Structure of TFIIH/Rad4-Rad23-Rad33/DNA in DNA opening

DNA repair protein RAD33

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q04231

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 × 9 DNA 2 PDB declaration: undecameric（11） Consistent with all polymer counts	Chain E； UniProt 1–177	Not recorded	General transcription and DNA repair factor IIH subunit TFB2 × 1 （Q02939） DNA repair helicase RAD3 × 1 （P06839） General transcription and DNA repair factor IIH subunit TFB1 × 1 （P32776） General transcription and DNA repair factor IIH subunit TFB4 × 1 （Q12004） General transcription and DNA repair factor IIH subunit SSL1 × 1 （Q04673） Damaged DNA strand × 1 Undamaged DNA strand × 1 DNA repair protein RAD4 × 1 （P14736） DNA repair helicase RAD25 × 1 （Q00578） RNA polymerase II transcription factor B subunit 5 × 1 （Q3E7C1） 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

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 7K04	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7M2U Nucleotide Excision Repair complex TFIIH Rad4-33 Deposited 2021-03-17	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain E 1–177（177 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

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RAD33_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain E； PDBConstruct 1–177； UniProt 1–177

General transcription and DNA repair factor IIH subunit TFB2

OrganismNot specified

UniProt Q02939

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–DNA Heteromer Protein × 9 DNA 2 PDB declaration: undecameric（11） Consistent with all polymer counts	Chain 2； UniProt 1–513	Not recorded	DNA repair protein RAD33 × 1 （Q04231） DNA repair helicase RAD3 × 1 （P06839） General transcription and DNA repair factor IIH subunit TFB1 × 1 （P32776） General transcription and DNA repair factor IIH subunit TFB4 × 1 （Q12004） General transcription and DNA repair factor IIH subunit SSL1 × 1 （Q04673） Damaged DNA strand × 1 Undamaged DNA strand × 1 DNA repair protein RAD4 × 1 （P14736） DNA repair helicase RAD25 × 1 （Q00578） RNA polymerase II transcription factor B subunit 5 × 1 （Q3E7C1） 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

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 7K04	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3DGP Crystal Structure of the complex between Tfb5 and the C-terminal domain of Tfb2 Deposited 2008-06-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 435–513（79 aa） Fragment：C-terminal Domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.9；277 K；Tris 20 mM, NaCl 50 mM, pH 8.9, EVAPORATION, temperature 277K	Resolution 1.80 Å R-free 0.237
3DOM Crystal Structure of the complex between Tfb5 and the C-terminal domain of Tfb2 Deposited 2008-07-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 412–513（102 aa） Fragment：C-terminal domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PEG3350 MME, NaCl, Hepes, pH 7.5, vapor diffusion, sitting drop, temperature 293K	Resolution 2.60 Å R-free 0.261
3DOM Crystal Structure of the complex between Tfb5 and the C-terminal domain of Tfb2 Deposited 2008-07-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 412–513（102 aa） Fragment：C-terminal domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PEG3350 MME, NaCl, Hepes, pH 7.5, vapor diffusion, sitting drop, temperature 293K	Resolution 2.60 Å R-free 0.261
5FMF the P-lobe of RNA polymerase II pre-initiation complex Deposited 2015-11-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric	Chain W 447–508（62 aa）	Not recorded	MG MAGNESIUM ION × 2 ZN ZINC ION × 9	ELECTRON MICROSCOPY cryo-EM buffer 20 MM HEPES (PH7.6), 5 MM DTT, 2 MM MG(OAC)2,AND 40 MM KOAC；pH 7.6；20 MM HEPES (PH7.6), 5 MM DTT, 2 MM MG(OAC)2,AND 40 MM KOAC cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 120, INSTRUMENT- FEI VITROBOT MARK III,	Resolution 6.00 Å
5OQJ STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH Deposited 2017-08-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric	Chain 2 1–112（112 aa） Chain 2 160–194（35 aa） Chain 2 215–281（67 aa） Chain 2 433–513（81 aa）	Not recorded	ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；GRIDS WERE BLOTTED FOR 8 S AND PLUNGE-FROZEN IN LIQUID ETHANE.	Resolution 4.70 Å
5OQM STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH AND CORE MEDIATOR Deposited 2017-08-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 44 PDB declaration: 46-meric	Chain 2 1–112（112 aa） Chain 2 160–194（35 aa） Chain 2 215–281（67 aa） Chain 2 282–513（232 aa）	Not recorded	ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 8 s and plunge-frozen in liquid ethane.	Resolution 5.80 Å
5SVA Mediator-RNA Polymerase II Pre-Initiation Complex Deposited 2016-08-05	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric	Chain a 1–513（513 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 15.30 Å
6GYM Structure of a yeast closed complex with distorted DNA (CCdist) Deposited 2018-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric	Chain 2 1–112（112 aa） Chain 2 160–194（35 aa） Chain 2 215–281（67 aa） Chain 2 433–513（81 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 16 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.70 Å
7K01 Structure of TFIIH in TFIIH/Rad4-Rad23-Rad33 DNA opening complex Deposited 2020-09-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain 2 1–513（513 aa）	Not recorded	ZN ZINC ION × 5 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；Sample dialyzed for 30 minutes into above buffer prior to grid making cryo-EM vitrification conditions Cryogen ETHANE；Grids were manually blotted for 2-3 seconds prior to plunge freezing	Resolution 3.90 Å
7M2U Nucleotide Excision Repair complex TFIIH Rad4-33 Deposited 2021-03-17	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain 2 1–513（513 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 5 CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.20 Å
7O4I Yeast RNA polymerase II transcription pre-initiation complex with initial transcription bubble Deposited 2021-04-06	Different oligomeric state Different ligand/ion Different 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 × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7O4J Yeast RNA polymerase II transcription pre-initiation complex (consensus) Deposited 2021-04-06	Different oligomeric state Different ligand/ion Different experimental 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 × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
7O4K Yeast TFIIH in the contracted state within the pre-initiation complex Deposited 2021-04-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric	Chain 2 1–513（513 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 10 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7O4L Yeast TFIIH in the expanded state within the pre-initiation complex Deposited 2021-04-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric	Chain 2 1–513（513 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 11 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7O72 Yeast RNA polymerase II transcription pre-initiation complex with closed promoter DNA Deposited 2021-04-12	Different oligomeric state Different ligand/ion Different 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 × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7O73 Yeast RNA polymerase II transcription pre-initiation complex with closed distorted promoter DNA Deposited 2021-04-12	Different oligomeric state Different ligand/ion Different experimental 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 × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7O75 Yeast RNA polymerase II transcription pre-initiation complex with open promoter DNA Deposited 2021-04-13	Different oligomeric state Different ligand/ion Different experimental 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 × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7ZS9 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome (complex A) Deposited 2022-05-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric	Chain 2 1–513（513 aa）	Not recorded	ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
7ZSA Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP (complex B) Deposited 2022-05-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric	Chain 2 1–513（513 aa）	Not recorded	ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
7ZSB Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP, complex C Deposited 2022-05-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric	Chain 2 1–513（513 aa）	Not recorded	ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.60 Å
8UOQ Composite map of PIC_delta_TFIIK form2 Deposited 2023-10-20	Different oligomeric state Different ligand/ion Different 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 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
8UOT Composite map of PICdeltaTFIIK form1 Deposited 2023-10-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain 2 1–513（513 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å

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

View Construct and Data Evidence

UniProt name	TFB2_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain 2； PDBConstruct 1–513； UniProt 1–513

DNA repair helicase RAD3

OrganismNot specified

UniProt P06839

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–DNA Heteromer Protein × 9 DNA 2 PDB declaration: undecameric（11） Consistent with all polymer counts	Chain 0； UniProt 1–778	Not recorded	DNA repair protein RAD33 × 1 （Q04231） General transcription and DNA repair factor IIH subunit TFB2 × 1 （Q02939） General transcription and DNA repair factor IIH subunit TFB1 × 1 （P32776） General transcription and DNA repair factor IIH subunit TFB4 × 1 （Q12004） General transcription and DNA repair factor IIH subunit SSL1 × 1 （Q04673） Damaged DNA strand × 1 Undamaged DNA strand × 1 DNA repair protein RAD4 × 1 （P14736） DNA repair helicase RAD25 × 1 （Q00578） RNA polymerase II transcription factor B subunit 5 × 1 （Q3E7C1） 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

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 7K04	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5FMF the P-lobe of RNA polymerase II pre-initiation complex Deposited 2015-11-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric	Chain Y 1–778（778 aa）	Not recorded	MG MAGNESIUM ION × 2 ZN ZINC ION × 9	ELECTRON MICROSCOPY cryo-EM buffer 20 MM HEPES (PH7.6), 5 MM DTT, 2 MM MG(OAC)2,AND 40 MM KOAC；pH 7.6；20 MM HEPES (PH7.6), 5 MM DTT, 2 MM MG(OAC)2,AND 40 MM KOAC cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 120, INSTRUMENT- FEI VITROBOT MARK III,	Resolution 6.00 Å
5OQJ STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH Deposited 2017-08-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric	Chain 0 1–293（293 aa） Chain 0 327–778（452 aa）	Not recorded	ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；GRIDS WERE BLOTTED FOR 8 S AND PLUNGE-FROZEN IN LIQUID ETHANE.	Resolution 4.70 Å
5OQM STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH AND CORE MEDIATOR Deposited 2017-08-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 44 PDB declaration: 46-meric	Chain 0 1–293（293 aa） Chain 0 328–778（451 aa）	Not recorded	ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 8 s and plunge-frozen in liquid ethane.	Resolution 5.80 Å
5SVA Mediator-RNA Polymerase II Pre-Initiation Complex Deposited 2016-08-05	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric	Chain Y 1–778（778 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 15.30 Å
6GYM Structure of a yeast closed complex with distorted DNA (CCdist) Deposited 2018-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric	Chain 0 1–293（293 aa） Chain 0 327–778（452 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 16 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.70 Å
7K01 Structure of TFIIH in TFIIH/Rad4-Rad23-Rad33 DNA opening complex Deposited 2020-09-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain 0 1–778（778 aa）	Not recorded	ZN ZINC ION × 5 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；Sample dialyzed for 30 minutes into above buffer prior to grid making cryo-EM vitrification conditions Cryogen ETHANE；Grids were manually blotted for 2-3 seconds prior to plunge freezing	Resolution 3.90 Å
7M2U Nucleotide Excision Repair complex TFIIH Rad4-33 Deposited 2021-03-17	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain 0 1–778（778 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 5 CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.20 Å
7O4I Yeast RNA polymerase II transcription pre-initiation complex with initial transcription bubble Deposited 2021-04-06	Different oligomeric state Different ligand/ion Different 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 × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7O4J Yeast RNA polymerase II transcription pre-initiation complex (consensus) Deposited 2021-04-06	Different oligomeric state Different ligand/ion Different experimental 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 × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
7O4K Yeast TFIIH in the contracted state within the pre-initiation complex Deposited 2021-04-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric	Chain 0 1–778（778 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 10 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7O4L Yeast TFIIH in the expanded state within the pre-initiation complex Deposited 2021-04-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric	Chain 0 1–778（778 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 11 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7O72 Yeast RNA polymerase II transcription pre-initiation complex with closed promoter DNA Deposited 2021-04-12	Different oligomeric state Different ligand/ion Different 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 × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7O73 Yeast RNA polymerase II transcription pre-initiation complex with closed distorted promoter DNA Deposited 2021-04-12	Different oligomeric state Different ligand/ion Different experimental 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 × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7O75 Yeast RNA polymerase II transcription pre-initiation complex with open promoter DNA Deposited 2021-04-13	Different oligomeric state Different ligand/ion Different experimental 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 × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7ZS9 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome (complex A) Deposited 2022-05-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric	Chain 0 1–778（778 aa）	Not recorded	ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
7ZSA Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP (complex B) Deposited 2022-05-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric	Chain 0 1–778（778 aa）	Not recorded	ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
7ZSB Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP, complex C Deposited 2022-05-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric	Chain 0 1–778（778 aa）	Not recorded	ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.60 Å
8CEN Yeast RNA polymerase II transcription pre-initiation complex with core Mediator Deposited 2023-02-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 44 PDB declaration: 46-meric	Chain 0 1–778（778 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8CEO Yeast RNA polymerase II transcription pre-initiation complex with core Mediator and the +1 nucleosome Deposited 2023-02-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 52 PDB declaration: 54-meric	Chain 0 1–778（778 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
8UOQ Composite map of PIC_delta_TFIIK form2 Deposited 2023-10-20	Different oligomeric state Different ligand/ion Different 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 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
8UOT Composite map of PICdeltaTFIIK form1 Deposited 2023-10-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain 0 1–778（778 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å

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

View Construct and Data Evidence

UniProt name	RAD3_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain 0； PDBConstruct 1–778； UniProt 1–778

General transcription and DNA repair factor IIH subunit TFB1

OrganismNot specified

UniProt P32776

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–DNA Heteromer Protein × 9 DNA 2 PDB declaration: undecameric（11） Consistent with all polymer counts	Chain 1； UniProt 2–642	Not recorded	DNA repair protein RAD33 × 1 （Q04231） General transcription and DNA repair factor IIH subunit TFB2 × 1 （Q02939） DNA repair helicase RAD3 × 1 （P06839） General transcription and DNA repair factor IIH subunit TFB4 × 1 （Q12004） General transcription and DNA repair factor IIH subunit SSL1 × 1 （Q04673） Damaged DNA strand × 1 Undamaged DNA strand × 1 DNA repair protein RAD4 × 1 （P14736） DNA repair helicase RAD25 × 1 （Q00578） RNA polymerase II transcription factor B subunit 5 × 1 （Q3E7C1） 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

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 7K04	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1Y5O NMR structure of the amino-terminal domain from the Tfb1 subunit of yeast TFIIH Deposited 2004-12-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–115（115 aa） Fragment：sequence database residues 1-115	Mutation：M1P	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 20 mM SODIUM PHOSPHATE；Pressure AMBIENT NMR sample composition 1.2 MM TFB1 [UNLABELED], 20 MM PHOSPHATE BUFFER, 1MM EDTA, 100% D2O; 1.2 MM TFB1 [U-15N], 20 MM PHOSPHATE BUFFER, 1MM EDTA, 90% H2O, 10% D2O; 1.2 MM TFB1 [U-15N,13C], 20 MM PHOSPHATE BUFFER, 1MM EDTA, 100% D2O	Resolution not provided
2GS0 NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and the activation domain of p53 Deposited 2006-04-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–115（115 aa）	Mutation：M1P	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 20 mM sodium phosphate；Pressure ambient NMR sample composition 1.0 mM Tfb1 U-15N, 1.0 mM p53 unlabeled, 1.00 mM EDTA, 20 mM phosphate buffer; 90% H2O, 10% D2O | 90% H2O/10% D2O NMR sample composition 1.0 mM Tfb1 U-15N,13C, 1.0 mM p53 unlabeled, 1.00 mM EDTA, 20 mM phosphate buffer; 100% D20 | 100% D20 NMR sample composition 1.0 mM p53 U-15N, 1.0 mM Tfb1 unlabeled, 1.00 mM EDTA, 20 mM phosphate buffer; 90% H2O, 10% D2O | 90% H2O/10% D2O NMR sample composition 1.0 mM p53 U-15N, 1.0 mM Tfb1 unlabeled, 1.00 mM EDTA, 20 mM phosphate buffer; 100% D20 | 100% D20	Resolution not provided
2K2U NMR Structure of the complex between Tfb1 subunit of TFIIH and the activation domain of VP16 Deposited 2008-04-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–115（115 aa） Fragment：PH domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 20mM Sodium Phosphate；Pressure Ambient NMR sample composition 1.0 mM [U-99% 15N] Tfb1, 1.0 mM VP16, 90% H2O, 10% D2O | 90% H2O/10% D2O NMR sample composition 1.0 mM [U-99% 13C; U-99% 15N] Tfb1, 1.0 mM VP16, 100% D2O | 100% D2O NMR sample composition 1.0 mM [U-99% 15N] VP16, 1.0 mM Tfb1, 90% H2O, 10% D2O | 90% H2O/10% D2O NMR sample composition 1.0 mM [U-99% 13C; U-99% 15N] VP16, 1.0 mM Tfb1, 100% D2O | 100% D2O	Resolution not provided
2L2I NMR Structure of the complex between the Tfb1 subunit of TFIIH and the activation domain of EKLF Deposited 2010-08-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–115（114 aa） Fragment：PH domain (UNP residues 2-115)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 20mM Sodium Phosphate；Pressure ambient NMR sample composition 1 mM [U-100% 15N] Tfb1, 2 mM EKLF, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Tfb1, 2 mM EKLF, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition 0.6 mM [U-100% 15N] EKLF, 1.2 mM Tfb1, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition 0.6 mM [U-100% 13C; U-100% 15N] EKLF, 1.2 mM Tfb1, 100% D2O | 100% D2O NMR sample composition 0.6 mM [U-100% 13C; U-100% 15N] EKLF, 1.2 mM Tfb1, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Tfb1, 2 mM EKLF, 100% D2O | 100% D2O	Resolution not provided
2LOX NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and Rad2 Deposited 2012-01-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–115（114 aa） Fragment：UNP residues 2-115	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；300 K；Pressure ambient NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Tfb1, 1.25 mM Rad2, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Tfb1, 1.25 mM Rad2, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 100% D2O | 100% D2O NMR sample composition 1 mM [U-100% 15N] Tfb1, 1.25 mM Rad2, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition 1.25 mM Tfb1, 1 mM [U-100% 13C; U-100% 15N] Rad2, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition 1.25 mM Tfb1, 1 mM [U-100% 13C; U-100% 15N] Rad2, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 100% D2O | 100% D2O NMR sample composition 1.25 mM Tfb1, 1 mM [U-100% 15N] Rad2, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O	Resolution not provided
2M14 NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and Rad4 Deposited 2012-11-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–115（114 aa） Fragment：UNP residues 2-115	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 20；Pressure ambient NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Tfb1, 1.25 mM Rad4, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Tfb1, 1.25 mM Rad4, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 100% D2O | 100% D2O NMR sample composition 1 mM [U-100% 15N] Tfb1, 1.25 mM Rad4, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition 1.25 mM Tfb1, 1 mM [U-100% 13C; U-100% 15N] Rad4, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition 1.25 mM Tfb1, 1 mM [U-100% 13C; U-100% 15N] Rad4, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 100% D2O | 100% D2O NMR sample composition 1.25 mM Tfb1, 1 mM [U-100% 15N] Rad4, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O	Resolution not provided
2MKR Structural Characterization of a Complex Between the Acidic Transactivation Domain of EBNA2 and the Tfb1/p62 subunit of TFIIH. Deposited 2014-02-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–115（115 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 20；Pressure ambient NMR sample composition 0.7 mM [U-13C; U-15N] Tfb1, 2.1 mM EBNA2, 20 mM sodium phosphate, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition 0.7 mM [U-15N] Tfb1, 2.1 mM EBNA2, 20 mM sodium phosphate, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition 0.7 mM [U-13C; U-15N] Tfb1, 2.1 mM EBNA2, 20 mM sodium phosphate, 1 mM DTT, 100% D2O | 100% D2O NMR sample composition 0.5 mM [U-13C; U-15N] EBNA2, 1.5 mM Tfb1, 20 mM sodium phosphate, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition 0.5 mM [U-100% 15N] EBNA2, 1.5 mM Tfb1, 20 mM sodium phosphate, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition 0.5 mM [U-13C; U-15N] EBNA2, 1.5 mM Tfb1, 20 mM sodium phosphate, 1 mM DTT-24, 100% D2O | 100% D2O	Resolution not provided
2N0Y NMR structure of the complex between the C-terminal domain of the Rift Valley fever virus protein NSs and the PH domain of the Tfb1 subunit of TFIIH Deposited 2015-03-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–115（115 aa） Fragment：Pleckstrin homology domain residues 1-115	Mutation：M1P	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 1 mM [U-13C; U-15N] RNA polymerase II transcription factor B subunit 1, 2 mM Non-structural protein NS-S, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition 1 mM [U-13C; U-15N] RNA polymerase II transcription factor B subunit 1, 2 mM Non-structural protein NS-S, 100% D2O | 100% D2O NMR sample composition 0.5 mM [U-15N] RNA polymerase II transcription factor B subunit 1, 1 mM Non-structural protein NS-S, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition 1 mM RNA polymerase II transcription factor B subunit 1, 0.5 mM [U-13C; U-15N] Non-structural protein NS-S, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition 0.5 mM RNA polymerase II transcription factor B subunit 1, 1 mM [U-13C; U-15N] Non-structural protein NS-S, 100% D2O | 100% D2O NMR sample composition 0.4 mM RNA polymerase II transcription factor B subunit 1, 0.2 mM [U-15N] Non-structural protein NS-S, 90% H2O/10% D2O | 90% H2O/10% D2O	Resolution not provided
2N23 NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and the N-terminal activation domain of EKLF (TAD1) Deposited 2015-04-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–115（114 aa） Fragment：Pleckstrin homology domain, UNP residues 2-115	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N] RNA polymerase II transcription factor B subunit 1, 2 mM N-terminal transactivation domain of Krueppel-like factor 1, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N] RNA polymerase II transcription factor B subunit 1, 2 mM N-terminal transactivation domain of Krueppel-like factor 1, 100% D2O | 100% D2O NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N] N-terminal transactivation domain of Krueppel-like factor 1, 2 mM RNA polymerase II transcription factor B subunit 1, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N] N-terminal transactivation domain of Krueppel-like factor 1, 2 mM RNA polymerase II transcription factor B subunit 1, 100% D2O | 100% D2O	Resolution not provided
5OQJ STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH Deposited 2017-08-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric	Chain 1 1–218（218 aa） Chain 1 250–295（46 aa） Chain 1 537–642（106 aa）	Not recorded	ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；GRIDS WERE BLOTTED FOR 8 S AND PLUNGE-FROZEN IN LIQUID ETHANE.	Resolution 4.70 Å
5OQM STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH AND CORE MEDIATOR Deposited 2017-08-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 44 PDB declaration: 46-meric	Chain 1 1–121（121 aa） Chain 1 176–218（43 aa） Chain 1 250–295（46 aa） Chain 1 522–642（121 aa）	Not recorded	ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 8 s and plunge-frozen in liquid ethane.	Resolution 5.80 Å
5URN NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and the transactivation domain 1 of p65 Deposited 2017-02-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–115（114 aa） Fragment：PLECKSTRIN HOMOLOGY DOMAIN, UNP RESIDUES 2-115	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0；Pressure AMBIENT NMR sample composition 0.8 mM [U-99% 13C; U-99% 15N] RNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT 1, 1.6 mM TRANSCRIPTION FACTOR P65, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition 0.8 mM [U-99% 13C; U-99% 15N] TRANSCRIPTION FACTOR P65, 1.6 mM RNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT 1, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition 0.8 mM [U-99% 13C; U-99% 15N] RNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT 1, 1.6 mM TRANSCRIPTION FACTOR P65, 100% D2O | 100% D2O NMR sample composition 0.8 mM [U-99% 13C; U-99% 15N] TRANSCRIPTION FACTOR P65, 1.6 mM RNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT 1, 100% D2O | 100% D2O	Resolution not provided
6GYM Structure of a yeast closed complex with distorted DNA (CCdist) Deposited 2018-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric	Chain 1 1–218（218 aa） Chain 1 250–295（46 aa） Chain 1 537–642（106 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 16 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.70 Å
7K01 Structure of TFIIH in TFIIH/Rad4-Rad23-Rad33 DNA opening complex Deposited 2020-09-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain 1 1–642（642 aa）	Not recorded	ZN ZINC ION × 5 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；Sample dialyzed for 30 minutes into above buffer prior to grid making cryo-EM vitrification conditions Cryogen ETHANE；Grids were manually blotted for 2-3 seconds prior to plunge freezing	Resolution 3.90 Å
7M2U Nucleotide Excision Repair complex TFIIH Rad4-33 Deposited 2021-03-17	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain 1 1–642（642 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 5 CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.20 Å
7O4I Yeast RNA polymerase II transcription pre-initiation complex with initial transcription bubble Deposited 2021-04-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain 1 1–642（642 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain 1 1–642（642 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric	Chain 1 1–642（642 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric	Chain 1 1–642（642 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 11 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7O72 Yeast RNA polymerase II transcription pre-initiation complex with closed promoter DNA Deposited 2021-04-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain 1 1–642（642 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain 1 1–642（642 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain 1 1–642（642 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric	Chain 1 1–642（642 aa）	Not recorded	ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
7ZSA Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP (complex B) Deposited 2022-05-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric	Chain 1 1–642（642 aa）	Not recorded	ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
7ZSB Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP, complex C Deposited 2022-05-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric	Chain 1 1–642（642 aa）	Not recorded	ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.60 Å
8UOQ Composite map of PIC_delta_TFIIK form2 Deposited 2023-10-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain 1 1–642（642 aa）	Not recorded	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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain 1 1–642（642 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å

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

View Construct and Data Evidence

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

General transcription and DNA repair factor IIH subunit TFB4

OrganismNot specified

UniProt Q12004

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–DNA Heteromer Protein × 9 DNA 2 PDB declaration: undecameric（11） Consistent with all polymer counts	Chain 4； UniProt 1–338	Not recorded	DNA repair protein RAD33 × 1 （Q04231） General transcription and DNA repair factor IIH subunit TFB2 × 1 （Q02939） DNA repair helicase RAD3 × 1 （P06839） General transcription and DNA repair factor IIH subunit TFB1 × 1 （P32776） General transcription and DNA repair factor IIH subunit SSL1 × 1 （Q04673） Damaged DNA strand × 1 Undamaged DNA strand × 1 DNA repair protein RAD4 × 1 （P14736） DNA repair helicase RAD25 × 1 （Q00578） RNA polymerase II transcription factor B subunit 5 × 1 （Q3E7C1） 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

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 7K04	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5OQJ STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH Deposited 2017-08-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric	Chain 4 1–88（88 aa） Chain 4 115–256（142 aa） Chain 4 274–338（65 aa）	Not recorded	ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；GRIDS WERE BLOTTED FOR 8 S AND PLUNGE-FROZEN IN LIQUID ETHANE.	Resolution 4.70 Å
5OQM STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH AND CORE MEDIATOR Deposited 2017-08-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 44 PDB declaration: 46-meric	Chain 4 1–88（88 aa） Chain 4 120–256（137 aa） Chain 4 274–338（65 aa）	Not recorded	ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 8 s and plunge-frozen in liquid ethane.	Resolution 5.80 Å
6GYM Structure of a yeast closed complex with distorted DNA (CCdist) Deposited 2018-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric	Chain 4 1–88（88 aa） Chain 4 115–338（224 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 16 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.70 Å
7K01 Structure of TFIIH in TFIIH/Rad4-Rad23-Rad33 DNA opening complex Deposited 2020-09-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain 4 1–338（338 aa）	Not recorded	ZN ZINC ION × 5 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；Sample dialyzed for 30 minutes into above buffer prior to grid making cryo-EM vitrification conditions Cryogen ETHANE；Grids were manually blotted for 2-3 seconds prior to plunge freezing	Resolution 3.90 Å
7M2U Nucleotide Excision Repair complex TFIIH Rad4-33 Deposited 2021-03-17	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain 4 1–338（338 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 5 CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.20 Å
7O4I Yeast RNA polymerase II transcription pre-initiation complex with initial transcription bubble Deposited 2021-04-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain 4 1–338（338 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7O4J Yeast RNA polymerase II transcription pre-initiation complex (consensus) Deposited 2021-04-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain 4 1–338（338 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
7O4K Yeast TFIIH in the contracted state within the pre-initiation complex Deposited 2021-04-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric	Chain 4 1–338（338 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 10 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7O4L Yeast TFIIH in the expanded state within the pre-initiation complex Deposited 2021-04-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric	Chain 4 1–338（338 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 11 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7O72 Yeast RNA polymerase II transcription pre-initiation complex with closed promoter DNA Deposited 2021-04-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain 4 1–338（338 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7O73 Yeast RNA polymerase II transcription pre-initiation complex with closed distorted promoter DNA Deposited 2021-04-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain 4 1–338（338 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7O75 Yeast RNA polymerase II transcription pre-initiation complex with open promoter DNA Deposited 2021-04-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain 4 1–338（338 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7ZS9 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome (complex A) Deposited 2022-05-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric	Chain 4 1–338（338 aa）	Not recorded	ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
7ZSA Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP (complex B) Deposited 2022-05-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric	Chain 4 1–338（338 aa）	Not recorded	ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
7ZSB Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP, complex C Deposited 2022-05-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric	Chain 4 1–338（338 aa）	Not recorded	ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.60 Å
8UOQ Composite map of PIC_delta_TFIIK form2 Deposited 2023-10-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain 4 1–338（338 aa）	Not recorded	ZN ZINC ION × 15 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
8UOT Composite map of PICdeltaTFIIK form1 Deposited 2023-10-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain 4 1–338（338 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å

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

View Construct and Data Evidence

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

General transcription and DNA repair factor IIH subunit SSL1

OrganismNot specified

UniProt Q04673

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–DNA Heteromer Protein × 9 DNA 2 PDB declaration: undecameric（11） Consistent with all polymer counts	Chain 6； UniProt 1–461	Not recorded	DNA repair protein RAD33 × 1 （Q04231） General transcription and DNA repair factor IIH subunit TFB2 × 1 （Q02939） DNA repair helicase RAD3 × 1 （P06839） General transcription and DNA repair factor IIH subunit TFB1 × 1 （P32776） General transcription and DNA repair factor IIH subunit TFB4 × 1 （Q12004） Damaged DNA strand × 1 Undamaged DNA strand × 1 DNA repair protein RAD4 × 1 （P14736） DNA repair helicase RAD25 × 1 （Q00578） RNA polymerase II transcription factor B subunit 5 × 1 （Q3E7C1） 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

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 7K04	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4WFQ Crystal structure of TFIIH subunit Deposited 2014-09-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 119–310（192 aa）	Not recorded	SO4 SULFATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；PEG	Resolution 2.40 Å R-free 0.214
5OQJ STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH Deposited 2017-08-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric	Chain 6 1–307（307 aa） Chain 6 325–372（48 aa） Chain 6 387–411（25 aa） Chain 6 425–461（37 aa）	Not recorded	ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；GRIDS WERE BLOTTED FOR 8 S AND PLUNGE-FROZEN IN LIQUID ETHANE.	Resolution 4.70 Å
5OQM STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH AND CORE MEDIATOR Deposited 2017-08-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 44 PDB declaration: 46-meric	Chain 6 1–307（307 aa） Chain 6 325–372（48 aa） Chain 6 387–411（25 aa） Chain 6 425–461（37 aa）	Not recorded	ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 8 s and plunge-frozen in liquid ethane.	Resolution 5.80 Å
6GYM Structure of a yeast closed complex with distorted DNA (CCdist) Deposited 2018-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric	Chain 6 1–307（307 aa） Chain 6 325–372（48 aa） Chain 6 387–411（25 aa） Chain 6 425–461（37 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 16 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.70 Å
7K01 Structure of TFIIH in TFIIH/Rad4-Rad23-Rad33 DNA opening complex Deposited 2020-09-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain 6 1–461（461 aa）	Not recorded	ZN ZINC ION × 5 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；Sample dialyzed for 30 minutes into above buffer prior to grid making cryo-EM vitrification conditions Cryogen ETHANE；Grids were manually blotted for 2-3 seconds prior to plunge freezing	Resolution 3.90 Å
7M2U Nucleotide Excision Repair complex TFIIH Rad4-33 Deposited 2021-03-17	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain 6 1–461（461 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 5 CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.20 Å
7O4I Yeast RNA polymerase II transcription pre-initiation complex with initial transcription bubble Deposited 2021-04-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain 6 1–461（461 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7O4J Yeast RNA polymerase II transcription pre-initiation complex (consensus) Deposited 2021-04-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain 6 1–461（461 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
7O4K Yeast TFIIH in the contracted state within the pre-initiation complex Deposited 2021-04-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric	Chain 6 1–461（461 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 10 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7O4L Yeast TFIIH in the expanded state within the pre-initiation complex Deposited 2021-04-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric	Chain 6 1–461（461 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 11 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7O72 Yeast RNA polymerase II transcription pre-initiation complex with closed promoter DNA Deposited 2021-04-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain 6 1–461（461 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7O73 Yeast RNA polymerase II transcription pre-initiation complex with closed distorted promoter DNA Deposited 2021-04-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain 6 1–461（461 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7O75 Yeast RNA polymerase II transcription pre-initiation complex with open promoter DNA Deposited 2021-04-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain 6 1–461（461 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7ZS9 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome (complex A) Deposited 2022-05-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric	Chain 6 1–461（461 aa）	Not recorded	ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
7ZSA Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP (complex B) Deposited 2022-05-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric	Chain 6 1–461（461 aa）	Not recorded	ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
7ZSB Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP, complex C Deposited 2022-05-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric	Chain 6 1–461（461 aa）	Not recorded	ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.60 Å
8UOQ Composite map of PIC_delta_TFIIK form2 Deposited 2023-10-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain 6 1–461（461 aa）	Not recorded	ZN ZINC ION × 15 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
8UOT Composite map of PICdeltaTFIIK form1 Deposited 2023-10-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain 6 1–461（461 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å

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

View Construct and Data Evidence

UniProt name	SSL1_YEAST
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain 6； PDBConstruct 1–461； UniProt 1–461

DNA repair protein RAD4

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P14736

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 × 9 DNA 2 PDB declaration: undecameric（11） Consistent with all polymer counts	Chain A； UniProt 1–754	Not recorded	DNA repair protein RAD33 × 1 （Q04231） General transcription and DNA repair factor IIH subunit TFB2 × 1 （Q02939） DNA repair helicase RAD3 × 1 （P06839） General transcription and DNA repair factor IIH subunit TFB1 × 1 （P32776） General transcription and DNA repair factor IIH subunit TFB4 × 1 （Q12004） General transcription and DNA repair factor IIH subunit SSL1 × 1 （Q04673） Damaged DNA strand × 1 Undamaged DNA strand × 1 DNA repair helicase RAD25 × 1 （Q00578） RNA polymerase II transcription factor B subunit 5 × 1 （Q3E7C1） 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

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 7K04	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2M14 NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and Rad4 Deposited 2012-11-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 76–115（40 aa） Fragment：UNP residues 76-115	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 20；Pressure ambient NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Tfb1, 1.25 mM Rad4, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Tfb1, 1.25 mM Rad4, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 100% D2O | 100% D2O NMR sample composition 1 mM [U-100% 15N] Tfb1, 1.25 mM Rad4, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition 1.25 mM Tfb1, 1 mM [U-100% 13C; U-100% 15N] Rad4, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition 1.25 mM Tfb1, 1 mM [U-100% 13C; U-100% 15N] Rad4, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 100% D2O | 100% D2O NMR sample composition 1.25 mM Tfb1, 1 mM [U-100% 15N] Rad4, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O	Resolution not provided
2QSF Crystal structure of the Rad4-Rad23 complex Deposited 2007-07-31	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 101–632（532 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；100 mM sodium phosphate, 8% (w/v) PEG 2000, 2 mM dithiothreitol, pH 6.5, hanging-drop vapor diffusion, temperature 277K, VAPOR DIFFUSION, HANGING DROP	Resolution 2.35 Å R-free 0.245
2QSG Crystal structure of Rad4-Rad23 bound to a UV-damaged DNA Deposited 2007-07-31	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 101–632（532 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；50 mM bis-tris propane, 100mM sodium chloride, 6% (v/v) isopropanol, 14 mM calcium chloride and 5 mM dithiothreitol, pH 6.8, hanging-drop vapor diffusion, temperature 277K, VAPOR DIFFUSION, HANGING DROP	Resolution 3.10 Å R-free 0.277
2QSH Crystal structure of Rad4-Rad23 bound to a mismatch DNA Deposited 2007-07-31	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 101–632（532 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；50 mM bis-tris propane, 100 mM sodium chloride, 15% (v/v) isopropanol, 10 mM calcium chloride and 5 mM dithiothreitol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.81 Å R-free 0.244
4YIR Crystal structure of Rad4-Rad23 crosslinked to an undamaged DNA Deposited 2015-03-02	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 101–632（532 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；50mM BTP-HCl, 100mM NaCl, 14% isopropanol and 100mM calcium chloride	Resolution 3.05 Å R-free 0.253
6CFI Crystal structure of Rad4-Rad23 bound to a 6-4 photoproduct UV lesion Deposited 2018-02-15	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 101–632（532 aa） Fragment：residues 101-632	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；bis-tris propane 5 mM sodium chloride 100 mM 1-propanol 14% spermidine-HCl 5 mM dithiothreitol 5 mM	Resolution 3.36 Å R-free 0.268
6UBF Role of Beta-hairpin motifs in the DNA duplex opening by the Rad4/XPC nucleotide excision repair complex Deposited 2019-09-11	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 101–632（532 aa） Fragment：UNP residues 101-632	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；50 mM BTP-HCl, 150 mM sodium chloride, 12% isopropanol	Resolution 4.60 Å R-free 0.356
6UG1 Sequence impact in DNA duplex opening by the Rad4/XPC nucleotide excision repair complex Deposited 2019-09-25	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 129–632（504 aa） Fragment：UNP residues 129-632	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；50 mM BTP-HCl, 150 mM sodium chloride, 12% isopropanol, 100 mM calcium chloride	Resolution 2.83 Å R-free 0.272
6UIN Role of Beta-hairpin motifs in the DNA duplex opening by the Rad4/XPC nucleotide excision repair complex Deposited 2019-10-01	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 101–632（532 aa） Fragment：UNP residues 101-632	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；50 mM BTP-HCl, 200 mM sodium chloride, 12% isopropanol, 100 mM calcium chloride	Resolution 3.35 Å R-free 0.262
7M2U Nucleotide Excision Repair complex TFIIH Rad4-33 Deposited 2021-03-17	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain A 1–754（754 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

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RAD4_YEAST
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain A； PDBConstruct 1–754； UniProt 1–754

DNA repair helicase RAD25

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q00578

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–DNA Heteromer Protein × 9 DNA 2 PDB declaration: undecameric（11） Consistent with all polymer counts	Chain 7； UniProt 1–843	Not recorded	DNA repair protein RAD33 × 1 （Q04231） General transcription and DNA repair factor IIH subunit TFB2 × 1 （Q02939） DNA repair helicase RAD3 × 1 （P06839） General transcription and DNA repair factor IIH subunit TFB1 × 1 （P32776） General transcription and DNA repair factor IIH subunit TFB4 × 1 （Q12004） General transcription and DNA repair factor IIH subunit SSL1 × 1 （Q04673） Damaged DNA strand × 1 Undamaged DNA strand × 1 DNA repair protein RAD4 × 1 （P14736） RNA polymerase II transcription factor B subunit 5 × 1 （Q3E7C1） 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

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 7K04	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
7M2U Nucleotide Excision Repair complex TFIIH Rad4-33 Deposited 2021-03-17	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain 7 1–843（843 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 5 CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.20 Å
7ML0 RNA polymerase II pre-initiation complex (PIC1) Deposited 2021-04-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric	Chain 7 1–843（843 aa）	Not recorded	ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
7ML1 RNA polymerase II pre-initiation complex (PIC2) Deposited 2021-04-27	Different oligomeric state Different ligand/ion Different 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 × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
7ML2 RNA polymerase II pre-initiation complex (PIC3) Deposited 2021-04-27	Different oligomeric state Different ligand/ion Different 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 × 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 experimental conditions 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 experimental conditions 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 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 × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7O4J Yeast RNA polymerase II transcription pre-initiation complex (consensus) Deposited 2021-04-06	Different oligomeric state Different ligand/ion Different experimental 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 × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
7O4K Yeast TFIIH in the contracted state within the pre-initiation complex Deposited 2021-04-06	Different oligomeric state Different ligand/ion Different experimental conditions 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 experimental conditions 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 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 × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7O73 Yeast RNA polymerase II transcription pre-initiation complex with closed distorted promoter DNA Deposited 2021-04-12	Different oligomeric state Different ligand/ion Different experimental 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 × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7O75 Yeast RNA polymerase II transcription pre-initiation complex with open promoter DNA Deposited 2021-04-13	Different oligomeric state Different ligand/ion Different experimental 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 × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7ZS9 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome (complex A) Deposited 2022-05-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric	Chain 7 1–843（843 aa）	Not recorded	ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
7ZSA Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP (complex B) Deposited 2022-05-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric	Chain 7 1–843（843 aa）	Not recorded	ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
7ZSB Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP, complex C Deposited 2022-05-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric	Chain 7 1–843（843 aa）	Not recorded	ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.60 Å
8CEN Yeast RNA polymerase II transcription pre-initiation complex with core Mediator Deposited 2023-02-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 44 PDB declaration: 46-meric	Chain 7 1–843（843 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8CEO Yeast RNA polymerase II transcription pre-initiation complex with core Mediator and the +1 nucleosome Deposited 2023-02-02	Different oligomeric state Different ligand/ion Different experimental conditions 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 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 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	10
Chains and sequence ranges	Author chain 7； PDBConstruct 1–843； UniProt 1–843

RNA polymerase II transcription factor B subunit 5

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q3E7C1

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–DNA Heteromer Protein × 9 DNA 2 PDB declaration: undecameric（11） Consistent with all polymer counts	Chain 5； UniProt 1–72	Not recorded	DNA repair protein RAD33 × 1 （Q04231） General transcription and DNA repair factor IIH subunit TFB2 × 1 （Q02939） DNA repair helicase RAD3 × 1 （P06839） General transcription and DNA repair factor IIH subunit TFB1 × 1 （P32776） General transcription and DNA repair factor IIH subunit TFB4 × 1 （Q12004） General transcription and DNA repair factor IIH subunit SSL1 × 1 （Q04673） Damaged DNA strand × 1 Undamaged DNA strand × 1 DNA repair protein RAD4 × 1 （P14736） DNA repair helicase RAD25 × 1 （Q00578） 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

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 7K04	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
7M2U Nucleotide Excision Repair complex TFIIH Rad4-33 Deposited 2021-03-17	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain 5 2–67（66 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 5 CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.20 Å
7ML0 RNA polymerase II pre-initiation complex (PIC1) Deposited 2021-04-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric	Chain 5 1–72（72 aa）	Not recorded	ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
7ML1 RNA polymerase II pre-initiation complex (PIC2) Deposited 2021-04-27	Different oligomeric state Different ligand/ion Different 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 × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
7ML2 RNA polymerase II pre-initiation complex (PIC3) Deposited 2021-04-27	Different oligomeric state Different ligand/ion Different 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 × 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 experimental conditions 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 experimental conditions 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 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 × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7O4J Yeast RNA polymerase II transcription pre-initiation complex (consensus) Deposited 2021-04-06	Different oligomeric state Different ligand/ion Different experimental 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 × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
7O4K Yeast TFIIH in the contracted state within the pre-initiation complex Deposited 2021-04-06	Different oligomeric state Different ligand/ion Different experimental conditions 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 experimental conditions 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 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 × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7O73 Yeast RNA polymerase II transcription pre-initiation complex with closed distorted promoter DNA Deposited 2021-04-12	Different oligomeric state Different ligand/ion Different experimental 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 × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7O75 Yeast RNA polymerase II transcription pre-initiation complex with open promoter DNA Deposited 2021-04-13	Different oligomeric state Different ligand/ion Different experimental 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 × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7ZS9 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome (complex A) Deposited 2022-05-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric	Chain 5 1–72（72 aa）	Not recorded	ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
7ZSA Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP (complex B) Deposited 2022-05-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric	Chain 5 1–72（72 aa）	Not recorded	ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
7ZSB Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP, complex C Deposited 2022-05-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric	Chain 5 1–72（72 aa）	Not recorded	ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.60 Å
8UMH Consensus map of PICdeltaTFIIK form2 Deposited 2023-10-17	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain 5 1–72（72 aa）	Not recorded	ZN ZINC ION × 15 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
8UMI consensus map of PICdeltaTFIIK form1 Deposited 2023-10-17	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain 5 1–72（72 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
8UOQ Composite map of PIC_delta_TFIIK form2 Deposited 2023-10-20	Different oligomeric state Different ligand/ion Different 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 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	11
Chains and sequence ranges	Author chain 5； PDBConstruct 1–72； UniProt 1–72

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.