 × 1 （P34087） Non-template DNA × 1 Template DNA × 1 Transcription initiation factor IIE subunit alpha × 1 （P36100） Transcription initiation factor IIE subunit beta × 1 （P36145） 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

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 7O4K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5OQJ STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH Deposited 2017-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 4 1–88（88 aa）
Chain 4 115–256（142 aa）
Chain 4 274–338（65 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 44 PDB declaration: 46-meric
Chain 4 1–88（88 aa）
Chain 4 120–256（137 aa）
Chain 4 274–338（65 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
6GYM Structure of a yeast closed complex with distorted DNA (CCdist) Deposited 2018-06-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 4 1–88（88 aa）
Chain 4 115–338（224 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
7K01 Structure of TFIIH in TFIIH/Rad4-Rad23-Rad33 DNA opening complex Deposited 2020-09-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain 4 1–338（338 aa）
Not recorded ZN ZINC ION × 5 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；Sample dialyzed for 30 minutes into above buffer prior to grid making
cryo-EM vitrification conditions Cryogen ETHANE；Grids were manually blotted for 2-3 seconds prior to plunge freezing
Resolution 3.90 Å
7K04 Structure of TFIIH/Rad4-Rad23-Rad33/DNA in DNA opening Deposited 2020-09-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain 4 1–338（338 aa）
Not recorded CA CALCIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Manually blotted by Leica EM CPC
Resolution 9.25 Å
7M2U Nucleotide Excision Repair complex TFIIH Rad4-33 Deposited 2021-03-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain 4 1–338（338 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 5 CA CALCIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.20 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 4 1–338（338 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 4 1–338（338 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
7O4L Yeast TFIIH in the expanded state within the pre-initiation complex Deposited 2021-04-06 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain 4 1–338（338 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 4 1–338（338 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 4 1–338（338 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 4 1–338（338 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
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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain 4 1–338（338 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain 4 1–338（338 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain 4 1–338（338 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
8UOQ Composite map of PIC_delta_TFIIK form2 Deposited 2023-10-20 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 4 1–338（338 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 4 1–338（338 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

17 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TFB4_YEAST
Isoform —
PDB entities 5
Chains and sequence ranges Author chain 4； PDBConstruct 4–341； UniProt 1–338

General transcription and DNA repair factor IIH subunit TFB5

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q3E7C1

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 15 DNA 2 PDB declaration: heptadecameric（17） Consistent with all polymer counts Chain 5； UniProt 1–72 Not recorded General transcription and DNA repair factor IIH helicase subunit XPD × 1 （P06839） General transcription and DNA repair factor IIH subunit TFB1 × 1 （P32776） General transcription and DNA repair factor IIH subunit TFB2 × 1 （Q02939） RNA polymerase II transcription factor B subunit 3 × 1 （Q03290） General transcription and DNA repair factor IIH subunit TFB4 × 1 （Q12004） General transcription and DNA repair factor IIH subunit SSL1 × 1 （Q04673） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） DNA-directed RNA polymerase II subunit RPB1 × 1 （P04050） DNA-directed RNA polymerase II subunit RPB2 × 1 （P08518） DNA-directed RNA polymerase II subunit RPB4 × 1 （P20433） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （P20435） DNA-directed RNA polymerase II subunit RPB7 × 1 （P34087） Non-template DNA × 1 Template DNA × 1 Transcription initiation factor IIE subunit alpha × 1 （P36100） Transcription initiation factor IIE subunit beta × 1 （P36145） 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

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 7O4K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3DGP Crystal Structure of the complex between Tfb5 and the C-terminal domain of Tfb2 Deposited 2008-06-14 Different construct 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 2–72（71 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8.9；277 K；Tris 20 mM, NaCl 50 mM, pH 8.9, EVAPORATION, temperature 277K
Resolution 1.80 Å R-free 0.237
3DOM Crystal Structure of the complex between Tfb5 and the C-terminal domain of Tfb2 Deposited 2008-07-04 Different construct 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 2–72（71 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PEG3350 MME, NaCl, Hepes, pH 7.5, vapor diffusion, sitting drop, temperature 293K
Resolution 2.60 Å R-free 0.261
3DOM Crystal Structure of the complex between Tfb5 and the C-terminal domain of Tfb2 Deposited 2008-07-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2–72（71 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PEG3350 MME, NaCl, Hepes, pH 7.5, vapor diffusion, sitting drop, temperature 293K
Resolution 2.60 Å R-free 0.261
5FMF the P-lobe of RNA polymerase II pre-initiation complex Deposited 2015-11-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain X 2–64（63 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
5OQJ STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH Deposited 2017-08-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 5 1–72（72 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 conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 44 PDB declaration: 46-meric
Chain 5 1–72（72 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
5SVA Mediator-RNA Polymerase II Pre-Initiation Complex Deposited 2016-08-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric
Chain b 1–72（72 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
6GYM Structure of a yeast closed complex with distorted DNA (CCdist) Deposited 2018-06-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 5 1–72（72 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
7K01 Structure of TFIIH in TFIIH/Rad4-Rad23-Rad33 DNA opening complex Deposited 2020-09-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain 5 1–72（72 aa）
Not recorded ZN ZINC ION × 5 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；Sample dialyzed for 30 minutes into above buffer prior to grid making
cryo-EM vitrification conditions Cryogen ETHANE；Grids were manually blotted for 2-3 seconds prior to plunge freezing
Resolution 3.90 Å
7K04 Structure of TFIIH/Rad4-Rad23-Rad33/DNA in DNA opening Deposited 2020-09-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain 5 1–72（72 aa）
Not recorded CA CALCIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Manually blotted by Leica EM CPC
Resolution 9.25 Å
7M2U Nucleotide Excision Repair complex TFIIH Rad4-33 Deposited 2021-03-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain 5 2–67（66 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 5 CA CALCIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.20 Å
7ML0 RNA polymerase II pre-initiation complex (PIC1) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain 5 1–72（72 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ML1 RNA polymerase II pre-initiation complex (PIC2) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 5 1–72（72 aa）
Not recorded ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7ML2 RNA polymerase II pre-initiation complex (PIC3) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 5 1–72（72 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7ML3 General transcription factor TFIIH (weak binding) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain 5 1–72（72 aa）
Not recorded ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
7ML4 RNA polymerase II initially transcribing complex (ITC) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 28 PDB declaration: 31-meric
Chain 5 1–72（72 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 5 1–72（72 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 5 1–72（72 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
7O4L Yeast TFIIH in the expanded state within the pre-initiation complex Deposited 2021-04-06 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain 5 1–72（72 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 5 1–72（72 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 5 1–72（72 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 5 1–72（72 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
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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain 5 1–72（72 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain 5 1–72（72 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain 5 1–72（72 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
8UMH Consensus map of PICdeltaTFIIK form2 Deposited 2023-10-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 5 1–72（72 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 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 4.10 Å
8UMI consensus map of PICdeltaTFIIK form1 Deposited 2023-10-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 5 1–72（72 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
8UOQ Composite map of PIC_delta_TFIIK form2 Deposited 2023-10-20 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 5 1–72（72 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 5 1–72（72 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

28 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TFB5_YEAST
Isoform —
PDB entities 6
Chains and sequence ranges Author chain 5； PDBConstruct 5–76； UniProt 1–72

General transcription and DNA repair factor IIH subunit SSL1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q04673

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 15 DNA 2 PDB declaration: heptadecameric（17） Consistent with all polymer counts Chain 6； UniProt 1–461 Not recorded General transcription and DNA repair factor IIH helicase subunit XPD × 1 （P06839） General transcription and DNA repair factor IIH subunit TFB1 × 1 （P32776） General transcription and DNA repair factor IIH subunit TFB2 × 1 （Q02939） RNA polymerase II transcription factor B subunit 3 × 1 （Q03290） General transcription and DNA repair factor IIH subunit TFB4 × 1 （Q12004） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） DNA-directed RNA polymerase II subunit RPB1 × 1 （P04050） DNA-directed RNA polymerase II subunit RPB2 × 1 （P08518） DNA-directed RNA polymerase II subunit RPB4 × 1 （P20433） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （P20435） DNA-directed RNA polymerase II subunit RPB7 × 1 （P34087） Non-template DNA × 1 Template DNA × 1 Transcription initiation factor IIE subunit alpha × 1 （P36100） Transcription initiation factor IIE subunit beta × 1 （P36145） 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

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 7O4K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4WFQ Crystal structure of TFIIH subunit Deposited 2014-09-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 119–310（192 aa）
Not recorded SO4 SULFATE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；PEG
Resolution 2.40 Å R-free 0.214
5OQJ STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH Deposited 2017-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 6 1–307（307 aa）
Chain 6 325–372（48 aa）
Chain 6 387–411（25 aa）
Chain 6 425–461（37 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 44 PDB declaration: 46-meric
Chain 6 1–307（307 aa）
Chain 6 325–372（48 aa）
Chain 6 387–411（25 aa）
Chain 6 425–461（37 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
6GYM Structure of a yeast closed complex with distorted DNA (CCdist) Deposited 2018-06-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 6 1–307（307 aa）
Chain 6 325–372（48 aa）
Chain 6 387–411（25 aa）
Chain 6 425–461（37 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
7K01 Structure of TFIIH in TFIIH/Rad4-Rad23-Rad33 DNA opening complex Deposited 2020-09-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain 6 1–461（461 aa）
Not recorded ZN ZINC ION × 5 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；Sample dialyzed for 30 minutes into above buffer prior to grid making
cryo-EM vitrification conditions Cryogen ETHANE；Grids were manually blotted for 2-3 seconds prior to plunge freezing
Resolution 3.90 Å
7K04 Structure of TFIIH/Rad4-Rad23-Rad33/DNA in DNA opening Deposited 2020-09-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain 6 1–461（461 aa）
Not recorded CA CALCIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Manually blotted by Leica EM CPC
Resolution 9.25 Å
7M2U Nucleotide Excision Repair complex TFIIH Rad4-33 Deposited 2021-03-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain 6 1–461（461 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 5 CA CALCIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.20 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 6 1–461（461 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 6 1–461（461 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
7O4L Yeast TFIIH in the expanded state within the pre-initiation complex Deposited 2021-04-06 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain 6 1–461（461 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 6 1–461（461 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 6 1–461（461 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 6 1–461（461 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
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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain 6 1–461（461 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain 6 1–461（461 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain 6 1–461（461 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
8UOQ Composite map of PIC_delta_TFIIK form2 Deposited 2023-10-20 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 6 1–461（461 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 6 1–461（461 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

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

View Construct and Data Evidence
UniProt name SSL1_YEAST
Isoform —
PDB entities 7
Chains and sequence ranges Author chain 6； PDBConstruct 4–464； UniProt 1–461

General transcription and DNA repair factor IIH helicase subunit XPB

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q00578

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 15 DNA 2 PDB declaration: heptadecameric（17） Consistent with all polymer counts Chain 7； UniProt 1–843 Not recorded General transcription and DNA repair factor IIH helicase subunit XPD × 1 （P06839） General transcription and DNA repair factor IIH subunit TFB1 × 1 （P32776） General transcription and DNA repair factor IIH subunit TFB2 × 1 （Q02939） RNA polymerase II transcription factor B subunit 3 × 1 （Q03290） General transcription and DNA repair factor IIH subunit TFB4 × 1 （Q12004） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH subunit SSL1 × 1 （Q04673） DNA-directed RNA polymerase II subunit RPB1 × 1 （P04050） DNA-directed RNA polymerase II subunit RPB2 × 1 （P08518） DNA-directed RNA polymerase II subunit RPB4 × 1 （P20433） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （P20435） DNA-directed RNA polymerase II subunit RPB7 × 1 （P34087） Non-template DNA × 1 Template DNA × 1 Transcription initiation factor IIE subunit alpha × 1 （P36100） Transcription initiation factor IIE subunit beta × 1 （P36145） 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

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 7O4K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5FMF the P-lobe of RNA polymerase II pre-initiation complex Deposited 2015-11-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain 1 294–785（492 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
5OQJ STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH Deposited 2017-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 7 1–425（425 aa）
Chain 7 452–462（11 aa）
Chain 7 482–843（362 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 44 PDB declaration: 46-meric
Chain 7 1–425（425 aa）
Chain 7 482–843（362 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
5SVA Mediator-RNA Polymerase II Pre-Initiation Complex Deposited 2016-08-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric
Chain Z 1–843（843 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
6GYM Structure of a yeast closed complex with distorted DNA (CCdist) Deposited 2018-06-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 7 1–425（425 aa）
Chain 7 482–843（362 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
7K01 Structure of TFIIH in TFIIH/Rad4-Rad23-Rad33 DNA opening complex Deposited 2020-09-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain 7 1–843（843 aa）
Not recorded ZN ZINC ION × 5 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；Sample dialyzed for 30 minutes into above buffer prior to grid making
cryo-EM vitrification conditions Cryogen ETHANE；Grids were manually blotted for 2-3 seconds prior to plunge freezing
Resolution 3.90 Å
7K04 Structure of TFIIH/Rad4-Rad23-Rad33/DNA in DNA opening Deposited 2020-09-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain 7 1–843（843 aa）
Not recorded CA CALCIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Manually blotted by Leica EM CPC
Resolution 9.25 Å
7M2U Nucleotide Excision Repair complex TFIIH Rad4-33 Deposited 2021-03-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain 7 1–843（843 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 5 CA CALCIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.20 Å
7ML0 RNA polymerase II pre-initiation complex (PIC1) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain 7 1–843（843 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ML1 RNA polymerase II pre-initiation complex (PIC2) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 7 1–843（843 aa）
Not recorded ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7ML2 RNA polymerase II pre-initiation complex (PIC3) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 7 1–843（843 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7ML3 General transcription factor TFIIH (weak binding) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain 7 1–843（843 aa）
Not recorded ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
7ML4 RNA polymerase II initially transcribing complex (ITC) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 28 PDB declaration: 31-meric
Chain 7 1–843（843 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 7 1–843（843 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 7 1–843（843 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
7O4L Yeast TFIIH in the expanded state within the pre-initiation complex Deposited 2021-04-06 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain 7 1–843（843 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 7 1–843（843 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 7 1–843（843 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 7 1–843（843 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
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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain 7 1–843（843 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain 7 1–843（843 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain 7 1–843（843 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 44 PDB declaration: 46-meric
Chain 7 1–843（843 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 conditions Assembly 1 Protein–DNA Heteromer；Protein × 52 PDB declaration: 54-meric
Chain 7 1–843（843 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
8UMH Consensus map of PICdeltaTFIIK form2 Deposited 2023-10-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 7 1–843（843 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 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 4.10 Å
8UMI consensus map of PICdeltaTFIIK form1 Deposited 2023-10-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 7 1–843（843 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
8UOQ Composite map of PIC_delta_TFIIK form2 Deposited 2023-10-20 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 7 1–843（843 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 7 1–843（843 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

28 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RAD25_YEAST
Isoform —
PDB entities 8
Chains and sequence ranges Author chain 7； PDBConstruct 1–843； UniProt 1–843

DNA-directed RNA polymerase II subunit RPB1

OrganismNot specified

UniProt P04050

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 15 DNA 2 PDB declaration: heptadecameric（17） Consistent with all polymer counts Chain A； UniProt 1–1733 Not recorded General transcription and DNA repair factor IIH helicase subunit XPD × 1 （P06839） General transcription and DNA repair factor IIH subunit TFB1 × 1 （P32776） General transcription and DNA repair factor IIH subunit TFB2 × 1 （Q02939） RNA polymerase II transcription factor B subunit 3 × 1 （Q03290） General transcription and DNA repair factor IIH subunit TFB4 × 1 （Q12004） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH subunit SSL1 × 1 （Q04673） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） DNA-directed RNA polymerase II subunit RPB2 × 1 （P08518） DNA-directed RNA polymerase II subunit RPB4 × 1 （P20433） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （P20435） DNA-directed RNA polymerase II subunit RPB7 × 1 （P34087） Non-template DNA × 1 Template DNA × 1 Transcription initiation factor IIE subunit alpha × 1 （P36100） Transcription initiation factor IIE subunit beta × 1 （P36145） 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

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 7O4K 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 ligand/ion Different experimental method 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 method 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 method 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 oligomeric state Different ligand/ion Different experimental method 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 method 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 method 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 method 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 method 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 method 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 oligomeric state Different ligand/ion Different experimental method 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 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 × 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 oligomeric state Different ligand/ion Different experimental method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 1–1733（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 method 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 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 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 method 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 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 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 ligand/ion Different experimental method 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 method 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 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 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 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 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 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 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 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 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 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 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 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 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 ligand/ion Different experimental method 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 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 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 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 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 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 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 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 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 method 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 method 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 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 × 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 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 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion 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 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 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 × 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 method 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 1–1733（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 ligand/ion 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） 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 ligand/ion 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） 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 method 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 ligand/ion 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） 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 method 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 ligand/ion 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） 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 ligand/ion 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） 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 oligomeric state Different ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 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 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 method 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 method 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 method 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 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 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 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 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 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 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 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 × 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 method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 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 oligomeric state Different ligand/ion Different experimental method 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 3.24 Å R-free 0.227
3S17 RNA Polymerase II Initiation Complex with a 9-nt RNA Deposited 2011-05-14 Different oligomeric state Different ligand/ion Different experimental method 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
3S1M RNA Polymerase II Initiation Complex with a 5-nt RNA (variant 1) Deposited 2011-05-15 Different oligomeric state Different ligand/ion Different experimental method 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 3.13 Å R-free 0.233
3S1N RNA Polymerase II Initiation Complex with a 5-nt RNA (variant 2) Deposited 2011-05-15 Different oligomeric state Different ligand/ion Different experimental method 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 3.10 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain A 1–1732（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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain A 1–1732（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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain A 1–1732（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 method 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 method 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain A 1–1732（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 ligand/ion Different experimental method 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 method 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain A 1–1732（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 method 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 method 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain A 1–1732（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 method 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 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 × 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 ligand/ion 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 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 ligand/ion Different experimental method 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 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 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 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 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 method 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 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 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 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 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 ligand/ion 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 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 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 × 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 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 × 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 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 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 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 × 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 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 × 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 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 × 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 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 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 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 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 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 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 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 ligand/ion 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 1–1733（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 method 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 method 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 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 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 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 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 ligand/ion 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 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 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 × 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 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 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 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 ligand/ion 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 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 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 ligand/ion 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 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 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 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 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 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 ligand/ion 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 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 ligand/ion 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 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 ligand/ion 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 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 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 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 ligand/ion 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 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 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 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 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 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 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 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 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 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
7O4L Yeast TFIIH in the expanded state within the pre-initiation complex Deposited 2021-04-06 Different ligand/ion 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 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 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 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 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 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 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 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 ligand/ion 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 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 ligand/ion 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 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 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 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 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 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 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 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 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 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 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 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 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 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 conditions 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 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 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 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion Different experimental conditions 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 ligand/ion 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 ligand/ion 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 method 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 method 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 ligand/ion Different experimental method 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 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 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 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 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 method 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 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 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 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 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 method 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 method 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 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 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 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 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 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 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 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 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 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 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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 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 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 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 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 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 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 ligand/ion 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 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 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 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 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 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 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 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 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 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 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 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 9
Chains and sequence ranges Author chain A； PDBConstruct 1–1733； UniProt 1–1733

DNA-directed RNA polymerase II subunit RPB2

OrganismNot specified

UniProt P08518

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 15 DNA 2 PDB declaration: heptadecameric（17） Consistent with all polymer counts Chain B； UniProt 1–1224 Not recorded General transcription and DNA repair factor IIH helicase subunit XPD × 1 （P06839） General transcription and DNA repair factor IIH subunit TFB1 × 1 （P32776） General transcription and DNA repair factor IIH subunit TFB2 × 1 （Q02939） RNA polymerase II transcription factor B subunit 3 × 1 （Q03290） General transcription and DNA repair factor IIH subunit TFB4 × 1 （Q12004） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH subunit SSL1 × 1 （Q04673） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） DNA-directed RNA polymerase II subunit RPB1 × 1 （P04050） DNA-directed RNA polymerase II subunit RPB4 × 1 （P20433） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （P20435） DNA-directed RNA polymerase II subunit RPB7 × 1 （P34087） Non-template DNA × 1 Template DNA × 1 Transcription initiation factor IIE subunit alpha × 1 （P36100） Transcription initiation factor IIE subunit beta × 1 （P36145） 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

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 7O4K 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain B 1–1224（1224 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain B 1–1224（1224 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 40 PDB declaration: 40-meric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain B 1–1224（1224 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain B 1–1224（1224 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain B 1–1224（1224 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: tridecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain B 1–1224（1224 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain B 1–1224（1224 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain B 1–1224（1224 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain N 1–1224（1224 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain B 1–1224（1224 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
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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain B 1–1224（1224 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 1–1224（1224 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: tridecameric
Chain B 1–1224（1224 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain B 1–1224（1224 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 1–1224（1224 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 aa） Fragment：DNA-directed RNA polymerase II 140 kDa polypeptide
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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 aa） Fragment：DNA-directed RNA polymerase II 140 kDa polypeptide
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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 aa） Fragment：DNA-directed RNA polymerase II 140 kDa polypeptide
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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 aa） Fragment：DNA-directed RNA polymerase II 140 kDa polypeptide
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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 11 PDB declaration: tetradecameric
Chain B 1–1224（1224 aa） Fragment：DNA-directed RNA polymerase II 140 kDa polypeptide
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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 aa） Fragment：DNA-directed RNA polymerase II 140 kDa polypeptide
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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 aa） Fragment：DNA-directed RNA polymerase II 140 kDa polypeptide
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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–1224（1224 aa） Fragment：DNA-directed RNA polymerase II 140 kDa polypeptide
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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain C 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain N 1–1224（1224 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain B 1–1224（1224 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain B 1–1224（1224 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain B 1–1224（1224 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain B 1–1224（1224 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain B 1–1224（1224 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain B 1–1224（1224 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain B 1–1224（1224 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 1–1224（1224 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–1224（1224 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–1224（1224 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–1224（1224 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–1224（1224 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–1224（1224 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–1224（1224 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
3S1M RNA Polymerase II Initiation Complex with a 5-nt RNA (variant 1) Deposited 2011-05-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–1224（1224 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 3.13 Å R-free 0.233
3S1N RNA Polymerase II Initiation Complex with a 5-nt RNA (variant 2) Deposited 2011-05-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–1224（1224 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–1224（1224 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–1224（1224 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–1224（1224 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–1224（1224 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 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 B 1–1224（1224 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 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 B 1–1224（1224 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 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 B 1–1224（1224 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 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 B 1–1224（1224 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 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 B 1–1224（1224 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 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 B 1–1224（1224 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 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 1–1224（1224 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 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 B 1–1224（1224 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 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 B 1–1224（1224 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 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 B 1–1224（1224 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 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 B 1–1224（1224 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 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 B 1–1224（1224 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 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain B 1–1224（1224 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain B 1–1224（1224 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain B 1–1224（1224 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
4V1M Architecture of the RNA polymerase II-Mediator core transcription initiation complex Deposited 2014-09-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: nonadecameric
Chain B 1–1224（1224 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 conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain B 1–1224（1224 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–1224（1224 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–1224（1224 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain B 1–1224（1224 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain B 1–1224（1224 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain B 1–1224（1224 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain B 1–1224（1224 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain B 2–1224（1223 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain B 2–1224（1223 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain B 1–1224（1224 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 conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 44 PDB declaration: 46-meric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain B 1–1224（1224 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric
Chain B 1–1224（1224 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 1–1224（1224 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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain B 1–1224（1224 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain B 1–1224（1224 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–1224（1224 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–1224（1224 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–1224（1224 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–1224（1224 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–1224（1224 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain B 1–1224（1224 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain B 1–1224（1224 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain B 1–1224（1224 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain B 1–1224（1224 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain B 1–1224（1224 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 conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 24 PDB declaration: 27-meric
Chain B 1–1224（1224 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain B 1–1224（1224 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain B 1–1224（1224 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
7O4L Yeast TFIIH in the expanded state within the pre-initiation complex Deposited 2021-04-06 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain B 1–1224（1224 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain B 1–1224（1224 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain B 1–1224（1224 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain B 1–1224（1224 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 oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain B 1–1224（1224 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 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 78 PDB declaration: 80-meric
Chain AB 1–1224（1224 aa）
Chain BB 1–1224（1224 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain B 1–1224（1224 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain B 1–1224（1224 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain B 1–1224（1224 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 44 PDB declaration: 46-meric
Chain B 1–1224（1224 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 conditions Assembly 1 Protein–DNA Heteromer；Protein × 52 PDB declaration: 54-meric
Chain B 1–1224（1224 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 conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: 18-meric
Chain B 1–1224（1224 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 conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: 18-meric
Chain B 1–1224（1224 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 conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: 19-meric
Chain B 1–1224（1224 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 conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: 19-meric
Chain B 1–1224（1224 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
8UKQ RNA polymerase II elongation complex with Fapy-dG lesion in apo state Deposited 2023-10-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: 13-meric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: 13-meric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain B 1–1224（1224 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain B 1–1224（1224 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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 11 PDB declaration: tetradecameric
Chain B 1–1224（1224 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain B 1–1224（1224 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain B 1–1224（1224 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain B 1–1224（1224 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain B 1–1224（1224 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain B 1–1224（1224 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain B 1–1224（1224 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: octadecameric
Chain B 1–1224（1224 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 1–1224（1224 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 conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain B 1–1224（1224 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 conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain B 1–1224（1224 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

195 other PDB entries and 202 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPB2_YEAST
Isoform —
PDB entities 10
Chains and sequence ranges Author chain B； PDBConstruct 1–1224； UniProt 1–1224

DNA-directed RNA polymerase II subunit RPB4

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P20433

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 15 DNA 2 PDB declaration: heptadecameric（17） Consistent with all polymer counts Chain D； UniProt 1–221 Not recorded General transcription and DNA repair factor IIH helicase subunit XPD × 1 （P06839） General transcription and DNA repair factor IIH subunit TFB1 × 1 （P32776） General transcription and DNA repair factor IIH subunit TFB2 × 1 （Q02939） RNA polymerase II transcription factor B subunit 3 × 1 （Q03290） General transcription and DNA repair factor IIH subunit TFB4 × 1 （Q12004） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH subunit SSL1 × 1 （Q04673） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） DNA-directed RNA polymerase II subunit RPB1 × 1 （P04050） DNA-directed RNA polymerase II subunit RPB2 × 1 （P08518） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （P20435） DNA-directed RNA polymerase II subunit RPB7 × 1 （P34087） Non-template DNA × 1 Template DNA × 1 Transcription initiation factor IIE subunit alpha × 1 （P36100） Transcription initiation factor IIE subunit beta × 1 （P36145） 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

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 7O4K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1NT9 Complete 12-subunit RNA polymerase II Deposited 2003-01-29 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 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 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
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 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 × 4 PDB declaration: tetrameric
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 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
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 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
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 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
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 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 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 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: pentadecameric
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 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 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 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: tridecameric
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 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 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 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 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 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 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 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 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 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
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 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 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 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 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 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: tetradecameric
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 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: tridecameric
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 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
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 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 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 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 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 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 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 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
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 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
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 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 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 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
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 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric
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 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 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 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 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 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 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 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 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 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 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 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 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 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
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 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 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 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 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 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 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 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 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 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 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 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
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 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
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 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
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 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
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 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
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 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: nonadecameric
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
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 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 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 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 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 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 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 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 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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
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 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
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 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 44 PDB declaration: 46-meric
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 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 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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric
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 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 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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
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 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 24 PDB declaration: 27-meric
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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
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
7O4L Yeast TFIIH in the expanded state within the pre-initiation complex Deposited 2021-04-06 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
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 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 78 PDB declaration: 80-meric
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 44 PDB declaration: 46-meric
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 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–DNA Heteromer；Protein × 52 PDB declaration: 54-meric
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: 18-meric
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: 18-meric
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: 19-meric
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: 19-meric
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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 11 PDB declaration: tetradecameric
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: octadecameric
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
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

103 other PDB entries and 107 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPB4_YEAST
Isoform —
PDB entities 11
Chains and sequence ranges Author chain D； PDBConstruct 1–221； UniProt 1–221

DNA-directed RNA polymerases I, II, and III subunit RPABC2

OrganismNot specified

UniProt P20435

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 15 DNA 2 PDB declaration: heptadecameric（17） Consistent with all polymer counts Chain F； UniProt 1–155 Not recorded General transcription and DNA repair factor IIH helicase subunit XPD × 1 （P06839） General transcription and DNA repair factor IIH subunit TFB1 × 1 （P32776） General transcription and DNA repair factor IIH subunit TFB2 × 1 （Q02939） RNA polymerase II transcription factor B subunit 3 × 1 （Q03290） General transcription and DNA repair factor IIH subunit TFB4 × 1 （Q12004） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH subunit SSL1 × 1 （Q04673） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） DNA-directed RNA polymerase II subunit RPB1 × 1 （P04050） DNA-directed RNA polymerase II subunit RPB2 × 1 （P08518） DNA-directed RNA polymerase II subunit RPB4 × 1 （P20433） DNA-directed RNA polymerase II subunit RPB7 × 1 （P34087） Non-template DNA × 1 Template DNA × 1 Transcription initiation factor IIE subunit alpha × 1 （P36100） Transcription initiation factor IIE subunit beta × 1 （P36145） 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

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 7O4K 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain F 1–155（155 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain F 1–155（155 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 40 PDB declaration: 40-meric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain F 1–155（155 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 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 × 12 PDB declaration: dodecameric
Chain F 1–155（155 aa）
Chain G 1–171（171 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain F 1–155（155 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain F 1–155（155 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: tridecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain F 1–155（155 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain F 1–155（155 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain F 1–155（155 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain R 1–155（155 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain F 1–155（155 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
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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain F 1–155（155 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain F 1–155（155 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: tridecameric
Chain F 1–155（155 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain F 1–155（155 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain F 1–155（155 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 aa） Fragment：DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide
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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 aa） Fragment：DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide
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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 aa） Fragment：DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide
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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 aa） Fragment：DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide
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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 11 PDB declaration: tetradecameric
Chain F 1–155（155 aa） Fragment：DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide
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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 aa） Fragment：DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide
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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 aa） Fragment：DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide
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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain F 1–155（155 aa） Fragment：DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide
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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain G 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain R 1–155（155 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain F 1–155（155 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain F 1–155（155 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain F 1–155（155 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain F 1–155（155 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain F 1–155（155 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain F 1–155（155 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain F 1–155（155 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 conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain F 72–155（84 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric
Chain F 1–155（155 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain F 1–155（155 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain F 1–155（155 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain F 1–155（155 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain F 1–155（155 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain F 1–155（155 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain F 1–155（155 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
3S1M RNA Polymerase II Initiation Complex with a 5-nt RNA (variant 1) Deposited 2011-05-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain F 1–155（155 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 3.13 Å R-free 0.233
3S1N RNA Polymerase II Initiation Complex with a 5-nt RNA (variant 2) Deposited 2011-05-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain F 1–155（155 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain F 1–155（155 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain F 1–155（155 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain F 1–155（155 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain F 1–155（155 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 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 F 1–155（155 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 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 F 1–155（155 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 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 F 1–155（155 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 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 F 1–155（155 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 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 F 1–155（155 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 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 F 1–155（155 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 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain F 1–155（155 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 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 F 1–155（155 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 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 F 1–155（155 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 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 F 1–155（155 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 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 F 1–155（155 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 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 F 1–155（155 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 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain F 1–155（155 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain F 1–155（155 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain F 1–155（155 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
4C2M Structure of RNA polymerase I at 2.8 A resolution Deposited 2013-08-19 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 7 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；10% PEG4000, 300MM AMMONIUM ACETATE, 50MM HEPES PH 7.5, 5MM TCEP
Resolution 2.80 Å R-free 0.210
4C2M Structure of RNA polymerase I at 2.8 A resolution Deposited 2013-08-19 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain U 1–155（155 aa）
Not recorded ZN ZINC ION × 7 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；10% PEG4000, 300MM AMMONIUM ACETATE, 50MM HEPES PH 7.5, 5MM TCEP
Resolution 2.80 Å R-free 0.210
4C3H Structure of 14-subunit RNA polymerase I at 3.27 A resolution, crystal form C2-93 Deposited 2013-08-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions 24% ETHYLENGLYCOL, 0.1M MES PH 6.8
Resolution 3.27 Å R-free 0.226
4C3I Structure of 14-subunit RNA polymerase I at 3.0 A resolution, crystal form C2-100 Deposited 2013-08-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain F 1–155（155 aa）
Not recorded SO4 SULFATE ION × 3 ZN ZINC ION × 7 MG MAGNESIUM ION × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 10% MPD, 0.1M TRIS HCL PH 7.4
Resolution 3.00 Å R-free 0.231
4C3J Structure of 14-subunit RNA polymerase I at 3.35 A resolution, crystal form C2-90 Deposited 2013-08-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions 10% MPD, 0.1M TRIS HCL, PH 7.5
Resolution 3.35 Å R-free 0.220
4V1M Architecture of the RNA polymerase II-Mediator core transcription initiation complex Deposited 2014-09-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: nonadecameric
Chain F 1–155（155 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 conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain F 1–155（155 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain F 1–155（155 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain F 1–155（155 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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
4YM7 RNA polymerase I structure with an alternative dimer hinge Deposited 2015-03-06 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain AF 1–155（155 aa）
Not recorded ZN ZINC ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；10% PEG 6000, 3% MPD, 100 mM Hepes, 300 mM di-ammonium-tartrate, 3 mM TCEP
Resolution 5.50 Å R-free 0.235
4YM7 RNA polymerase I structure with an alternative dimer hinge Deposited 2015-03-06 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain BF 1–155（155 aa）
Not recorded ZN ZINC ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；10% PEG 6000, 3% MPD, 100 mM Hepes, 300 mM di-ammonium-tartrate, 3 mM TCEP
Resolution 5.50 Å R-free 0.235
4YM7 RNA polymerase I structure with an alternative dimer hinge Deposited 2015-03-06 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain CF 1–155（155 aa）
Not recorded ZN ZINC ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；10% PEG 6000, 3% MPD, 100 mM Hepes, 300 mM di-ammonium-tartrate, 3 mM TCEP
Resolution 5.50 Å R-free 0.235
4YM7 RNA polymerase I structure with an alternative dimer hinge Deposited 2015-03-06 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain DF 1–155（155 aa）
Not recorded ZN ZINC ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；10% PEG 6000, 3% MPD, 100 mM Hepes, 300 mM di-ammonium-tartrate, 3 mM TCEP
Resolution 5.50 Å R-free 0.235
4YM7 RNA polymerase I structure with an alternative dimer hinge Deposited 2015-03-06 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain EF 1–155（155 aa）
Not recorded ZN ZINC ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；10% PEG 6000, 3% MPD, 100 mM Hepes, 300 mM di-ammonium-tartrate, 3 mM TCEP
Resolution 5.50 Å R-free 0.235
4YM7 RNA polymerase I structure with an alternative dimer hinge Deposited 2015-03-06 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain FF 1–155（155 aa）
Not recorded ZN ZINC ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；10% PEG 6000, 3% MPD, 100 mM Hepes, 300 mM di-ammonium-tartrate, 3 mM TCEP
Resolution 5.50 Å R-free 0.235
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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain F 1–155（155 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
5FJ8 Cryo-EM structure of yeast RNA polymerase III elongation complex at 3. 9 A Deposited 2015-10-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer 150MM (NH4)2SO4, 15MM TRIS, 10MM DTT, 5MM MGCL2；pH 7.5；150MM (NH4)2SO4, 15MM TRIS, 10MM DTT, 5MM MGCL2
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 95, INSTRUMENT- FEI VITROBOT MARK III, METHOD- 2.5 UL OF SAMPLE WAS APPLIED 15 SECONDS WAIT TIME BLOT FOR 9 SECONDS BEFORE PLUNGING,
Resolution 3.90 Å
5FJ9 Cryo-EM structure of yeast apo RNA polymerase III at 4.6 A Deposited 2015-10-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer 150MM (NH4)2SO4, 15MM TRIS, 10MM DTT；pH 7.5；150MM (NH4)2SO4, 15MM TRIS, 10MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 95, INSTRUMENT- FEI VITROBOT MARK III, METHOD- 2.5 UL OF SAMPLE WAS APPLIED 15 SECONDS WAIT TIME BLOT FOR 9 SECONDS BEFORE PLUNGING,
Resolution 4.60 Å
5FJA Cryo-EM structure of yeast RNA polymerase III at 4.7 A Deposited 2015-10-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer 150MM (NH4)2SO4, 15MM TRIS, 10MM DTT；pH 7.5；150MM (NH4)2SO4, 15MM TRIS, 10MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 95, INSTRUMENT - FEI VITROBOT MARK III, METHOD- 2.5 UL OF SAMPLE WAS APPLIED 15 SECONDS WAIT TIME BLOT FOR 9 SECONDS BEFORE PLUNGING,
Resolution 4.65 Å
5FMF the P-lobe of RNA polymerase II pre-initiation complex Deposited 2015-11-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain F 72–155（84 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain F 1–155（155 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain F 1–155（155 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
5G5L RNA polymerase I-Rrn3 complex at 4.8 A resolution Deposited 2016-05-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer 150MM NACL, 5MM HEPES, 1MM MGCL2, 0.01 MM ZNCL2, 5 MM DTT；pH 7.8；150MM NACL, 5MM HEPES, 1MM MGCL2, 0.01 MM ZNCL2, 5 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；VITROBOT MARK IV, METHOD- 4.5 MICROLITERS OF SAMPLE WAS APPLIED TO GLOW- DISCHARGED QUANTIFOIL R 2- 1 HOLEY CARBON GRIDS, WHICH WERE THEN BLOTTED FOR 8.5S AND PLUNGE- FROZEN IN LIQUID ETHANE.
Resolution 4.80 Å
5IP7 Structure of RNA Polymerase II-Tfg1 peptide complex Deposited 2016-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain F 69–155（87 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain F 69–155（87 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
5LMX Monomeric RNA polymerase I at 4.9 A resolution Deposited 2016-08-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.90 Å
5M3F Yeast RNA polymerase I elongation complex at 3.8A Deposited 2016-10-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE；blot force 13, blotting time 8.5s
Resolution 3.80 Å
5M3M Free monomeric RNA polymerase I at 4.0A resolution Deposited 2016-10-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 7 SO4 SULFATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE；blot force 13, blotting time 8.5s
Resolution 4.00 Å
5M5W RNA Polymerase I open complex Deposited 2016-10-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；2.5 ul of sample 15 seconds wait time Blot for 8 seconds
Resolution 3.80 Å
5M5X RNA Polymerase I elongation complex 1 Deposited 2016-10-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；2.5 ul of sample 15 seconds wait time Blot time for 8 seconds
Resolution 4.00 Å
5M5Y RNA Polymerase I elongation complex 2 Deposited 2016-10-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；2.5 ul of sample 15 seconds wait time Blot for 8 seconds
Resolution 4.00 Å
5M64 RNA Polymerase I elongation complex with A49 tandem winged helix domain Deposited 2016-10-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；2.5 ul of sample 15 seconds wait time Blot for 8 seconds
Resolution 4.60 Å
5N5Y Cryo-EM structure of RNA polymerase I in complex with Rrn3 and Core Factor (Orientation III) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 8 SO4 SULFATE ION × 5 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.70 Å
5N5Z Cryo-EM structure of RNA polymerase I in complex with Rrn3 and Core Factor (Orientation II) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.70 Å
5N60 Cryo-EM structure of RNA polymerase I in complex with Rrn3 and Core Factor (Orientation I) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.70 Å
5N61 RNA polymerase I initially transcribing complex Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
5OA1 RNA polymerase I pre-initiation complex Deposited 2017-06-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 32 PDB declaration: 34-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
5OQJ STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH Deposited 2017-08-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain F 1–155（155 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 conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 44 PDB declaration: 46-meric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain F 1–155（155 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric
Chain F 1–155（155 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain F 1–155（155 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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain F 1–155（155 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain F 1–155（155 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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
5W5Y RNA polymerase I Initial Transcribing Complex Deposited 2017-06-16 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
5W64 RNA Polymerase I Initial Transcribing Complex State 1 Deposited 2017-06-16 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
5W65 RNA polymerase I Initial Transcribing Complex State 2 Deposited 2017-06-16 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
5W66 RNA polymerase I Initial Transcribing Complex State 3 Deposited 2017-06-16 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6BLO Pol II elongation complex with an abasic lesion at i+1 position Deposited 2017-11-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain F 1–155（155 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain F 1–155（155 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain F 1–155（155 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain F 1–155（155 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: dodecameric
Chain F 1–155（155 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
6CNB Yeast RNA polymerase III initial transcribing complex Deposited 2018-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 19 PDB declaration: 21-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6CNC Yeast RNA polymerase III open complex Deposited 2018-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 19 PDB declaration: 21-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6CND Yeast RNA polymerase III natural open complex (nOC) Deposited 2018-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 19 PDB declaration: 21-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
6CNF Yeast RNA polymerase III elongation complex Deposited 2018-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 19 PDB declaration: 21-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6EU0 RNA Polymerase III open pre-initiation complex (OC-PIC) Deposited 2017-10-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6EU1 RNA Polymerase III - open DNA complex (OC-POL3). Deposited 2017-10-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6EU2 Apo RNA Polymerase III - open conformation (oPOL3) Deposited 2017-10-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6EU3 Apo RNA Polymerase III - closed conformation (cPOL3) Deposited 2017-10-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6F40 RNA Polymerase III open complex Deposited 2017-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6F41 RNA Polymerase III initially transcribing complex Deposited 2017-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6F42 RNA Polymerase III closed complex CC1. Deposited 2017-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.50 Å
6F44 RNA Polymerase III closed complex CC2. Deposited 2017-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6GYK Structure of a yeast closed complex (core CC1) Deposited 2018-06-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain F 2–155（154 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain F 1–155（155 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain F 1–155（155 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
6H67 Yeast RNA polymerase I elongation complex stalled by cyclobutane pyrimidine dimer (CPD) Deposited 2018-07-26 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6H68 Yeast RNA polymerase I elongation complex stalled by cyclobutane pyrimidine dimer (CPD) with fully-ordered A49 Deposited 2018-07-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
6HKO Yeast RNA polymerase I elongation complex bound to nucleotide analog GMPCPP Deposited 2018-09-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain F 1–155（155 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 6 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；30 seconds incubation 3 seconds blotting blotting force 3
Resolution 3.42 Å
6HLQ Yeast RNA polymerase I* elongation complex bound to nucleotide analog GMPCPP Deposited 2018-09-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 1 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；30 seconds incubation 3 seconds blotting blotting force 3
Resolution 3.18 Å
6HLR Yeast RNA polymerase I elongation complex bound to nucleotide analog GMPCPP (core focused) Deposited 2018-09-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain F 1–155（155 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 6 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；30 seconds incubation 3 seconds blotting blotting force 3
Resolution 3.18 Å
6HLS Yeast apo RNA polymerase I* Deposited 2018-09-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；30 seconds incubation 3 seconds blotting blotting force 3
Resolution 3.21 Å
6I84 Structure of transcribing RNA polymerase II-nucleosome complex Deposited 2018-11-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain F 1–155（155 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain E 1–155（155 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
6RQH RNA Polymerase I Closed Conformation 1 (CC1) Deposited 2019-05-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain F 1–155（155 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6RQL RNA Polymerase I Closed Conformation 2 (CC2) Deposited 2019-05-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain F 1–155（155 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
6RQT RNA Polymerase I-tWH-Rrn3-DNA Deposited 2019-05-16 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6RRD RNA Polymerase I Pre-initiation complex DNA opening intermediate 1 Deposited 2019-05-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6RUI RNA Polymerase I Pre-initiation complex DNA opening intermediate 2 Deposited 2019-05-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
6RUO RNA Polymerase I Open Complex conformation 1 Deposited 2019-05-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6RWE RNA Polymerase I Open Complex conformation 2 Deposited 2019-06-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6TPS early intermediate RNA Polymerase I Pre-initiation complex - eiPIC Deposited 2019-12-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
6TUT Cryo-EM structure of the RNA Polymerase III-Maf1 complex Deposited 2020-01-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM HEPES, 150 mM (NH4)2SO4, 5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE；Blot time 6, blot force 2
Resolution 3.25 Å
6UPX RNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 1 Deposited 2019-10-18 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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
7MEI Composite structure of EC+EC Deposited 2021-04-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 30-meric
Chain F 1–155（155 aa）
Chain f 1–155（155 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 4 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 3.54 Å
7NKX RNA polymerase II-Spt4/5-nucleosome-Chd1 structure Deposited 2021-02-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain F 1–155（155 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 conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 24 PDB declaration: 27-meric
Chain F 1–155（155 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain F 1–155（155 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain F 1–155（155 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
7O4L Yeast TFIIH in the expanded state within the pre-initiation complex Deposited 2021-04-06 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain F 1–155（155 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain F 1–155（155 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain F 1–155（155 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain F 1–155（155 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 oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain F 1–155（155 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 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 78 PDB declaration: 80-meric
Chain AF 1–155（155 aa）
Chain BF 1–155（155 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
7Z0H Structure of yeast RNA Polymerase III-Ty1 integrase complex at 2.6 A (focus subunit AC40). Deposited 2022-02-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: nonadecameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
7Z1L Structure of yeast RNA Polymerase III Pre-Termination Complex (PTC) Deposited 2022-02-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 1 4QM (3R,5S,7R,8R,9S,10S,12S,13R,14S,17R)-10,13-dimethyl-17-[(2R)-pentan-2-yl]-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthrene-3,7,12-triol × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7Z1M Structure of yeast RNA Polymerase III Elongation Complex (EC) Deposited 2022-02-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 1 4QM (3R,5S,7R,8R,9S,10S,12S,13R,14S,17R)-10,13-dimethyl-17-[(2R)-pentan-2-yl]-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthrene-3,7,12-triol × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7Z1N Structure of yeast RNA Polymerase III Delta C53-C37-C11 Deposited 2022-02-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 5 MG MAGNESIUM ION × 1 1N7 CHAPSO × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7Z1O Structure of yeast RNA Polymerase III PTC + NTPs Deposited 2022-02-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 1 1N7 CHAPSO × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7Z2Z Structure of yeast RNA Polymerase III-DNA-Ty1 integrase complex (Pol III-DNA-IN1) at 3.1 A Deposited 2022-03-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 19 PDB declaration: 22-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 2 4QM (3R,5S,7R,8R,9S,10S,12S,13R,14S,17R)-10,13-dimethyl-17-[(2R)-pentan-2-yl]-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthrene-3,7,12-triol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
7Z30 Structure of yeast RNA Polymerase III-Ty1 integrase complex at 2.9 A (focus subunit C11 terminal Zn-ribbon in the funnel pore). Deposited 2022-03-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: nonadecameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7Z31 Structure of yeast RNA Polymerase III-Ty1 integrase complex at 2.7 A (focus subunit C11, no C11 C-terminal Zn-ribbon in the funnel pore). Deposited 2022-03-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: nonadecameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.76 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain F 1–155（155 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain F 1–155（155 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain F 1–155（155 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
8BWS Structure of yeast RNA Polymerase III elongation complex at 3.3 A Deposited 2022-12-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 4QM (3R,5S,7R,8R,9S,10S,12S,13R,14S,17R)-10,13-dimethyl-17-[(2R)-pentan-2-yl]-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthrene-3,7,12-triol × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 44 PDB declaration: 46-meric
Chain F 1–155（155 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 conditions Assembly 1 Protein–DNA Heteromer；Protein × 52 PDB declaration: 54-meric
Chain F 1–155（155 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 conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: 18-meric
Chain F 1–155（155 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 conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: 18-meric
Chain F 1–155（155 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 conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: 19-meric
Chain F 1–155（155 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 conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: 19-meric
Chain F 1–155（155 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric
Chain F 1–155（155 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric
Chain F 1–155（155 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 11 PDB declaration: 14-meric
Chain F 1–155（155 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
8TVS Cryo-EM structure of backtracked Pol II in complex with Rad26 Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric
Chain F 1–155（155 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
8TVV Cryo-EM structure of backtracked Pol II Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain F 1–155（155 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 ligand/ion Different experimental conditions Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain F 1–155（155 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain F 1–155（155 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: 17-meric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain F 1–155（155 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: 13-meric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: 13-meric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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
8UMH Consensus map of PICdeltaTFIIK form2 Deposited 2023-10-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 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 4.10 Å
8UMI consensus map of PICdeltaTFIIK form1 Deposited 2023-10-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain F 1–155（155 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
8UOQ Composite map of PIC_delta_TFIIK form2 Deposited 2023-10-20 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain F 1–155（155 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain F 1–155（155 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
9G1V Yeast RNA polymerase I elongation complex stalled by an apurinic site Deposited 2024-07-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: 17-meric
Chain F 1–155（155 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen METHANE
Resolution 2.70 Å
9G1X Yeast RNA polymerase I elongation complex stalled by an apurinic site, 11-subunit Deposited 2024-07-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 11 PDB declaration: 14-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen METHANE
Resolution 3.50 Å
9G23 Yeast RNA polymerase I elongation complex stalled by an apurinic site bound to nucleotide analog AMPCPP at A-site Deposited 2024-07-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: 17-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen METHANE
Resolution 3.40 Å
9G24 Yeast RNA polymerase I elongation complex stalled by an apurinic site bound to nucleotide analog AMPCPP at E-site Deposited 2024-07-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 6 APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen METHANE
Resolution 3.50 Å
9G26 Yeast RNA polymerase I elongation complex stalled by an apurinic site, closed state Deposited 2024-07-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: 17-meric
Chain F 1–155（155 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen METHANE
Resolution 3.40 Å
9G27 Yeast RNA polymerase I elongation complex stalled by an apurinic site, pre-translocation state Deposited 2024-07-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen METHANE
Resolution 2.80 Å
9G29 Yeast RNA polymerase I elongation complex stalled by an apurinic site with the C-terminal of A12 in the funnel Deposited 2024-07-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: 17-meric
Chain F 1–155（155 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen METHANE
Resolution 3.30 Å
9G2B Yeast RNA polymerase I elongation complex stalled by an apurinic site, 12-subunit Deposited 2024-07-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen METHANE
Resolution 3.20 Å
9G2C Yeast RNA polymerase I elongation complex stalled by an apurinic site, open state Deposited 2024-07-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen METHANE
Resolution 3.50 Å
9JA1 The RNA polymerase II elongation complex from Saccharomyces cerevisiae Deposited 2024-08-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 11 PDB declaration: tetradecameric
Chain F 1–155（155 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain F 1–155（155 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain F 1–155（155 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain F 1–155（155 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain F 1–155（155 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain F 1–155（155 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain F 1–155（155 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: octadecameric
Chain F 1–155（155 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 1–155（155 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 conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain F 1–155（155 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 conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain F 1–155（155 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

280 other PDB entries and 293 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPAB2_YEAST
Isoform —
PDB entities 12
Chains and sequence ranges Author chain F； PDBConstruct 1–155； UniProt 1–155

DNA-directed RNA polymerase II subunit RPB7

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P34087

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 15 DNA 2 PDB declaration: heptadecameric（17） Consistent with all polymer counts Chain G； UniProt 1–171 Not recorded General transcription and DNA repair factor IIH helicase subunit XPD × 1 （P06839） General transcription and DNA repair factor IIH subunit TFB1 × 1 （P32776） General transcription and DNA repair factor IIH subunit TFB2 × 1 （Q02939） RNA polymerase II transcription factor B subunit 3 × 1 （Q03290） General transcription and DNA repair factor IIH subunit TFB4 × 1 （Q12004） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH subunit SSL1 × 1 （Q04673） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） DNA-directed RNA polymerase II subunit RPB1 × 1 （P04050） DNA-directed RNA polymerase II subunit RPB2 × 1 （P08518） DNA-directed RNA polymerase II subunit RPB4 × 1 （P20433） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （P20435） Non-template DNA × 1 Template DNA × 1 Transcription initiation factor IIE subunit alpha × 1 （P36100） Transcription initiation factor IIE subunit beta × 1 （P36145） 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

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 7O4K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1NT9 Complete 12-subunit RNA polymerase II Deposited 2003-01-29 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 G 1–171（171 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain G 1–171（171 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 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 × 4 PDB declaration: tetrameric
Chain B 1–171（171 aa）
Chain D 1–171（171 aa）
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 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–171（171 aa）
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 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–171（171 aa）
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 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain G 1–171（171 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain G 1–171（171 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain G 1–171（171 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain G 1–171（171 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: tridecameric
Chain G 1–171（171 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain G 1–171（171 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 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 G 1–171（171 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain G 1–171（171 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain G 1–171（171 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain S 1–171（171 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain G 1–171（171 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 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 G 1–171（171 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain G 1–171（171 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: tridecameric
Chain G 1–171（171 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain G 1–171（171 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 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 G 1–171（171 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 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 H 1–171（171 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain G 1–171（171 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 method Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain S 1–171（171 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain G 1–171（171 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain G 1–171（171 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain G 1–171（171 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain G 1–171（171 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain G 1–171（171 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain G 1–171（171 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain G 1–171（171 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain G 1–171（171 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain G 1–171（171 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 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 G 1–171（171 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain G 1–171（171 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric
Chain G 1–171（171 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 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 G 1–171（171 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 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 G 1–171（171 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 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 G 1–171（171 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 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 G 1–171（171 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 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 G 1–171（171 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 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 G 1–171（171 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 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain G 1–171（171 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 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 G 1–171（171 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 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 G 1–171（171 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 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 G 1–171（171 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 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 G 1–171（171 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 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 G 1–171（171 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 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain G 1–171（171 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain G 1–171（171 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain G 1–171（171 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain G 1–171（171 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain G 1–171（171 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain G 1–171（171 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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: nonadecameric
Chain G 1–171（171 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 conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain G 1–171（171 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 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 G 1–171（171 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain G 1–171（171 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain G 1–171（171 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 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 G 1–171（171 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain G 1–171（171 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain G 1–171（171 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain G 1–171（171 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain G 1–171（171 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain G 1–171（171 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain G 1–171（171 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 conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 44 PDB declaration: 46-meric
Chain G 1–171（171 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain G 1–171（171 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric
Chain G 1–171（171 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain G 1–171（171 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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain G 1–171（171 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain G 1–171（171 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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain G 1–171（171 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain G 1–171（171 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain G 1–171（171 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain G 1–171（171 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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain G 1–171（171 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 conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 24 PDB declaration: 27-meric
Chain G 1–171（171 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain G 1–171（171 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain G 1–171（171 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
7O4L Yeast TFIIH in the expanded state within the pre-initiation complex Deposited 2021-04-06 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain G 1–171（171 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain G 1–171（171 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain G 1–171（171 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain G 1–171（171 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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain G 1–171（171 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 oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain G 1–171（171 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 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 78 PDB declaration: 80-meric
Chain AG 1–171（171 aa）
Chain BG 1–171（171 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain G 1–171（171 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain G 1–171（171 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain G 1–171（171 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 44 PDB declaration: 46-meric
Chain G 1–171（171 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 conditions Assembly 1 Protein–DNA Heteromer；Protein × 52 PDB declaration: 54-meric
Chain G 1–171（171 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 conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: 18-meric
Chain G 1–171（171 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 conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: 18-meric
Chain G 1–171（171 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 conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: 19-meric
Chain G 1–171（171 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 conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: 19-meric
Chain G 1–171（171 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 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain G 1–171（171 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain G 1–171（171 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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 11 PDB declaration: tetradecameric
Chain G 1–171（171 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain G 1–171（171 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain G 1–171（171 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain G 1–171（171 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain G 1–171（171 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain G 1–171（171 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain G 1–171（171 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: octadecameric
Chain G 1–171（171 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 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain G 1–171（171 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 conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain G 1–171（171 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

104 other PDB entries and 108 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPB7_YEAST
Isoform —
PDB entities 13
Chains and sequence ranges Author chain G； PDBConstruct 1–171； UniProt 1–171

Transcription initiation factor IIE subunit alpha

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P36100

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 15 DNA 2 PDB declaration: heptadecameric（17） Consistent with all polymer counts Chain W； UniProt 1–482 Not recorded General transcription and DNA repair factor IIH helicase subunit XPD × 1 （P06839） General transcription and DNA repair factor IIH subunit TFB1 × 1 （P32776） General transcription and DNA repair factor IIH subunit TFB2 × 1 （Q02939） RNA polymerase II transcription factor B subunit 3 × 1 （Q03290） General transcription and DNA repair factor IIH subunit TFB4 × 1 （Q12004） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH subunit SSL1 × 1 （Q04673） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） DNA-directed RNA polymerase II subunit RPB1 × 1 （P04050） DNA-directed RNA polymerase II subunit RPB2 × 1 （P08518） DNA-directed RNA polymerase II subunit RPB4 × 1 （P20433） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （P20435） DNA-directed RNA polymerase II subunit RPB7 × 1 （P34087） Non-template DNA × 1 Template DNA × 1 Transcription initiation factor IIE subunit beta × 1 （P36145） 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

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 7O4K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5FMF the P-lobe of RNA polymerase II pre-initiation complex Deposited 2015-11-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain R 1–160（160 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain W 1–482（482 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain W 1–482（482 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
5OQJ STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH Deposited 2017-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain W 1–194（194 aa）
Chain W 410–482（73 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 44 PDB declaration: 46-meric
Chain W 195–482（288 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
5SVA Mediator-RNA Polymerase II Pre-Initiation Complex Deposited 2016-08-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric
Chain h 1–482（482 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
6GYL Structure of a yeast closed complex with distorted DNA (core CCdist) Deposited 2018-06-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain W 1–194（194 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain W 1–194（194 aa）
Chain W 410–482（73 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
7O4I Yeast RNA polymerase II transcription pre-initiation complex with initial transcription bubble Deposited 2021-04-06 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain W 1–482（482 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain W 1–482（482 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
7O4L Yeast TFIIH in the expanded state within the pre-initiation complex Deposited 2021-04-06 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain W 1–482（482 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain W 1–482（482 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain W 1–482（482 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain W 1–482（482 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
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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain W 1–482（482 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain W 1–482（482 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain W 1–482（482 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 44 PDB declaration: 46-meric
Chain W 1–482（482 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 conditions Assembly 1 Protein–DNA Heteromer；Protein × 52 PDB declaration: 54-meric
Chain W 1–482（482 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
8UOQ Composite map of PIC_delta_TFIIK form2 Deposited 2023-10-20 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain W 1–482（482 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain W 1–482（482 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

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

View Construct and Data Evidence
UniProt name T2EA_YEAST
Isoform —
PDB entities 16
Chains and sequence ranges Author chain W； PDBConstruct 1–482； UniProt 1–482

Transcription initiation factor IIE subunit beta

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P36145

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 15 DNA 2 PDB declaration: heptadecameric（17） Consistent with all polymer counts Chain X； UniProt 1–328 Not recorded General transcription and DNA repair factor IIH helicase subunit XPD × 1 （P06839） General transcription and DNA repair factor IIH subunit TFB1 × 1 （P32776） General transcription and DNA repair factor IIH subunit TFB2 × 1 （Q02939） RNA polymerase II transcription factor B subunit 3 × 1 （Q03290） General transcription and DNA repair factor IIH subunit TFB4 × 1 （Q12004） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH subunit SSL1 × 1 （Q04673） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） DNA-directed RNA polymerase II subunit RPB1 × 1 （P04050） DNA-directed RNA polymerase II subunit RPB2 × 1 （P08518） DNA-directed RNA polymerase II subunit RPB4 × 1 （P20433） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （P20435） DNA-directed RNA polymerase II subunit RPB7 × 1 （P34087） Non-template DNA × 1 Template DNA × 1 Transcription initiation factor IIE subunit alpha × 1 （P36100） 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

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 7O4K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5FMF the P-lobe of RNA polymerase II pre-initiation complex Deposited 2015-11-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain S 125–247（123 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain X 1–328（328 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain X 1–328（328 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
5OQJ STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH Deposited 2017-08-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain X 1–328（328 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 conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 44 PDB declaration: 46-meric
Chain X 1–328（328 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
5SVA Mediator-RNA Polymerase II Pre-Initiation Complex Deposited 2016-08-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric
Chain i 1–328（328 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
6GYL Structure of a yeast closed complex with distorted DNA (core CCdist) Deposited 2018-06-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain X 1–328（328 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain X 1–328（328 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
7O4I Yeast RNA polymerase II transcription pre-initiation complex with initial transcription bubble Deposited 2021-04-06 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain X 1–328（328 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain X 1–328（328 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
7O4L Yeast TFIIH in the expanded state within the pre-initiation complex Deposited 2021-04-06 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain X 1–328（328 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain X 1–328（328 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain X 1–328（328 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain X 1–328（328 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
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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain X 1–328（328 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain X 1–328（328 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain X 1–328（328 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 44 PDB declaration: 46-meric
Chain X 1–328（328 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 conditions Assembly 1 Protein–DNA Heteromer；Protein × 52 PDB declaration: 54-meric
Chain X 1–328（328 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
8UOQ Composite map of PIC_delta_TFIIK form2 Deposited 2023-10-20 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain X 1–328（328 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain X 1–328（328 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

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

View Construct and Data Evidence
UniProt name T2EB_YEAST
Isoform —
PDB entities 17
Chains and sequence ranges Author chain X； PDBConstruct 1–328； UniProt 1–328

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 7o4k

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7o4k
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▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id7o4k
Deposition date deposition_date2021-04-06
Structure title titleYeast TFIIH in the contracted state within the pre-initiation complex
Keywords keywordsPre-initiation complex, TRANSCRIPTION; TRANSCRIPTION
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier63.70 Å
Radius of gyration Rg (electron density) rg_electron64.16 Å
Forward intensity I(0) i03351640000.00
Molecular weight molecular_weight489060.0 kDa
Excluded volume excluded_volume613290 ų
Envelope volume envelope_volume990030 ų
Hydration-shell volume shell_volume131310 ų
Envelope diameter envelope_diameter221.8 Å
Shell Rg shell_rg62.87 Å
Envelope Rg envelope_rg62.73 Å
Shape Rg shape_rg64.16 Å
Total Rg total_rg64.12 Å
Total atoms total_atoms34264
Residues n_residues4236
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

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

Maximum dimension Dmax dmax197.5 Å
Rg (real space) rg_real63.90 Å
Rg uncertainty (real space) rg_real_error1.24 Å
I(0) (real space) i0_real3.3500e+09
I(0) uncertainty (real space) i0_real_error6.6820e+07
Rg (reciprocal space) rg_reciprocal63.44 Å
I(0) (reciprocal space) i0_reciprocal3349000000.0000
Solution quality estimate total_estimate0.8388
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary79.0 Å
Skewness Skewness skewness0.478
Kurtosis Kurtosis kurtosis-0.115
Angular range angular_range— – 0.1250 Å−1
Current regularization parameter α current_alpha0.0009
Highest regularization parameter α highest_alpha201600000.0000
Real-space data points n_real_points26
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.905; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.196
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (22)

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id7o4k001
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id7o4k101
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
Domain ID domain_id7o4k301
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology40 — Herpes Virus-1
Homologous superfamily homologous superfamily10 — Zinc/RING finger domain, C3HC4 (zinc finger)
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8. Citations (1)

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9. Files and Curves (10)