7ml0

RNA polymerase II pre-initiation complex (PIC1)

Method: ELECTRON MICROSCOPY D_max: 209.2 Å Quality: EXCELLENT

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

DNA-directed RNA polymerase subunit

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–DNA Heteromer Protein × 26 DNA 2 PDB declaration: 28-meric（28） Consistent with all polymer counts	Chain A； UniProt 1–1733	Not recorded	DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） TATA-box-binding protein × 1 （P13393） template strand DNA × 1 non-template strand DNA × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） DNA-directed RNA polymerase subunit × 1 DNA-directed RNA polymerase II subunit RPB4 × 1 General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） 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

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 7ML0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 A 1–1733（1733 aa） Chain a 1–1733（1733 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
7MK9 Complex structure of trailing EC of EC+EC (trailing EC-focused) Deposited 2021-04-22	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 × 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 3.54 Å
7MKA Structure of EC+EC (leading EC-focused) Deposited 2021-04-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric	Chain a 1–1733（1733 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 2	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
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 A 1–1733（1733 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 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 × 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
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 A 1–1733（1733 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
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 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
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 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；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 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

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A6A5Q1P2_YEASX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1733； UniProt 1–1733

DNA-directed RNA polymerase subunit beta

OrganismNot specified

UniProt A0A6A5Q4H2

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 × 26 DNA 2 PDB declaration: 28-meric（28） Consistent with all polymer counts	Chain B； UniProt 1–1224	Not recorded	DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） TATA-box-binding protein × 1 （P13393） template strand DNA × 1 non-template strand DNA × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） DNA-directed RNA polymerase subunit × 1 DNA-directed RNA polymerase II subunit RPB4 × 1 General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7ML0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 B 1–1224（1224 aa） Chain b 1–1224（1224 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
7MK9 Complex structure of trailing EC of EC+EC (trailing EC-focused) Deposited 2021-04-22	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 × 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 3.54 Å
7MKA Structure of EC+EC (leading EC-focused) Deposited 2021-04-22	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 × 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 3.54 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 B 1–1224（1224 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 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 × 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
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 B 1–1224（1224 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
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 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 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 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 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 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 4.60 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 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
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 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 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 Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-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 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 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 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 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 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 B 1–1224（1224 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 B 1–1224（1224 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
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 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；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 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
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 B 1–1224（1224 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 B 1–1224（1224 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

20 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A6A5Q4H2_YEASX
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–1224； UniProt 1–1224

DNA-directed RNA polymerase II subunit RPB3

OrganismNot specified

UniProt A0A6A5Q0Z3

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 × 26 DNA 2 PDB declaration: 28-meric（28） Consistent with all polymer counts	Chain C； UniProt 1–318	Not recorded	DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） TATA-box-binding protein × 1 （P13393） template strand DNA × 1 non-template strand DNA × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） DNA-directed RNA polymerase subunit × 1 DNA-directed RNA polymerase II subunit RPB4 × 1 General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7ML0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 C 1–318（318 aa） Chain c 1–318（318 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
7MK9 Complex structure of trailing EC of EC+EC (trailing EC-focused) Deposited 2021-04-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric	Chain C 1–318（318 aa）	Not recorded	ZN ZINC ION × 8 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 3.54 Å
7MKA Structure of EC+EC (leading EC-focused) Deposited 2021-04-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric	Chain c 1–318（318 aa）	Not recorded	ZN ZINC ION × 8 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 3.54 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 C 1–318（318 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 structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain C 1–318（318 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
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 C 1–318（318 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
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 C 1–318（318 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 C 1–318（318 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 C 1–318（318 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 C 1–318（318 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 C 1–318（318 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 Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric	Chain C 1–318（318 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 C 1–318（318 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 C 1–318（318 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 C 1–318（318 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 C 1–318（318 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
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 C 1–318（318 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 C 1–318（318 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 C 1–318（318 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 C 1–318（318 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

20 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A6A5Q0Z3_YEASX
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–318； UniProt 1–318

DNA-directed RNA polymerase II subunit RPB4

OrganismNot specified

UniProt A0A6A5PTI6

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 × 26 DNA 2 PDB declaration: 28-meric（28） Consistent with all polymer counts	Chain D； UniProt 1–221	Not recorded	DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） TATA-box-binding protein × 1 （P13393） template strand DNA × 1 non-template strand DNA × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） DNA-directed RNA polymerase subunit × 1 DNA-directed RNA polymerase II subunit RPB4 × 1 General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7ML0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 D 1–221（221 aa） Chain d 1–221（221 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
7MK9 Complex structure of trailing EC of EC+EC (trailing EC-focused) Deposited 2021-04-22	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 × 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 3.54 Å
7MKA Structure of EC+EC (leading EC-focused) Deposited 2021-04-22	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 × 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 3.54 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 D 1–221（221 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 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 × 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
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 D 1–221（221 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
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 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 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 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 3.70 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 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
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 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 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 Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-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 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 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 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 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 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 D 1–221（221 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 D 1–221（221 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
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 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；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 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
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 D 1–221（221 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 D 1–221（221 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

19 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A6A5PTI6_YEASX
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–221； UniProt 1–221

DNA-directed RNA polymerases I, II, and III subunit RPABC1

OrganismNot specified

UniProt A0A6A5Q456

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 × 26 DNA 2 PDB declaration: 28-meric（28） Consistent with all polymer counts	Chain E； UniProt 1–215	Not recorded	DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） TATA-box-binding protein × 1 （P13393） template strand DNA × 1 non-template strand DNA × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） DNA-directed RNA polymerase subunit × 1 DNA-directed RNA polymerase II subunit RPB4 × 1 General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7ML0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 E 1–215（215 aa） Chain e 1–215（215 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
7MK9 Complex structure of trailing EC of EC+EC (trailing EC-focused) Deposited 2021-04-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric	Chain E 1–215（215 aa）	Not recorded	ZN ZINC ION × 8 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 3.54 Å
7MKA Structure of EC+EC (leading EC-focused) Deposited 2021-04-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric	Chain e 1–215（215 aa）	Not recorded	ZN ZINC ION × 8 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 3.54 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 E 1–215（215 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 structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain E 1–215（215 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
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 E 1–215（215 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
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 E 1–215（215 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 E 1–215（215 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 E 1–215（215 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 E 1–215（215 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 E 1–215（215 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 Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric	Chain E 1–215（215 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 E 1–215（215 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 E 1–215（215 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 E 1–215（215 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 E 1–215（215 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
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 E 1–215（215 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 E 1–215（215 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 E 1–215（215 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 E 1–215（215 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

20 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A6A5Q456_YEASX
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–215； UniProt 1–215

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

OrganismNot specified

UniProt A0A6L0ZRI7

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 × 26 DNA 2 PDB declaration: 28-meric（28） Consistent with all polymer counts	Chain F； UniProt 1–155	Not recorded	DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） TATA-box-binding protein × 1 （P13393） template strand DNA × 1 non-template strand DNA × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） DNA-directed RNA polymerase subunit × 1 DNA-directed RNA polymerase II subunit RPB4 × 1 General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7ML0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7MK9 Complex structure of trailing EC of EC+EC (trailing EC-focused) Deposited 2021-04-22	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 × 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 3.54 Å
7MKA Structure of EC+EC (leading EC-focused) Deposited 2021-04-22	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 × 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 3.54 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 F 1–155（155 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 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 × 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
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 F 1–155（155 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

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A6L0ZRI7_YEASX
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain F； PDBConstruct 1–155； UniProt 1–155

DNA-directed RNA polymerase II subunit RPB7

OrganismNot specified

UniProt A0A6A5Q270

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 × 26 DNA 2 PDB declaration: 28-meric（28） Consistent with all polymer counts	Chain G； UniProt 1–171	Not recorded	DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） TATA-box-binding protein × 1 （P13393） template strand DNA × 1 non-template strand DNA × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） DNA-directed RNA polymerase subunit × 1 DNA-directed RNA polymerase II subunit RPB4 × 1 General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7ML0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 G 1–171（171 aa） Chain g 1–171（171 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
7MK9 Complex structure of trailing EC of EC+EC (trailing EC-focused) Deposited 2021-04-22	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 × 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 3.54 Å
7MKA Structure of EC+EC (leading EC-focused) Deposited 2021-04-22	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 × 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 3.54 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 G 1–171（171 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 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 × 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
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 G 1–171（171 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
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 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 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 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 3.70 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 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
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 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 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 Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-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 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 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 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 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 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 G 1–171（171 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 G 1–171（171 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
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 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；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 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
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 G 1–171（171 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 G 1–171（171 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

19 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A6A5Q270_YEASX
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain G； PDBConstruct 1–171； UniProt 1–171

DNA-directed RNA polymerases I, II, and III subunit RPABC3

OrganismNot specified

UniProt A0A6A5Q8C2

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 × 26 DNA 2 PDB declaration: 28-meric（28） Consistent with all polymer counts	Chain H； UniProt 1–146	Not recorded	DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） TATA-box-binding protein × 1 （P13393） template strand DNA × 1 non-template strand DNA × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） DNA-directed RNA polymerase subunit × 1 DNA-directed RNA polymerase II subunit RPB4 × 1 General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7ML0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 H 1–146（146 aa） Chain h 1–146（146 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
7MK9 Complex structure of trailing EC of EC+EC (trailing EC-focused) Deposited 2021-04-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric	Chain H 1–146（146 aa）	Not recorded	ZN ZINC ION × 8 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 3.54 Å
7MKA Structure of EC+EC (leading EC-focused) Deposited 2021-04-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric	Chain h 1–146（146 aa）	Not recorded	ZN ZINC ION × 8 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 3.54 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 H 1–146（146 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 structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain H 1–146（146 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
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 H 1–146（146 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
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 H 1–146（146 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 H 1–146（146 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 H 1–146（146 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 H 1–146（146 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 H 1–146（146 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 Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric	Chain H 1–146（146 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 H 1–146（146 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 H 1–146（146 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 H 1–146（146 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 H 1–146（146 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
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 H 1–146（146 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 H 1–146（146 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 H 1–146（146 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 H 1–146（146 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

20 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A6A5Q8C2_YEASX
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain H； PDBConstruct 1–146； UniProt 1–146

DNA-directed RNA polymerase II subunit RPB9

OrganismNot specified

UniProt A0A7I9EWC2

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 × 26 DNA 2 PDB declaration: 28-meric（28） Consistent with all polymer counts	Chain I； UniProt 1–122	Not recorded	DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） TATA-box-binding protein × 1 （P13393） template strand DNA × 1 non-template strand DNA × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） DNA-directed RNA polymerase subunit × 1 DNA-directed RNA polymerase II subunit RPB4 × 1 General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7ML0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 I 1–122（122 aa） Chain i 1–122（122 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
7MK9 Complex structure of trailing EC of EC+EC (trailing EC-focused) Deposited 2021-04-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric	Chain I 1–122（122 aa）	Not recorded	ZN ZINC ION × 8 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 3.54 Å
7MKA Structure of EC+EC (leading EC-focused) Deposited 2021-04-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric	Chain i 1–122（122 aa）	Not recorded	ZN ZINC ION × 8 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 3.54 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 I 1–122（122 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 structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain I 1–122（122 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
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 I 1–122（122 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
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 I 1–122（122 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 I 1–122（122 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 I 1–122（122 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 I 1–122（122 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 I 1–122（122 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 Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric	Chain I 1–122（122 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 I 1–122（122 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 I 1–122（122 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 I 1–122（122 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 I 1–122（122 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
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 I 1–122（122 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 I 1–122（122 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 I 1–122（122 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 I 1–122（122 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

20 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A7I9EWC2_YEASX
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain I； PDBConstruct 1–122； UniProt 1–122

DNA-directed RNA polymerases II subunit RPABC5

OrganismNot specified

UniProt A0A6A5Q7Q6

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 × 26 DNA 2 PDB declaration: 28-meric（28） Consistent with all polymer counts	Chain J； UniProt 1–70	Not recorded	DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） TATA-box-binding protein × 1 （P13393） template strand DNA × 1 non-template strand DNA × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） DNA-directed RNA polymerase subunit × 1 DNA-directed RNA polymerase II subunit RPB4 × 1 General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7ML0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 J 1–70（70 aa） Chain j 1–70（70 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
7MK9 Complex structure of trailing EC of EC+EC (trailing EC-focused) Deposited 2021-04-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric	Chain J 1–70（70 aa）	Not recorded	ZN ZINC ION × 8 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 3.54 Å
7MKA Structure of EC+EC (leading EC-focused) Deposited 2021-04-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric	Chain j 1–70（70 aa）	Not recorded	ZN ZINC ION × 8 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 3.54 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 J 1–70（70 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 structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain J 1–70（70 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
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 J 1–70（70 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
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 J 1–70（70 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 J 1–70（70 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 J 1–70（70 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 J 1–70（70 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 J 1–70（70 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 Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric	Chain J 1–70（70 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 J 1–70（70 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 J 1–70（70 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 J 1–70（70 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 J 1–70（70 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
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 J 1–70（70 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 J 1–70（70 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 J 1–70（70 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 J 1–70（70 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

20 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A6A5Q7Q6_YEASX
Isoform	—
PDB entities	10
Chains and sequence ranges	Author chain J； PDBConstruct 1–70； UniProt 1–70

DNA-directed RNA polymerase II subunit RPB11

OrganismNot specified

UniProt A0A6A5Q7A1

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 × 26 DNA 2 PDB declaration: 28-meric（28） Consistent with all polymer counts	Chain K； UniProt 1–120	Not recorded	DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） TATA-box-binding protein × 1 （P13393） template strand DNA × 1 non-template strand DNA × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） DNA-directed RNA polymerase subunit × 1 DNA-directed RNA polymerase II subunit RPB4 × 1 General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7ML0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 K 1–120（120 aa） Chain k 1–120（120 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
7MK9 Complex structure of trailing EC of EC+EC (trailing EC-focused) Deposited 2021-04-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric	Chain K 1–120（120 aa）	Not recorded	ZN ZINC ION × 8 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 3.54 Å
7MKA Structure of EC+EC (leading EC-focused) Deposited 2021-04-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric	Chain k 1–120（120 aa）	Not recorded	ZN ZINC ION × 8 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 3.54 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 K 1–120（120 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 structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain K 1–120（120 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
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 K 1–120（120 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
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 K 1–120（120 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 K 1–120（120 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 K 1–120（120 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 K 1–120（120 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 K 1–120（120 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 Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric	Chain K 1–120（120 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 K 1–120（120 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 K 1–120（120 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 K 1–120（120 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 K 1–120（120 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
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 K 1–120（120 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 K 1–120（120 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 K 1–120（120 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 K 1–120（120 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

20 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A6A5Q7A1_YEASX
Isoform	—
PDB entities	11
Chains and sequence ranges	Author chain K； PDBConstruct 1–120； UniProt 1–120

DNA-directed RNA polymerases II subunit RPABC4

OrganismNot specified

UniProt A0A6A5PY05

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 × 26 DNA 2 PDB declaration: 28-meric（28） Consistent with all polymer counts	Chain L； UniProt 1–70	Not recorded	DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） TATA-box-binding protein × 1 （P13393） template strand DNA × 1 non-template strand DNA × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） DNA-directed RNA polymerase subunit × 1 DNA-directed RNA polymerase II subunit RPB4 × 1 General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7ML0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 L 1–70（70 aa） Chain l 1–70（70 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
7MK9 Complex structure of trailing EC of EC+EC (trailing EC-focused) Deposited 2021-04-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric	Chain L 1–70（70 aa）	Not recorded	ZN ZINC ION × 8 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 3.54 Å
7MKA Structure of EC+EC (leading EC-focused) Deposited 2021-04-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric	Chain l 1–70（70 aa）	Not recorded	ZN ZINC ION × 8 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 3.54 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 L 1–70（70 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 structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain L 1–70（70 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
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 L 1–70（70 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
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 L 1–70（70 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 L 1–70（70 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 L 1–70（70 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 L 1–70（70 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 L 1–70（70 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 Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric	Chain L 1–70（70 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 L 1–70（70 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 L 1–70（70 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 L 1–70（70 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 L 1–70（70 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
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 L 1–70（70 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 L 1–70（70 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 L 1–70（70 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 L 1–70（70 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

20 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A6A5PY05_YEASX
Isoform	—
PDB entities	12
Chains and sequence ranges	Author chain L； PDBConstruct 1–70； UniProt 1–70

Transcription initiation factor IIB

OrganismNot specified

UniProt P29055

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 × 26 DNA 2 PDB declaration: 28-meric（28） Consistent with all polymer counts	Chain M； UniProt 1–345	Not recorded	DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） TATA-box-binding protein × 1 （P13393） template strand DNA × 1 non-template strand DNA × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） DNA-directed RNA polymerase subunit × 1 DNA-directed RNA polymerase II subunit RPB4 × 1 General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7ML0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 M 1–345（345 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
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 M 1–345（345 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 M 1–345（345 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
4V1N Architecture of the RNA polymerase II-Mediator core transcription initiation complex Deposited 2014-09-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: nonadecameric	Chain M 1–345（345 aa） Chain Q 1–734（734 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 M 1–345（345 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
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 P 1–345（345 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 M 1–345（345 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 M 1–345（345 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 M 1–345（345 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 M 1–345（345 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 c 1–345（345 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
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 M 1–345（345 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 M 1–345（345 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 M 1–345（345 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
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 M 1–345（345 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 structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain M 1–345（345 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
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 M 1–345（345 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 M 1–345（345 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 M 1–345（345 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
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 M 1–345（345 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 M 1–345（345 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 M 1–345（345 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 M 1–345（345 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 M 1–345（345 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 AM 1–345（345 aa） Chain BM 1–345（345 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 experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric	Chain M 1–345（345 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 experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric	Chain M 1–345（345 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 experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric	Chain M 1–345（345 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 experimental conditions	Assembly 1 Protein–DNA Heteromer；Protein × 44 PDB declaration: 46-meric	Chain M 1–345（345 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 experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 52 PDB declaration: 54-meric	Chain M 1–345（345 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 M 1–345（345 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 M 1–345（345 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 M 1–345（345 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 M 1–345（345 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

34 other PDB entries and 34 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TF2B_YEAST
Isoform	—
PDB entities	13
Chains and sequence ranges	Author chain M； PDBConstruct 1–345； UniProt 1–345

Transcription initiation factor IIF subunit alpha

OrganismNot specified

UniProt P41895

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 × 26 DNA 2 PDB declaration: 28-meric（28） Consistent with all polymer counts	Chain Q； UniProt 1–735	Not recorded	DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） TATA-box-binding protein × 1 （P13393） template strand DNA × 1 non-template strand DNA × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） DNA-directed RNA polymerase subunit × 1 DNA-directed RNA polymerase II subunit RPB4 × 1 General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7ML0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 Q 1–735（735 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 Q 1–735（735 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 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 Q 1–735（735 aa）	Mutation：;Residues indicated as UNK are of uncertain amino acid register and may deviate from the given register by few amino acids. For details about modelling of the subunits refer to the associated publication. Residues indicated as UNK with the chain identifier Z are part of an assembly between the clutch domains of Tfb2 and Ssl2 but could not be assigned to any of the two proteins with confidence since domain swapping/beta-strand exchange may occur. To account for this uncertainty, a theoretical chain Z was introduced for this residue range but not assigned to any of the PIC components. Submission based on experimental data from EMDB EMD-3846. ;	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 Q 1–403（403 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 f 1–735（735 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
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 Q 1–735（735 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 Q 1–735（735 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 Q 1–735（735 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
7MEI Composite structure of EC+EC Deposited 2021-04-06	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 Q 1–735（735 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
7MK9 Complex structure of trailing EC of EC+EC (trailing EC-focused) Deposited 2021-04-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric	Chain Q 1–735（735 aa）	Not recorded	ZN ZINC ION × 8 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 3.54 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 Q 1–735（735 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 structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain Q 1–735（735 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
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 Q 1–735（735 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 Q 1–735（735 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 Q 1–735（735 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
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 Q 1–735（735 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 Q 1–735（735 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 Q 1–735（735 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 P 1–735（735 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 P 1–735（735 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 AP 1–735（735 aa） Chain BP 1–735（735 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 experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric	Chain Q 1–735（735 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 experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric	Chain Q 1–735（735 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 experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric	Chain Q 1–735（735 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 Q 1–735（735 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 Q 1–735（735 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 Q 1–735（735 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 Q 1–735（735 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	T2FA_YEAST
Isoform	—
PDB entities	14
Chains and sequence ranges	Author chain Q； PDBConstruct 1–735； UniProt 1–735

Transcription initiation factor IIF subunit beta

OrganismNot specified

UniProt A0A6A5PZ00

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 × 26 DNA 2 PDB declaration: 28-meric（28） Consistent with all polymer counts	Chain R； UniProt 1–400	Not recorded	DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） TATA-box-binding protein × 1 （P13393） template strand DNA × 1 non-template strand DNA × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） DNA-directed RNA polymerase subunit × 1 DNA-directed RNA polymerase II subunit RPB4 × 1 General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7ML0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7MEI Composite structure of EC+EC Deposited 2021-04-06	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 M 1–400（400 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
7MK9 Complex structure of trailing EC of EC+EC (trailing EC-focused) Deposited 2021-04-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric	Chain M 1–400（400 aa）	Not recorded	ZN ZINC ION × 8 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 3.54 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 R 1–400（400 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 structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain R 1–400（400 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
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 R 1–400（400 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
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 P 1–400（400 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 P 1–400（400 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

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A6A5PZ00_YEASX
Isoform	—
PDB entities	15
Chains and sequence ranges	Author chain R； PDBConstruct 1–400； UniProt 1–400

Transcription initiation factor IIE subunit alpha

OrganismNot specified

UniProt A0A6A5PTU5

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 × 26 DNA 2 PDB declaration: 28-meric（28） Consistent with all polymer counts	Chain W； UniProt 1–482	Not recorded	DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） TATA-box-binding protein × 1 （P13393） template strand DNA × 1 non-template strand DNA × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） DNA-directed RNA polymerase subunit × 1 DNA-directed RNA polymerase II subunit RPB4 × 1 General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7ML0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 W 1–482（482 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 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 × 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
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 W 1–482（482 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
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 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；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 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

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A6A5PTU5_YEASX
Isoform	—
PDB entities	16
Chains and sequence ranges	Author chain W； PDBConstruct 1–482； UniProt 1–482

Transcription initiation factor IIE subunit beta

OrganismNot specified

UniProt A0A6A5PS93

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 × 26 DNA 2 PDB declaration: 28-meric（28） Consistent with all polymer counts	Chain X； UniProt 1–328	Not recorded	DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） TATA-box-binding protein × 1 （P13393） template strand DNA × 1 non-template strand DNA × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） DNA-directed RNA polymerase subunit × 1 DNA-directed RNA polymerase II subunit RPB4 × 1 General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7ML0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 X 1–328（328 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 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 × 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
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 X 1–328（328 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
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 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；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 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

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A6A5PS93_YEASX
Isoform	—
PDB entities	17
Chains and sequence ranges	Author chain X； PDBConstruct 1–328； UniProt 1–328

TATA-box-binding protein

OrganismNot specified

UniProt P13393

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 × 26 DNA 2 PDB declaration: 28-meric（28） Consistent with all polymer counts	Chain O； UniProt 1–240	Not recorded	DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） template strand DNA × 1 non-template strand DNA × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） DNA-directed RNA polymerase subunit × 1 DNA-directed RNA polymerase II subunit RPB4 × 1 General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7ML0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1NGM Crystal structure of a yeast Brf1-TBP-DNA ternary complex Deposited 2002-12-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 60–239（180 aa） Fragment：C-terminal core domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；MES, NaCl, BME, glycerol, MgCl2, PEG2000MME, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.95 Å R-free 0.308
1NGM Crystal structure of a yeast Brf1-TBP-DNA ternary complex Deposited 2002-12-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain E 60–239（180 aa） Fragment：C-terminal core domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；MES, NaCl, BME, glycerol, MgCl2, PEG2000MME, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.95 Å R-free 0.308
1NGM Crystal structure of a yeast Brf1-TBP-DNA ternary complex Deposited 2002-12-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain I 60–239（180 aa） Fragment：C-terminal core domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；MES, NaCl, BME, glycerol, MgCl2, PEG2000MME, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.95 Å R-free 0.308
1NGM Crystal structure of a yeast Brf1-TBP-DNA ternary complex Deposited 2002-12-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain M 60–239（180 aa） Fragment：C-terminal core domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；MES, NaCl, BME, glycerol, MgCl2, PEG2000MME, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.95 Å R-free 0.308
1NH2 Crystal structure of a yeast TFIIA/TBP/DNA complex Deposited 2002-12-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain A 60–239（180 aa） Fragment：C-TERMINAL 180 RESIDUES	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å R-free 0.226
1RM1 Structure of a Yeast TFIIA/TBP/TATA-box DNA Complex Deposited 2003-11-26	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain A 1–239（239 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；PEG 4000, ammonium citrate, MES, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.50 Å R-free 0.252
1TBA SOLUTION STRUCTURE OF A TBP-TAFII230 COMPLEX: PROTEIN MIMICRY OF THE MINOR GROOVE SURFACE OF THE TATA BOX UNWOUND BY TBP, NMR, 25 STRUCTURES Deposited 1998-08-16	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 B 60–239（180 aa） Fragment：CORE DOMAIN RESIDUES 60-249	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K	Resolution not provided
1TBP CRYSTAL STRUCTURE OF YEAST TATA-BINDING PROTEIN AND MODEL FOR INTERACTION WITH DNA Deposited 1993-08-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 61–239（179 aa） Chain B 61–239（179 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å
1YTB CRYSTAL STRUCTURE OF A YEAST TBP/TATA-BOX COMPLEX Deposited 1994-09-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 60–239（180 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 295.00K	Resolution 1.80 Å R-free 0.261
1YTB CRYSTAL STRUCTURE OF A YEAST TBP/TATA-BOX COMPLEX Deposited 1994-09-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 60–239（180 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 295.00K	Resolution 1.80 Å R-free 0.261
1YTF YEAST TFIIA/TBP/DNA COMPLEX Deposited 1996-04-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain A 60–239（180 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.297
4B0A The high-resolution structure of yTBP-yTAF1 identifies conserved and competing interaction surfaces in transcriptional activation Deposited 2012-06-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 61–240（180 aa） Fragment：TAF1 RESIDUES 8-71, LINKER, TBP RESIDUE 61-240	Mutation：YES	CA CALCIUM ION × 3 GOL GLYCEROL × 6 CL CHLORIDE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.97 Å R-free 0.223
4V1N Architecture of the RNA polymerase II-Mediator core transcription initiation complex Deposited 2014-09-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: nonadecameric	Chain O 61–240（180 aa） Fragment：RESIDUES 61-240	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 construct 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 O 61–240（180 aa） Fragment：RESIDUES 61-240	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
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 Q 61–240（180 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 O 1–240（240 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 O 1–240（240 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 O 1–240（240 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 O 1–240（240 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 j 1–240（240 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
6CNB Yeast RNA polymerase III initial transcribing complex Deposited 2018-03-08	Different construct 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 R 61–240（180 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 construct Different mutation/modification 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 R 61–240（180 aa）	Mutation：C438S	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 construct Different mutation/modification 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 R 61–240（180 aa）	Mutation：C438S	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 construct Different mutation/modification 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 R 61–240（180 aa）	Mutation：C438S	ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.50 Å
6E16 Ternary structure of c-Myc-TBP-TAF1 Deposited 2018-07-09	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 61–240（180 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；291 K；20% (w/w) PEG8000, 0.2M ammonium sulfare, and 0.1M HEPES pH7.5	Resolution 2.40 Å R-free 0.220
6E24 Ternary structure of c-Myc-TBP-TAF1 Deposited 2018-07-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 61–240（180 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；16% W/V PEG3350 0.05M CITRIC ACID 0.05M BIS-TRIS PROPANE pH5.0	Resolution 3.00 Å R-free 0.224
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 Y 1–240（240 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
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 U 1–240（240 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 U 1–240（240 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 U 1–240（240 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 U 1–240（240 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric	Chain O 1–240（240 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 O 1–240（240 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 O 1–240（240 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
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 O 1–240（240 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
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 O 1–240（240 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 O 1–240（240 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 O 1–240（240 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
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 O 1–240（240 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 O 1–240（240 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 O 1–240（240 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
7Q5B Cryo-EM structure of Ty3 retrotransposon targeting a TFIIIB-bound tRNA gene Deposited 2021-11-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: tridecameric	Chain Y 1–240（240 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.98 Å
7Z0O Structure of transcription factor UAF in complex with TBP and 35S rRNA promoter DNA Deposited 2022-02-23	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain H 1–240（240 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
7ZS9 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome (complex A) Deposited 2022-05-06	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric	Chain O 1–240（240 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 experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric	Chain O 1–240（240 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 experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric	Chain O 1–240（240 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
8FFZ TFIIIA-TFIIIC-Brf1-TBP complex bound to 5S rRNA gene Deposited 2022-12-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: decameric	Chain H 61–240（180 aa）	Not recorded	ZN ZINC ION × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
8H5B The cryo-EM structure of nuclear transport receptor Kap114p complex with yeast TATA-box binding protein Deposited 2022-10-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 61–240（180 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.03 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 O 1–240（240 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 O 1–240（240 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 O 1–240（240 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 O 1–240（240 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

48 other PDB entries and 52 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TBP_YEAST
Isoform	—
PDB entities	18
Chains and sequence ranges	Author chain O； PDBConstruct 1–240； UniProt 1–240

General transcription and DNA repair factor IIH helicase subunit XPD

OrganismNot specified

UniProt A0A6A5Q1C1

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 × 26 DNA 2 PDB declaration: 28-meric（28） Consistent with all polymer counts	Chain 0； UniProt 1–778	Not recorded	DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） TATA-box-binding protein × 1 （P13393） template strand DNA × 1 non-template strand DNA × 1 DNA-directed RNA polymerase subunit × 1 DNA-directed RNA polymerase II subunit RPB4 × 1 General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7ML0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 0 1–778（778 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 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 × 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 0 1–778（778 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 0 1–778（778 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
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 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；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 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

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A6A5Q1C1_YEASX
Isoform	—
PDB entities	21
Chains and sequence ranges	Author chain 0； PDBConstruct 1–778； UniProt 1–778

RNA polymerase II transcription factor B subunit 2

OrganismNot specified

UniProt A0A6A5Q2X3

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 × 26 DNA 2 PDB declaration: 28-meric（28） Consistent with all polymer counts	Chain 2； UniProt 1–513	Not recorded	DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） TATA-box-binding protein × 1 （P13393） template strand DNA × 1 non-template strand DNA × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） DNA-directed RNA polymerase subunit × 1 DNA-directed RNA polymerase II subunit RPB4 × 1 General transcription and DNA repair factor IIH subunit SSL1 × 1 General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7ML0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 2 1–513（513 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 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 × 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 2 1–513（513 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 2 1–513（513 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
8CEO Yeast RNA polymerase II transcription pre-initiation complex with core Mediator and the +1 nucleosome Deposited 2023-02-02	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 52 PDB declaration: 54-meric	Chain 2 1–513（513 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 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；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 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

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A6A5Q2X3_YEASX
Isoform	—
PDB entities	25
Chains and sequence ranges	Author chain 2； PDBConstruct 1–513； UniProt 1–513

General transcription and DNA repair factor IIH subunit TFB5

OrganismNot specified

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 × 26 DNA 2 PDB declaration: 28-meric（28） Consistent with all polymer counts	Chain 5； UniProt 1–72	Not recorded	DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） TATA-box-binding protein × 1 （P13393） template strand DNA × 1 non-template strand DNA × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） DNA-directed RNA polymerase subunit × 1 DNA-directed RNA polymerase II subunit RPB4 × 1 General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7ML0	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
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 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
7O4K Yeast TFIIH in the contracted state within the pre-initiation complex Deposited 2021-04-06	Different oligomeric state 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 × 10 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7O4L Yeast TFIIH in the expanded state within the pre-initiation complex Deposited 2021-04-06	Different oligomeric state Different ligand/ion Different 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 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 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 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	26
Chains and sequence ranges	Author chain 5； PDBConstruct 1–72； UniProt 1–72

BJ4_G0050160.mRNA.1.CDS.1

OrganismNot specified

UniProt A0A7I9BTI9

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 × 26 DNA 2 PDB declaration: 28-meric（28） Consistent with all polymer counts	Chain 3； UniProt 1–321	Not recorded	DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） TATA-box-binding protein × 1 （P13393） template strand DNA × 1 non-template strand DNA × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） DNA-directed RNA polymerase subunit × 1 DNA-directed RNA polymerase II subunit RPB4 × 1 General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7ML0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 3 1–321（321 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 structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-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 7.6 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 3 1–321（321 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 3 1–321（321 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
8CEO Yeast RNA polymerase II transcription pre-initiation complex with core Mediator and the +1 nucleosome Deposited 2023-02-02	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 52 PDB declaration: 54-meric	Chain 3 1–321（321 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

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A7I9BTI9_YEASX
Isoform	—
PDB entities	27
Chains and sequence ranges	Author chain 3； PDBConstruct 1–321； UniProt 1–321

General transcription and DNA repair factor IIH helicase subunit XPB

OrganismNot specified

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 × 26 DNA 2 PDB declaration: 28-meric（28） Consistent with all polymer counts	Chain 7； UniProt 1–843	Not recorded	DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） TATA-box-binding protein × 1 （P13393） template strand DNA × 1 non-template strand DNA × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） DNA-directed RNA polymerase subunit × 1 DNA-directed RNA polymerase II subunit RPB4 × 1 General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7ML0	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
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 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
7O4K Yeast TFIIH in the contracted state within the pre-initiation complex Deposited 2021-04-06	Different oligomeric state 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 × 10 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7O4L Yeast TFIIH in the expanded state within the pre-initiation complex Deposited 2021-04-06	Different oligomeric state Different ligand/ion Different 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 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 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 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 experimental conditions	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 experimental conditions Different structure-quality metrics	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	28
Chains and sequence ranges	Author chain 7； PDBConstruct 1–843； UniProt 1–843

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7ml0
Deposition date deposition_date	2021-04-27
Structure title title	RNA polymerase II pre-initiation complex (PIC1)
Keywords keywords	PIC, TFIIH, transcription, ITC, RNA polymerase II; TRANSCRIPTION
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	79.68 Å
Radius of gyration Rg (electron density) rg_electron	79.89 Å
Forward intensity I(0) i0	12632400000.00
Molecular weight molecular_weight	917010.0 kDa
Excluded volume excluded_volume	1131900 Å³
Envelope volume envelope_volume	1892000 Å³
Hydration-shell volume shell_volume	199630 Å³
Envelope diameter envelope_diameter	277.9 Å
Shell Rg shell_rg	77.82 Å
Envelope Rg envelope_rg	77.42 Å
Shape Rg shape_rg	79.96 Å
Total Rg total_rg	79.62 Å
Total atoms total_atoms	64213
Residues n_residues	8237
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	209.2 Å
Rg (real space) rg_real	76.40 Å
Rg uncertainty (real space) rg_real_error	0.59 Å
I(0) (real space) i0_real	1.2200e+10
I(0) uncertainty (real space) i0_real_error	2.3810e+08
Rg (reciprocal space) rg_reciprocal	78.99 Å
I(0) (reciprocal space) i0_reciprocal	12610000000.0000
Solution quality estimate total_estimate	0.9071
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	83.7 Å
Skewness Skewness skewness	0.275
Kurtosis Kurtosis kurtosis	-0.570
Angular range angular_range	— – 0.1000 Å⁻¹
Current regularization parameter α current_alpha	0.1741
Highest regularization parameter α highest_alpha	635800000.0000
Real-space data points n_real_points	21
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.970; Stabil: 0.976; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.010

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (31)

Entity 1 Entity 1 polymer

Description description	DNA-directed RNA polymerase subunit
Molecular weight formula_weight	191821.6 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	64214

MVGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQLVSRGGCGNTQPTIRKDGLKLVGSWKKDRATGDADEPELRVLSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPSISFNESQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNIRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDEEAEQSFDQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMIDEESLVKYMPEQKITEIEDGQDGGVTPYSNESGLVNADLDVKDELMFSPLVDSGSNDAMAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYSPTSPGYSPGSPAYSPKQDEQKHNENENSR

Entity 2 Entity 2 polymer

Description description	DNA-directed RNA polymerase subunit beta
Molecular weight formula_weight	138937.3 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MSDLANSEKYYDEDPYGFEDESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHTTESDNISRKYEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEESEDDSESGKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGRRGTALGIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAEANEENDLDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYTDRSRDF

Entity 3 Entity 3 polymer

Description description	DNA-directed RNA polymerase II subunit RPB3
Molecular weight formula_weight	35330.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MSEEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDIEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQMDQDKVNFASGDNNTASNMLGSNEDVMMTGAEQDPYSNASQMGNTGSGGYDNAW

Entity 4 Entity 4 polymer

Description description	DNA-directed RNA polymerase II subunit RPB4
Molecular weight formula_weight	25451.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MNVSTSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIKEALVERRRAFKRSQKKHKKKHLKHENANDETTAVEDEDDDLDEDDVNADDDDFMHSETREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETLY

Entity 5 Entity 5 polymer

Description description	DNA-directed RNA polymerases I, II, and III subunit RPABC1
Molecular weight formula_weight	25117.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQRADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM

Entity 6 Entity 6 polymer

Description description	DNA-directed RNA polymerases I,II,and III subunit RPABC2
Molecular weight formula_weight	17931.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MSDYEEAFNDGNENFEDFDVEHFSDEETYEEKPQFKDGETTDANGKTIVTGGNGPEDFQQHEQIRRKTLKEKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL

Entity 7 Entity 7 polymer

Description description	DNA-directed RNA polymerase II subunit RPB7
Molecular weight formula_weight	19081.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MFFIKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFKPFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHAIGSIKEDYLGAI

Entity 8 Entity 8 polymer

Description description	DNA-directed RNA polymerases I, II, and III subunit RPABC3
Molecular weight formula_weight	16525.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIASSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGGLLMRLEGNYRNLNNLKQENAYLLIRR

Entity 9 Entity 9 polymer

Description description	DNA-directed RNA polymerase II subunit RPB9
Molecular weight formula_weight	14308.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

MTTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSPLVYRHELITNIGETAGVVQDIGSDPTLPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQKNKRTQFS

Entity 10 Entity 10 polymer

Description description	DNA-directed RNA polymerases II subunit RPABC5
Molecular weight formula_weight	8290.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRYCCRRMILTHVDLIEKFLRYNPLEKRD

Entity 11 Entity 11 polymer

Description description	DNA-directed RNA polymerase II subunit RPB11
Molecular weight formula_weight	13633.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEGYDPKDALKNACNSIINKLGALKTNFETEWNLQTLAADDAF

Entity 12 Entity 12 polymer

Description description	DNA-directed RNA polymerases II subunit RPABC4
Molecular weight formula_weight	7730.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

MSREGFQIPTNLDAAAAGTSQARTATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQFEAR

Entity 13 Entity 13 polymer

Description description	Transcription initiation factor IIB
Molecular weight formula_weight	38257.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

MMTRESIDKRAGRRGPNLNIVLTCPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRSEWRTFSNDDHNGDDPSRVGEASNPLLDGNNLSTRIGKGETTDMRFTKELNKAQGKNVMDKKDNEVQAAFAKITMLCDAAELPKIVKDCAKEAYKLCHDEKTLKGKSMESIMAASILIGCRRAEVARTFKEIQSLIHVKTKEFGKTLNIMKNILRGKSEDGFLKIDTDNMSGAQNLTYIPRFCSHLGLPMQVTTSAEYTAKKCKEIKEIAGKSPITIAVVSIYLNILLFQIPITAAKVGQTLQVTEGTIKSGYKILYEHRDKLVDPQLIANGVVSLDNLPGVEKK

Entity 14 Entity 14 polymer

Description description	Transcription initiation factor IIF subunit alpha
Molecular weight formula_weight	82320.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Q

MSRRNPPGSRNGGGPTNASPFIKRDRMRRNFLRMRMGQNGSNSSSPGVPNGDNSRGSLVKKDDPEYAEEREKMLLQIGVEADAGRSNVKVKDEDPNEYNEFPLRAIPKEDLENMRTHLLKFQSKKKINPVTDFHLPVRLHRKDTRNLQFQLTRAEIVQRQKEISEYKKKAEQERSTPNSGGMNKSGTVSLNNTVKDGSQTPTVDSVTKDNTANGVNSSIPTVTGSSVPPASPTTVSAVESNGLSNGSTSAANGLDGNASTANLANGRPLVTKLEDAGPAEDPTKVGMVKYDGKEVTNEPEFEEGTMDPLADVAPDGGGRAKRGNLRRKTRQLKVLDENAKKLRFEEFYPWVMEDFDGYNTWVGSYEAGNSDSYVLLSVEDDGSFTMIPADKVYKFTARNKYATLTIDEAEKRMDKKSGEVPRWLMKHLDNIGTTTTRYDRTRRKLKAVADQQAMDEDDRDDNSEVELDYDEEFADDEEAPIIDGNEQENKESEQRIKKEMLQANAMGLRDEEAPSENEEDELFGEKKIDEDGERIKKALQKTELAALYSSDENEINPYLSESDIENKENESPVKKEEDSDTLSKSKRSSPKKQQKKATNAHVHKEPTLRVKSIKNCVIILKGDKKILKSFPEGEWNPQTTKAVDSSNNASNTVPSPIKQEEGLNSTVAEREETPAPTITEKDIIEAIGDGKVNIKEFGKFIRRKYPGAENKKLMFAIVKKLCRKVGNDHMELKKE

Entity 15 Entity 15 polymer

Description description	Transcription initiation factor IIF subunit beta
Molecular weight formula_weight	46684.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R

MSSGSAGAPALSNNSTNSVAKEKSGNISGDEYLSQEEEVFDGNDIENNETKVYEESLDLDLERSNRQVWLVRLPMFLAEKWRDRNNLHGQELGKIRINKDGSKITLLLNENDNDSIPHEYDLELTKKVVENEYVFTEQNLKKYQQRKKELEADPEKQRQAYLKKQEREEELKKKQQQQKRRNNRKKFNHRVMTDRDGRDRYIPYVKTIPKKTAIVGTVCHECQVMPSMNDPNYHKIVEQRRNIVKLNNKERITTLDETVGVTMSHTGMSMRSDNSNFLKVGREKAKSNIKSIRMPKKEILDYLFKLFDEYDYWSLKGLKERTRQPEAHLKECLDKVATLVKKGPYAFKYTLRPEYKKLKEEERKATLGELADEQTGSAGDNAQGDAEADLEDEIEMEDVV

Entity 16 Entity 16 polymer

Description description	Transcription initiation factor IIE subunit alpha
Molecular weight formula_weight	54804.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	W

MDRPIDDIVKNLLKFVVRGFYGGSFVLVLDAILFHSVLAEDDLKQLLSINKTELGPLIARLRSDRLISIHKQREYPPNSKSVERVYYYVKYPHAIDAIKWKVHQVVQRLKDDLDKNSEPNGYMCPICLTKYTQLEAVQLLNFDRTEFLCSLCDEPLVEDDSGKKNKEKQDKLNRLMDQIQPIIDSLKKIDDSRIEENTFEIALARLIPPQNQSHAAYTYNPKKGSTMFRPGDSAPLPNLMGTALGNDSSRRAGANSQATLHINITTASDEVAQRELQERQAEEKRKQNAVPEWHKQSTIGKTALGRLDNEEEFDPVVTASAMDSINPDNEPAQETSYQNNRTLTEQEMEERENEKTLNDYYAALAKKQAKLNKEEEEEEEEEEDEEEEEEEEMEDVMDDNDETARENALEDEFEDVTDTAGTAKTESNTSNDVKQESINDKTEDAVNATATASGPSANAKPNDGDDDDDDDDDEMDIEFEDV

Entity 17 Entity 17 polymer

Description description	Transcription initiation factor IIE subunit beta
Molecular weight formula_weight	37050.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X

MSKNRDPLLANLNAFKSKVKSAPVIAPAKVGQKKTNDTVITIDGNTRKRTASERAQENTLNSAKNPVLVDIKKEAGSNSSNAISLDDDDDDEDFGSSPSKKVRPGSIAAAALQANQTDISKSHDSSKLLWATEYIQKKGKPVLVNELLDYLSMKKDDKVIELLKKLDRIEFDPKKGTFKYLSTYDVHSPSELLKLLRSQVTFKGISCKDLKDGWPQCDETINQLEEDSKILVLRTKKDKTPRYVWYNSGGNLKCIDEEFVKMWENVQLPQFAELPRKLQDLGLKPASVDPATIKRQTKRVEVKKKRQRKGKITNTHMTGILKDYSHRV

Entity 18 Entity 18 polymer

Description description	TATA-box-binding protein
Molecular weight formula_weight	27042.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O

MADEERLKEFKEANKIVFDPNTRQVWENQNRDGTKPATTFQSEEDIKRAAPESEKDTSATSGIVPTLQNIVATVTLGCRLDLKTVALHARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVVTGAKSEDDSKLASRKYARIIQKIGFAAKFTDFKIQNIVGSCDVKFPIRLEGLAFSHGTFSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKQREEIYQAFEAIYPVLSEFRKM

Entity 19 Entity 19 polymer

Description description	template strand DNA
Molecular weight formula_weight	20240.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	T

ATGTACAAACACACATCAAAGGTTTATAGATACATTGAAACTTTTATATACGCGCCTTTTTTTTTT

Entity 20 Entity 20 polymer

Description description	non-template strand DNA
Molecular weight formula_weight	20436.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	N

AAAAAAAAAAGGCGCGTATATAAAAGTTTCAATGTATCTATAAACCTTTGATGTGTGTTTGTACAT

Entity 21 Entity 21 polymer

Description description	General transcription and DNA repair factor IIH helicase subunit XPD
Molecular weight formula_weight	89899.0 kDa
EC 编号 ec_number	3.6.4.12
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	0

MKFYIDDLPVLFPYPKIYPEQYNYMCDIKKTLDVGGNSILEMPSGTGKTVSLLSLTIAYQMHYPEHRKIIYCSRTMSEIEKALVELENLMDYRTKELGYQEDFRGLGLTSRKNLCLHPEVSKERKGTVVDEKCRRMTNGQAKRKLEEDPEANVELCEYHENLYNIEVEDYLPKGVFSFEKLLKYCEEKTLCPYFIVRRMISLCNIIIYSYHYLLDPKIAERVSNEVSKDSIVIFDEAHNIDNVCIESLSLDLTTDALRRATRGANALDERISEVRKVDSQKLQDEYEKLVQGLHSADILTDQEEPFVETPVLPQDLLTEAIPGNIRRAEHFVSFLKRLIEYLKTRMKVLHVISETPKSFLQHLKQLTFIERKPLRFCSERLSLLVRTLEVTEVEDFTALKDIATFATLISTYEEGFLLIIEPYEIENAAVPNPIMRFTCLDASIAIKPVFERFSSVIITSGTISPLDMYPRMLNFKTVLQKSYAMTLAKKSFLPMIITKGSDQVAISSRFEIRNDPSIVRNYGSMLVEFAKITPDGMVVFFPSYLYMESIVSMWQTMGILDEVWKHKLILVETPDAQETSLALETYRKACSNGRGAILLSVARGKVSEGIDFDHQYGRTVLMIGIPFQYTESRILKARLEFMRENYRIRENDFLSFDAMRHAAQCLGRVLRGKDDYGVMVLADRRFSRKRSQLPKWIAQGLSDADLNLSTDMAISNTKQFLRTMAQPTDPKDQEGVSVWSYEDLIKHQNSRKDQGGFIENENKEGEQDEDEDEDIEMQ

Entity 22 Entity 22 polymer

Description description	DNA-directed RNA polymerase subunit
Molecular weight formula_weight	58551.3 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	1

MSHSGAAIFEKVSGIIAINEDVSPAELTWRSTDGDKVHTVVLSTIDKLQATPASSEKMMLRLIGKVDESKKRKDNEGNEVVPKPQRHMFSFNNRTVMDNIKMTLQQIISRYKDADIYEEKRRREESAQHTETPMSSSSVTAGTPTPHLDTPQLNNGAPLINTAKLDDSLSKEKLLTNLKLQQSLLKGNKVLMKVFQETVINAGLPPSEFWSTRIPLLRXFALXXSQKXGPXXVXXXXXPXXXXXXXXXXNLSREKILNIFENYPIVKKAYTDNVPKNFKEPEFWARFFSSKLFRKLXXXXXXXXXXXXXXXXXXLXXXXXFXXKXXXXLLHPVKKIIXLDGNIQDDPVVRGXXXXXXXXVDILKGMNRLSEKMIMXLKXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXRVITXIKINAKQAXHXXXEVKSTLPIDLLESCRMLHTTCCEFLKHFAIHXXXXQKQASTVKKLYNHLKDCIEKLNELFQDVLNGDGESMSNTCTAYLKPVLNSITLATHKYDEYFNEYNNNSN

Entity 23 Entity 23 polymer

Description description	DNA-directed RNA polymerase II subunit RPB4
Molecular weight formula_weight	37430.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	4

MDAISDPTFKHARSRKQVTEESPSLLTVIIEIAPKLWTTFDEEGNEKGSIIKVLEALIVFLNAHLAFNSANKVAVIAAYSQGIKYLYPESTSALKASESENKTRSDLKIINSXXYRRFRNVDETLVEEIYKLFELEKKQIEQNSQRSTLAGAMSAGLTYVNRISKESVTTSLKSRLLVLTCGSGSSKDEIFQYIPIMNCIFSATKMKCPIDVVKIGGSKESTFLQQTTDATNGVYLHVESTEGLIQYLATAMFIDPSLRPIIVKPNHGSVDFRTSCYLTGRVVAVGFICSVCLCVLSIIPPGNKCPACDSQFDEHVIAKLKRKPVVPRLKAKKKVTKP

Entity 24 Entity 24 polymer

Description description	General transcription and DNA repair factor IIH subunit SSL1
Molecular weight formula_weight	52024.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	6

MAPVVISESEEDEDRVAITRRTKRQVHFDGEGDDRVDQQQQQHSSSHRDRDKHVQRKKKKRLSNRNLQGSNGGYAWEDEIKRSWDLVKVDDEGDMASLVASIVEARKKRTAKKNITPYQRGIIRSLILTLDCSEAMLEKDLRPNRHAMIIQYAIDFVHEFFDQNPISQMGIIIMRNGLAQLVSQVSGNPQDHIDALKSIRKQEPKGNPSLQNALEMARGLLLPVPAHCTREVLIVFGSLSTTDPGDIHQTIDSLVSEKIRVKVLGLSAQVAICKELCKATNYGDESFYKILLDETHLKELFNEAVTPLPVNKINKGFTLVKMGFPTRIFEDTPTFCSCHSKLVYGGYFCPNCHSKVCSLPTVCPCCDLMLILSTHLARSYHHLMPLKTFAEVPTTEKFRSEDCFSCQSRFPXXXXXXXXXXXXXSRYRCEDCKQEFCVDCDVFIHEILHNCPGCESKPVIT

Entity 25 Entity 25 polymer

Description description	RNA polymerase II transcription factor B subunit 2
Molecular weight formula_weight	58602.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	2

MSDYSLKHSVTQYLEEIPQQVQNRLYTSPATCLAIYRILPPLAKFFIMAMVFNENEVPLLDLDKWVNSNGKLQFQNAIKSMKSLHLLIPNKSSGTLMINLNPTFKISLRNALTGGEVQNSFGVVVEENVVSLDLLDEYSANKWETILHFMVGTPLAKIPSEKVLNLLKHSKLMEEVNSTGEFKITNEGFQFLLQEINSQLWTLLLQYLKMIETSKMDLVDVLHFIFMLGALEVGKAYKIDALSETQRIMLQDMRDYGLVFQKHSNDSIFYPTKLALMLTSDTKTIRSASNAMDSVLRQNREEPSVNEDGANGKSTTDITTSDDLNKAGLKNQDIPDGSLIVETNFKIYSYSNSPLQIAVLSLFVHLKARFVNMVLGQITRESIRRALTNGITADQIIAYLETHAHPQMRRLAEEKLEKKLELDPNCKEPLQVLPPTVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGVLLWKDDKKKKFFISKEGNSQVLDFAKRKLKKKQ

Entity 26 Entity 26 polymer

Description description	General transcription and DNA repair factor IIH subunit TFB5
Molecular weight formula_weight	8243.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	5

MARARKGALVQCDPSIKALILQIDAKMSDIVLEELDDTHLLVNPSKVEFVKHELNRLLSKNIYNPMDEEENQ

Entity 27 Entity 27 polymer

Description description	BJ4_G0050160.mRNA.1.CDS.1
Molecular weight formula_weight	38188.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	3

MLMDEYEENKDMCPICKTDRYLSPDVKFLVNPECYHRICESCVDRIFSLGPAQCPYKGCDKILRKNKFKTQIFDDVEVEKEVDIRKRVFNVFNKTIDDFNGDLVEYNKYLEEVEDIIYKLDHGIDVAKTEEKLRTYEELNKQLIMNNLERSRTEIESFEQRQKFEKEMKLKKRLLERQIEEEERMNKEWTKKEIVNRLSTTTQDINETIEGVKNTVKLKKSSARRKLEELNRVLKNNPYFNSNVNVQNSRLKDAVPFTPFNGDREAHPRFTLKGSVYNDPFIKDLEHRKEFIASGFNTNYAYERVLTEAFMGLGCVISEEL

Entity 28 Entity 28 polymer

Description description	General transcription and DNA repair factor IIH helicase subunit XPB
Molecular weight formula_weight	95461.7 kDa
EC 编号 ec_number	3.6.4.12
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	7

MTDVEGYQPKSKGKIFPDMGESFFSSDEDSPATDAEIDENYDDNRETSEGRGERDTGAMVTGLKKPRKKTKSSRHTAADSSMNQMDAKDKALLQDTNSDIPADFVPDSVSGMFRSHDFSYLRLRPDHASRPLWISPSDGRIILESFSPLAEQAQDFLVTIAEPISRPSHIHEYKITAYSLYAAVSVGLETDDIISVLDRLSKVPVAESIINFIKGATISYGKVKLVIKHNRYFVETTQADILQMLLNDSVIGPLRIDSDHQVQPPEDVLQQQLQQTAGKPATNVNPNDVEAVFSAVIGGDNEREEEDDDIDAVHSFEIANESVEVVKKRCQEIDYPVLEEYDFRNDHRNPDLDIDLKPSTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGITAACTIKKSVIVLCTSSVSVMQWRQQFLQWCTLQPENCAVFTSDNKEMFQTESGLVVSTYSMVANTRNRSHDSQKVMDFLTGREWGFIILDEVHVVPAAMFRRVVSTIAAHAKLGLTATLVREDDKIGDLNFLIGPKLYEANWMELSQKGHIANVQCAEVWCPMTAEFYQEYLRETARKRMLLYIMNPTKFQACQFLIQYHERRGDKIIVFSDNVYALQEYALKMGKPFIYGSTPQQERMNILQNFQYNDQINTIFLSKVGDTSIDLPEATCLIQISSHYGSRRQEAQRLGRILRAKRRNDEGFNAFFYSLVSKDTQEMYYSTKRQAFLVDQGYAFKVITHLHGMENIPNLAYASPRERRELLQEVLLKNEEAAGIEVGDDADNSVGRGSNGHKRFKSKAVRGEGSLSGLAGGEDMAYMEYSTNKNKELKEHHPLIRKMYYKNLKK

Entity 29 Entity 29 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	17

Entity 30 Entity 30 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 31 Entity 31 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	1

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7. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id	7ml0001
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7ml0A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	274 — Enzyme I; Chain A, domain 2
Homologous superfamily homologous superfamily	100 — RNA polymerase Rpb1, domain 3

Domain ID domain_id	7ml0A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	7ml0K01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	10 — RNA polymerase, RBP11-like subunit

Domain ID domain_id	7ml0M01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily	10 — Cyclin-like

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

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

Resolution resolution	3.00 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	137466

fit	/app/data/saxs_computation/ml/7ml0/7ml0.fit
pddf	/app/data/pr_computation/ml/7ml0/7ml0.pr.out
profile	/app/data/saxs_computation/ml/7ml0/7ml0.dat

RNA polymerase II pre-initiation complex (PIC1)

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

DNA-directed RNA polymerase subunit

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerase subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerase II subunit RPB3

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerase II subunit RPB4

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerases I, II, and III subunit RPABC1

State in the Current Structure

Other States of the Same Protein in the Database

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

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerase II subunit RPB7

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerases I, II, and III subunit RPABC3

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerase II subunit RPB9

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerases II subunit RPABC5

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerase II subunit RPB11

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerases II subunit RPABC4

State in the Current Structure

Other States of the Same Protein in the Database

Transcription initiation factor IIB

State in the Current Structure

Other States of the Same Protein in the Database

Transcription initiation factor IIF subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Transcription initiation factor IIF subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

Transcription initiation factor IIE subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Transcription initiation factor IIE subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

TATA-box-binding protein

State in the Current Structure

Other States of the Same Protein in the Database

General transcription and DNA repair factor IIH helicase subunit XPD

State in the Current Structure

Other States of the Same Protein in the Database

RNA polymerase II transcription factor B subunit 2

State in the Current Structure

Other States of the Same Protein in the Database

General transcription and DNA repair factor IIH subunit TFB5

State in the Current Structure

Other States of the Same Protein in the Database

BJ4_G0050160.mRNA.1.CDS.1

State in the Current Structure

Other States of the Same Protein in the Database

General transcription and DNA repair factor IIH helicase subunit XPB

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D