← Back to search
7ml1

RNA polymerase II pre-initiation complex (PIC2)

Method: ELECTRON MICROSCOPY Dmax: 275.2 Å Quality: GOOD
▼

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

General transcription and DNA repair factor IIH helicase subunit XPD

OrganismNot specified

UniProt A0A6A5Q1C1

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 28 DNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain 0； UniProt 1–778 Not recorded Tfb1 × 1 General transcription and DNA repair factor IIH subunit TFB4 × 1 General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） TATA-box-binding protein × 1 （P13393） non-template strand DNA × 1 template strand DNA × 1 DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIA large subunit × 1 （A0A6A5Q2T8） Transcription initiation factor IIA subunit 2 × 1 （A0A6A5PRZ0） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） 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

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 7ML1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7ML0 RNA polymerase II pre-initiation complex (PIC1) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain 0 1–778（778 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ML2 RNA polymerase II pre-initiation complex (PIC3) Deposited 2021-04-27 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 0 1–778（778 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7ML3 General transcription factor TFIIH (weak binding) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain 0 1–778（778 aa）
Not recorded ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
7ML4 RNA polymerase II initially transcribing complex (ITC) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 28 PDB declaration: 31-meric
Chain 0 1–778（778 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8UMH Consensus map of PICdeltaTFIIK form2 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 0 1–778（778 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8UMI consensus map of PICdeltaTFIIK form1 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 0 1–778（778 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å

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

View Construct and Data Evidence
UniProt name A0A6A5Q1C1_YEASX
Isoform —
PDB entities 3
Chains and sequence ranges Author chain 0； PDBConstruct 1–778； UniProt 1–778

RNA polymerase II transcription factor B subunit 2

OrganismNot specified

UniProt A0A6A5Q2X3

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 28 DNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain 2； UniProt 1–513 Not recorded Tfb1 × 1 General transcription and DNA repair factor IIH subunit TFB4 × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） General transcription and DNA repair factor IIH subunit SSL1 × 1 General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） TATA-box-binding protein × 1 （P13393） non-template strand DNA × 1 template strand DNA × 1 DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIA large subunit × 1 （A0A6A5Q2T8） Transcription initiation factor IIA subunit 2 × 1 （A0A6A5PRZ0） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） 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

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 7ML1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7ML0 RNA polymerase II pre-initiation complex (PIC1) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain 2 1–513（513 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ML2 RNA polymerase II pre-initiation complex (PIC3) Deposited 2021-04-27 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 2 1–513（513 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7ML3 General transcription factor TFIIH (weak binding) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain 2 1–513（513 aa）
Not recorded ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
7ML4 RNA polymerase II initially transcribing complex (ITC) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 28 PDB declaration: 31-meric
Chain 2 1–513（513 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8CEO Yeast RNA polymerase II transcription pre-initiation complex with core Mediator and the +1 nucleosome Deposited 2023-02-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 52 PDB declaration: 54-meric
Chain 2 1–513（513 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8UMH Consensus map of PICdeltaTFIIK form2 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 2 1–513（513 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8UMI consensus map of PICdeltaTFIIK form1 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 2 1–513（513 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å

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

View Construct and Data Evidence
UniProt name A0A6A5Q2X3_YEASX
Isoform —
PDB entities 5
Chains and sequence ranges Author chain 2； PDBConstruct 1–513； UniProt 1–513

General transcription and DNA repair factor IIH subunit TFB5

OrganismNot specified

UniProt Q3E7C1

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 28 DNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain 5； UniProt 1–72 Not recorded Tfb1 × 1 General transcription and DNA repair factor IIH subunit TFB4 × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） TATA-box-binding protein × 1 （P13393） non-template strand DNA × 1 template strand DNA × 1 DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIA large subunit × 1 （A0A6A5Q2T8） Transcription initiation factor IIA subunit 2 × 1 （A0A6A5PRZ0） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） 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

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 7ML1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3DGP Crystal Structure of the complex between Tfb5 and the C-terminal domain of Tfb2 Deposited 2008-06-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–72（71 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8.9；277 K；Tris 20 mM, NaCl 50 mM, pH 8.9, EVAPORATION, temperature 277K
Resolution 1.80 Å R-free 0.237
3DOM Crystal Structure of the complex between Tfb5 and the C-terminal domain of Tfb2 Deposited 2008-07-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–72（71 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PEG3350 MME, NaCl, Hepes, pH 7.5, vapor diffusion, sitting drop, temperature 293K
Resolution 2.60 Å R-free 0.261
3DOM Crystal Structure of the complex between Tfb5 and the C-terminal domain of Tfb2 Deposited 2008-07-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2–72（71 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PEG3350 MME, NaCl, Hepes, pH 7.5, vapor diffusion, sitting drop, temperature 293K
Resolution 2.60 Å R-free 0.261
5FMF the P-lobe of RNA polymerase II pre-initiation complex Deposited 2015-11-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain X 2–64（63 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer 20 MM HEPES (PH7.6), 5 MM DTT, 2 MM MG(OAC)2,AND 40 MM KOAC；pH 7.6；20 MM HEPES (PH7.6), 5 MM DTT, 2 MM MG(OAC)2,AND 40 MM KOAC
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 120, INSTRUMENT- FEI VITROBOT MARK III,
Resolution 6.00 Å
5OQJ STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH Deposited 2017-08-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 5 1–72（72 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；GRIDS WERE BLOTTED FOR 8 S AND PLUNGE-FROZEN IN LIQUID ETHANE.
Resolution 4.70 Å
5OQM STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH AND CORE MEDIATOR Deposited 2017-08-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 44 PDB declaration: 46-meric
Chain 5 1–72（72 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 8 s and plunge-frozen in liquid ethane.
Resolution 5.80 Å
5SVA Mediator-RNA Polymerase II Pre-Initiation Complex Deposited 2016-08-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric
Chain b 1–72（72 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 15.30 Å
6GYM Structure of a yeast closed complex with distorted DNA (CCdist) Deposited 2018-06-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 5 1–72（72 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 16 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.70 Å
7K01 Structure of TFIIH in TFIIH/Rad4-Rad23-Rad33 DNA opening complex Deposited 2020-09-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain 5 1–72（72 aa）
Not recorded ZN ZINC ION × 5 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；Sample dialyzed for 30 minutes into above buffer prior to grid making
cryo-EM vitrification conditions Cryogen ETHANE；Grids were manually blotted for 2-3 seconds prior to plunge freezing
Resolution 3.90 Å
7K04 Structure of TFIIH/Rad4-Rad23-Rad33/DNA in DNA opening Deposited 2020-09-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain 5 1–72（72 aa）
Not recorded CA CALCIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Manually blotted by Leica EM CPC
Resolution 9.25 Å
7M2U Nucleotide Excision Repair complex TFIIH Rad4-33 Deposited 2021-03-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain 5 2–67（66 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 5 CA CALCIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.20 Å
7ML0 RNA polymerase II pre-initiation complex (PIC1) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain 5 1–72（72 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ML2 RNA polymerase II pre-initiation complex (PIC3) Deposited 2021-04-27 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 5 1–72（72 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7ML3 General transcription factor TFIIH (weak binding) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain 5 1–72（72 aa）
Not recorded ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
7ML4 RNA polymerase II initially transcribing complex (ITC) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 28 PDB declaration: 31-meric
Chain 5 1–72（72 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7O4I Yeast RNA polymerase II transcription pre-initiation complex with initial transcription bubble Deposited 2021-04-06 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 5 1–72（72 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7O4J Yeast RNA polymerase II transcription pre-initiation complex (consensus) Deposited 2021-04-06 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 5 1–72（72 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7O4K Yeast TFIIH in the contracted state within the pre-initiation complex Deposited 2021-04-06 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain 5 1–72（72 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 10 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7O4L Yeast TFIIH in the expanded state within the pre-initiation complex Deposited 2021-04-06 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain 5 1–72（72 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 11 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7O72 Yeast RNA polymerase II transcription pre-initiation complex with closed promoter DNA Deposited 2021-04-12 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 5 1–72（72 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7O73 Yeast RNA polymerase II transcription pre-initiation complex with closed distorted promoter DNA Deposited 2021-04-12 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 5 1–72（72 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7O75 Yeast RNA polymerase II transcription pre-initiation complex with open promoter DNA Deposited 2021-04-13 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 5 1–72（72 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7ZS9 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome (complex A) Deposited 2022-05-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain 5 1–72（72 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7ZSA Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP (complex B) Deposited 2022-05-06 Different oligomeric state Different ligand/ion Different experimental conditions 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 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 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 ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 5 1–72（72 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8UOT Composite map of PICdeltaTFIIK form1 Deposited 2023-10-20 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 5 1–72（72 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å

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

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

General transcription and DNA repair factor IIH helicase subunit XPB

OrganismNot specified

UniProt Q00578

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 28 DNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain 7； UniProt 1–843 Not recorded Tfb1 × 1 General transcription and DNA repair factor IIH subunit TFB4 × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） TATA-box-binding protein × 1 （P13393） non-template strand DNA × 1 template strand DNA × 1 DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIA large subunit × 1 （A0A6A5Q2T8） Transcription initiation factor IIA subunit 2 × 1 （A0A6A5PRZ0） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） 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

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 7ML1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5FMF the P-lobe of RNA polymerase II pre-initiation complex Deposited 2015-11-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain 1 294–785（492 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer 20 MM HEPES (PH7.6), 5 MM DTT, 2 MM MG(OAC)2,AND 40 MM KOAC；pH 7.6；20 MM HEPES (PH7.6), 5 MM DTT, 2 MM MG(OAC)2,AND 40 MM KOAC
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 120, INSTRUMENT- FEI VITROBOT MARK III,
Resolution 6.00 Å
5OQJ STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH Deposited 2017-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 7 1–425（425 aa）
Chain 7 452–462（11 aa）
Chain 7 482–843（362 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；GRIDS WERE BLOTTED FOR 8 S AND PLUNGE-FROZEN IN LIQUID ETHANE.
Resolution 4.70 Å
5OQM STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH AND CORE MEDIATOR Deposited 2017-08-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 44 PDB declaration: 46-meric
Chain 7 1–425（425 aa）
Chain 7 482–843（362 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 8 s and plunge-frozen in liquid ethane.
Resolution 5.80 Å
5SVA Mediator-RNA Polymerase II Pre-Initiation Complex Deposited 2016-08-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric
Chain Z 1–843（843 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 15.30 Å
6GYM Structure of a yeast closed complex with distorted DNA (CCdist) Deposited 2018-06-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 7 1–425（425 aa）
Chain 7 482–843（362 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 16 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.70 Å
7K01 Structure of TFIIH in TFIIH/Rad4-Rad23-Rad33 DNA opening complex Deposited 2020-09-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain 7 1–843（843 aa）
Not recorded ZN ZINC ION × 5 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；Sample dialyzed for 30 minutes into above buffer prior to grid making
cryo-EM vitrification conditions Cryogen ETHANE；Grids were manually blotted for 2-3 seconds prior to plunge freezing
Resolution 3.90 Å
7K04 Structure of TFIIH/Rad4-Rad23-Rad33/DNA in DNA opening Deposited 2020-09-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain 7 1–843（843 aa）
Not recorded CA CALCIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Manually blotted by Leica EM CPC
Resolution 9.25 Å
7M2U Nucleotide Excision Repair complex TFIIH Rad4-33 Deposited 2021-03-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain 7 1–843（843 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 5 CA CALCIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.20 Å
7ML0 RNA polymerase II pre-initiation complex (PIC1) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain 7 1–843（843 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ML2 RNA polymerase II pre-initiation complex (PIC3) Deposited 2021-04-27 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 7 1–843（843 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7ML3 General transcription factor TFIIH (weak binding) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain 7 1–843（843 aa）
Not recorded ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
7ML4 RNA polymerase II initially transcribing complex (ITC) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 28 PDB declaration: 31-meric
Chain 7 1–843（843 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7O4I Yeast RNA polymerase II transcription pre-initiation complex with initial transcription bubble Deposited 2021-04-06 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 7 1–843（843 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7O4J Yeast RNA polymerase II transcription pre-initiation complex (consensus) Deposited 2021-04-06 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 7 1–843（843 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7O4K Yeast TFIIH in the contracted state within the pre-initiation complex Deposited 2021-04-06 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain 7 1–843（843 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 10 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7O4L Yeast TFIIH in the expanded state within the pre-initiation complex Deposited 2021-04-06 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain 7 1–843（843 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 11 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7O72 Yeast RNA polymerase II transcription pre-initiation complex with closed promoter DNA Deposited 2021-04-12 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 7 1–843（843 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7O73 Yeast RNA polymerase II transcription pre-initiation complex with closed distorted promoter DNA Deposited 2021-04-12 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 7 1–843（843 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7O75 Yeast RNA polymerase II transcription pre-initiation complex with open promoter DNA Deposited 2021-04-13 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 7 1–843（843 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7ZS9 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome (complex A) Deposited 2022-05-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain 7 1–843（843 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7ZSA Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP (complex B) Deposited 2022-05-06 Different oligomeric state Different ligand/ion Different experimental conditions 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 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 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 ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 7 1–843（843 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8UOT Composite map of PICdeltaTFIIK form1 Deposited 2023-10-20 Different 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 7
Chains and sequence ranges Author chain 7； PDBConstruct 1–843； UniProt 1–843

BJ4_G0050160.mRNA.1.CDS.1

OrganismNot specified

UniProt A0A7I9BTI9

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 28 DNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain 3； UniProt 1–321 Not recorded Tfb1 × 1 General transcription and DNA repair factor IIH subunit TFB4 × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） TATA-box-binding protein × 1 （P13393） non-template strand DNA × 1 template strand DNA × 1 DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIA large subunit × 1 （A0A6A5Q2T8） Transcription initiation factor IIA subunit 2 × 1 （A0A6A5PRZ0） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） 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

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 7ML1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7ML0 RNA polymerase II pre-initiation complex (PIC1) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain 3 1–321（321 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ML2 RNA polymerase II pre-initiation complex (PIC3) Deposited 2021-04-27 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 3 1–321（321 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7ML3 General transcription factor TFIIH (weak binding) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain 3 1–321（321 aa）
Not recorded ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
7ML4 RNA polymerase II initially transcribing complex (ITC) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 28 PDB declaration: 31-meric
Chain 3 1–321（321 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8CEO Yeast RNA polymerase II transcription pre-initiation complex with core Mediator and the +1 nucleosome Deposited 2023-02-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 52 PDB declaration: 54-meric
Chain 3 1–321（321 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å

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

View Construct and Data Evidence
UniProt name A0A7I9BTI9_YEASX
Isoform —
PDB entities 8
Chains and sequence ranges Author chain 3； PDBConstruct 1–321； UniProt 1–321

TATA-box-binding protein

OrganismNot specified

UniProt P13393

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 28 DNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain O； UniProt 1–240 Not recorded Tfb1 × 1 General transcription and DNA repair factor IIH subunit TFB4 × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） non-template strand DNA × 1 template strand DNA × 1 DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIA large subunit × 1 （A0A6A5Q2T8） Transcription initiation factor IIA subunit 2 × 1 （A0A6A5PRZ0） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） 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

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 7ML1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1NGM Crystal structure of a yeast Brf1-TBP-DNA ternary complex Deposited 2002-12-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain A 60–239（180 aa） Fragment：C-terminal core domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；MES, NaCl, BME, glycerol, MgCl2, PEG2000MME, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.95 Å R-free 0.308
1NGM Crystal structure of a yeast Brf1-TBP-DNA ternary complex Deposited 2002-12-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain E 60–239（180 aa） Fragment：C-terminal core domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；MES, NaCl, BME, glycerol, MgCl2, PEG2000MME, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.95 Å R-free 0.308
1NGM Crystal structure of a yeast Brf1-TBP-DNA ternary complex Deposited 2002-12-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain I 60–239（180 aa） Fragment：C-terminal core domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；MES, NaCl, BME, glycerol, MgCl2, PEG2000MME, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.95 Å R-free 0.308
1NGM Crystal structure of a yeast Brf1-TBP-DNA ternary complex Deposited 2002-12-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain M 60–239（180 aa） Fragment：C-terminal core domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；MES, NaCl, BME, glycerol, MgCl2, PEG2000MME, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.95 Å R-free 0.308
1NH2 Crystal structure of a yeast TFIIA/TBP/DNA complex Deposited 2002-12-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 60–239（180 aa） Fragment：C-TERMINAL 180 RESIDUES
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.90 Å R-free 0.226
1RM1 Structure of a Yeast TFIIA/TBP/TATA-box DNA Complex Deposited 2003-11-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 1–239（239 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；PEG 4000, ammonium citrate, MES, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.50 Å R-free 0.252
1TBA SOLUTION STRUCTURE OF A TBP-TAFII230 COMPLEX: PROTEIN MIMICRY OF THE MINOR GROOVE SURFACE OF THE TATA BOX UNWOUND BY TBP, NMR, 25 STRUCTURES Deposited 1998-08-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 60–239（180 aa） Fragment：CORE DOMAIN RESIDUES 60-249
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K
Resolution not provided
1TBP CRYSTAL STRUCTURE OF YEAST TATA-BINDING PROTEIN AND MODEL FOR INTERACTION WITH DNA Deposited 1993-08-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 61–239（179 aa）
Chain B 61–239（179 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.60 Å
1YTB CRYSTAL STRUCTURE OF A YEAST TBP/TATA-BOX COMPLEX Deposited 1994-09-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric
Chain A 60–239（180 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 295.00K
Resolution 1.80 Å R-free 0.261
1YTB CRYSTAL STRUCTURE OF A YEAST TBP/TATA-BOX COMPLEX Deposited 1994-09-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric
Chain B 60–239（180 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 295.00K
Resolution 1.80 Å R-free 0.261
1YTF YEAST TFIIA/TBP/DNA COMPLEX Deposited 1996-04-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 60–239（180 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å R-free 0.297
4B0A The high-resolution structure of yTBP-yTAF1 identifies conserved and competing interaction surfaces in transcriptional activation Deposited 2012-06-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 61–240（180 aa） Fragment：TAF1 RESIDUES 8-71, LINKER, TBP RESIDUE 61-240
Mutation：YES CA CALCIUM ION × 3 GOL GLYCEROL × 6 CL CHLORIDE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.97 Å R-free 0.223
4V1N Architecture of the RNA polymerase II-Mediator core transcription initiation complex Deposited 2014-09-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: nonadecameric
Chain O 61–240（180 aa） Fragment：RESIDUES 61-240
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer 25 MM HEPES-KOH PH 7.5, 180 MM POTASSIUM ACETATE, 5 % GLYCEROL, 5 MM DTT；pH 7.5；25 MM HEPES-KOH PH 7.5, 180 MM POTASSIUM ACETATE, 5 % GLYCEROL, 5 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；GRIDS WERE GLOW- DISCHARGED FOR 20 S BEFORE DEPOSITION OF 4 MICROLITERS SAMPLE AND INCUBATED FOR 30 S. GRIDS WERE WASHED TWICE WITH 4 MICROLITERS DISTILLED WATER, BLOTTED, AND VITRIFIED BY PLUNGING INTO LIQUID ETHANE WITH A MANUAL PLUNGER.
Resolution 7.80 Å
4V1O Architecture of the RNA polymerase II-Mediator core transcription initiation complex Deposited 2014-09-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain O 61–240（180 aa） Fragment：RESIDUES 61-240
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer 25 MM HEPES-KOH PH 7.5, 180 MM POTASSIUM ACETATE, 5 % GLYCEROL, 5 MM DTT；pH 7.5；25 MM HEPES-KOH PH 7.5, 180 MM POTASSIUM ACETATE, 5 % GLYCEROL, 5 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；GRIDS WERE GLOW- DISCHARGED FOR 20 S BEFORE DEPOSITION OF 4 MICROLITERS SAMPLE AND INCUBATED FOR 30 S. GRIDS WERE WASHED TWICE WITH 4 MICROLITERS DISTILLED WATER, BLOTTED, AND VITRIFIED BY PLUNGING INTO LIQUID ETHANE WITH A MANUAL PLUNGER.
Resolution 9.70 Å
5FMF the P-lobe of RNA polymerase II pre-initiation complex Deposited 2015-11-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain Q 61–240（180 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer 20 MM HEPES (PH7.6), 5 MM DTT, 2 MM MG(OAC)2,AND 40 MM KOAC；pH 7.6；20 MM HEPES (PH7.6), 5 MM DTT, 2 MM MG(OAC)2,AND 40 MM KOAC
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 120, INSTRUMENT- FEI VITROBOT MARK III,
Resolution 6.00 Å
5FYW Transcription initiation complex structures elucidate DNA opening (OC) Deposited 2016-03-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain O 1–240（240 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer 25 MM HEPES-KOH PH 7.5, 150 MM POTASSIUM ACETATE, 2 MM MGCL2, 5 MM DTT；pH 7.5；25 MM HEPES-KOH PH 7.5, 150 MM POTASSIUM ACETATE, 2 MM MGCL2, 5 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；CRYOGEN - ETHANE. INSTRUMENT - FEI VITROBOT MARK IV. QUANTIFOIL R 3.5- 1 HOLEY CARBON GRIDS WERE GLOW-DISCHARGED BEFORE DEPOSITION OF 4.5 MICROLITERS OF SAMPLE. GRIDS WERE THEN BLOTTED FOR 8.5 S AND PLUNGE- FROZEN IN LIQUID ETHANE.
Resolution 4.35 Å
5FZ5 Transcription initiation complex structures elucidate DNA opening (CC) Deposited 2016-03-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain O 1–240（240 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer 25 MM HEPES-KOH PH 7.5, 150 MM POTASSIUM ACETATE, 2 MM MGCL2, 5 MM DTT；pH 7.5；25 MM HEPES-KOH PH 7.5, 150 MM POTASSIUM ACETATE, 2 MM MGCL2, 5 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE
Resolution 8.80 Å
5OQJ STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH Deposited 2017-08-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain O 1–240（240 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；GRIDS WERE BLOTTED FOR 8 S AND PLUNGE-FROZEN IN LIQUID ETHANE.
Resolution 4.70 Å
5OQM STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH AND CORE MEDIATOR Deposited 2017-08-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 44 PDB declaration: 46-meric
Chain O 1–240（240 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 8 s and plunge-frozen in liquid ethane.
Resolution 5.80 Å
5SVA Mediator-RNA Polymerase II Pre-Initiation Complex Deposited 2016-08-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric
Chain j 1–240（240 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 15.30 Å
6CNB Yeast RNA polymerase III initial transcribing complex Deposited 2018-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 19 PDB declaration: 21-meric
Chain R 61–240（180 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6CNC Yeast RNA polymerase III open complex Deposited 2018-03-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 19 PDB declaration: 21-meric
Chain R 61–240（180 aa）
Mutation：C438S ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6CND Yeast RNA polymerase III natural open complex (nOC) Deposited 2018-03-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 19 PDB declaration: 21-meric
Chain R 61–240（180 aa）
Mutation：C438S ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
6CNF Yeast RNA polymerase III elongation complex Deposited 2018-03-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 19 PDB declaration: 21-meric
Chain R 61–240（180 aa）
Mutation：C438S ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6E16 Ternary structure of c-Myc-TBP-TAF1 Deposited 2018-07-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 61–240（180 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions BATCH MODE；291 K；20% (w/w) PEG8000, 0.2M ammonium sulfare, and 0.1M HEPES pH7.5
Resolution 2.40 Å R-free 0.220
6E24 Ternary structure of c-Myc-TBP-TAF1 Deposited 2018-07-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 61–240（180 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；293 K；16% W/V PEG3350 0.05M CITRIC ACID 0.05M BIS-TRIS PROPANE pH5.0
Resolution 3.00 Å R-free 0.224
6EU0 RNA Polymerase III open pre-initiation complex (OC-PIC) Deposited 2017-10-27 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain Y 1–240（240 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6F40 RNA Polymerase III open complex Deposited 2017-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain U 1–240（240 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6F41 RNA Polymerase III initially transcribing complex Deposited 2017-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain U 1–240（240 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6F42 RNA Polymerase III closed complex CC1. Deposited 2017-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain U 1–240（240 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.50 Å
6F44 RNA Polymerase III closed complex CC2. Deposited 2017-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain U 1–240（240 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6GYK Structure of a yeast closed complex (core CC1) Deposited 2018-06-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain O 1–240（240 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
6GYL Structure of a yeast closed complex with distorted DNA (core CCdist) Deposited 2018-06-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain O 1–240（240 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
6GYM Structure of a yeast closed complex with distorted DNA (CCdist) Deposited 2018-06-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain O 1–240（240 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 16 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.70 Å
7ML0 RNA polymerase II pre-initiation complex (PIC1) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain O 1–240（240 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ML4 RNA polymerase II initially transcribing complex (ITC) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 28 PDB declaration: 31-meric
Chain O 1–240（240 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7O4I Yeast RNA polymerase II transcription pre-initiation complex with initial transcription bubble Deposited 2021-04-06 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain O 1–240（240 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7O4J Yeast RNA polymerase II transcription pre-initiation complex (consensus) Deposited 2021-04-06 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain O 1–240（240 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7O72 Yeast RNA polymerase II transcription pre-initiation complex with closed promoter DNA Deposited 2021-04-12 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain O 1–240（240 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7O73 Yeast RNA polymerase II transcription pre-initiation complex with closed distorted promoter DNA Deposited 2021-04-12 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain O 1–240（240 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7O75 Yeast RNA polymerase II transcription pre-initiation complex with open promoter DNA Deposited 2021-04-13 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain O 1–240（240 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7Q5B Cryo-EM structure of Ty3 retrotransposon targeting a TFIIIB-bound tRNA gene Deposited 2021-11-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: tridecameric
Chain Y 1–240（240 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.98 Å
7Z0O Structure of transcription factor UAF in complex with TBP and 35S rRNA promoter DNA Deposited 2022-02-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain H 1–240（240 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7ZS9 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome (complex A) Deposited 2022-05-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain O 1–240（240 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7ZSA Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP (complex B) Deposited 2022-05-06 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain O 1–240（240 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7ZSB Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP, complex C Deposited 2022-05-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain O 1–240（240 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.60 Å
8FFZ TFIIIA-TFIIIC-Brf1-TBP complex bound to 5S rRNA gene Deposited 2022-12-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: decameric
Chain H 61–240（180 aa）
Not recorded ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8H5B The cryo-EM structure of nuclear transport receptor Kap114p complex with yeast TATA-box binding protein Deposited 2022-10-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 61–240（180 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.03 Å
8UMH Consensus map of PICdeltaTFIIK form2 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain O 1–240（240 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8UMI consensus map of PICdeltaTFIIK form1 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain O 1–240（240 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8UOQ Composite map of PIC_delta_TFIIK form2 Deposited 2023-10-20 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain O 1–240（240 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8UOT Composite map of PICdeltaTFIIK form1 Deposited 2023-10-20 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain O 1–240（240 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å

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

View Construct and Data Evidence
UniProt name TBP_YEAST
Isoform —
PDB entities 9
Chains and sequence ranges Author chain O； PDBConstruct 1–240； UniProt 1–240

DNA-directed RNA polymerase subunit

OrganismNot specified

UniProt A0A6A5Q1P2

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 × 28 DNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain A； UniProt 1–1733 Not recorded Tfb1 × 1 General transcription and DNA repair factor IIH subunit TFB4 × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） TATA-box-binding protein × 1 （P13393） non-template strand DNA × 1 template strand DNA × 1 DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIA large subunit × 1 （A0A6A5Q2T8） Transcription initiation factor IIA subunit 2 × 1 （A0A6A5PRZ0） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） 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

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 7ML1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7MEI Composite structure of EC+EC Deposited 2021-04-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 30-meric
Chain A 1–1733（1733 aa）
Chain a 1–1733（1733 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7MK9 Complex structure of trailing EC of EC+EC (trailing EC-focused) Deposited 2021-04-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain A 1–1733（1733 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7MKA Structure of EC+EC (leading EC-focused) Deposited 2021-04-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain a 1–1733（1733 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7ML0 RNA polymerase II pre-initiation complex (PIC1) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain A 1–1733（1733 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ML2 RNA polymerase II pre-initiation complex (PIC3) Deposited 2021-04-27 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain A 1–1733（1733 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7ML4 RNA polymerase II initially transcribing complex (ITC) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 28 PDB declaration: 31-meric
Chain A 1–1733（1733 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8TVS Cryo-EM structure of backtracked Pol II in complex with Rad26 Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric
Chain A 1–1733（1733 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
8UMH Consensus map of PICdeltaTFIIK form2 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain A 1–1733（1733 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8UMI consensus map of PICdeltaTFIIK form1 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain A 1–1733（1733 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å

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

View Construct and Data Evidence
UniProt name A0A6A5Q1P2_YEASX
Isoform —
PDB entities 12
Chains and sequence ranges Author chain A； PDBConstruct 1–1733； UniProt 1–1733

DNA-directed RNA polymerase subunit beta

OrganismNot specified

UniProt A0A6A5Q4H2

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 28 DNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain B； UniProt 1–1224 Not recorded Tfb1 × 1 General transcription and DNA repair factor IIH subunit TFB4 × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） TATA-box-binding protein × 1 （P13393） non-template strand DNA × 1 template strand DNA × 1 DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIA large subunit × 1 （A0A6A5Q2T8） Transcription initiation factor IIA subunit 2 × 1 （A0A6A5PRZ0） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） 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

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 7ML1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7MEI Composite structure of EC+EC Deposited 2021-04-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 30-meric
Chain B 1–1224（1224 aa）
Chain b 1–1224（1224 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7MK9 Complex structure of trailing EC of EC+EC (trailing EC-focused) Deposited 2021-04-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain B 1–1224（1224 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7MKA Structure of EC+EC (leading EC-focused) Deposited 2021-04-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain b 1–1224（1224 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7ML0 RNA polymerase II pre-initiation complex (PIC1) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain B 1–1224（1224 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ML2 RNA polymerase II pre-initiation complex (PIC3) Deposited 2021-04-27 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain B 1–1224（1224 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7ML4 RNA polymerase II initially transcribing complex (ITC) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 28 PDB declaration: 31-meric
Chain B 1–1224（1224 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8TUG Cryo-EM structure of CPD-stalled Pol II in complex with Rad26 (engaged state) Deposited 2023-08-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric
Chain B 1–1224（1224 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8TVP Cryo-EM structure of CPD-stalled Pol II in complex with Rad26 (open state) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric
Chain B 1–1224（1224 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8TVQ Cryo-EM structure of CPD stalled 10-subunit Pol II in complex with Rad26 Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 11 PDB declaration: 14-meric
Chain B 1–1224（1224 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8TVS Cryo-EM structure of backtracked Pol II in complex with Rad26 Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric
Chain B 1–1224（1224 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
8TVV Cryo-EM structure of backtracked Pol II Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain B 1–1224（1224 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8TVW Cryo-EM structure of CPD-stalled Pol II (conformation 1) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain B 1–1224（1224 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8TVX Cryo-EM structure of CPD-stalled Pol II (Conformation 2) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain B 1–1224（1224 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8TVY Cryo-EM structure of CPD lesion containing RNA Polymerase II elongation complex with Rad26 and Elf1 (closed state) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: 17-meric
Chain B 1–1224（1224 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8U9R STRUCTURAL BASIS OF TRANSCRIPTION: RNA POLYMERASE II SUBSTRATE BINDING AND METAL COORDINATION USING A FREE-ELECTRON LASER Deposited 2023-09-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 1–1224（1224 aa）
Not recorded ZN ZINC ION × 8 GOL GLYCEROL × 1 MG MAGNESIUM ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；10-15 % tacsimate 100mM Hepes pH 7.5
Resolution 3.34 Å R-free 0.261
8U9X STRUCTURAL BASIS OF TRANSCRIPTION: RNA POLYMERASE II SUBSTRATE BINDING AND METAL COORDINATION AT 3.0 A OF T834P MUTANT USING A FREE-ELECTRON LASER Deposited 2023-09-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 1–1224（1224 aa）
Not recorded ZN ZINC ION × 8 MN MANGANESE (II) ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；10-15 % tacsimate 100mM Hepes
Resolution 3.05 Å R-free 0.307
8UMH Consensus map of PICdeltaTFIIK form2 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain B 1–1224（1224 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8UMI consensus map of PICdeltaTFIIK form1 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain B 1–1224（1224 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9BVT RNA Pol II - High Mn(+2) concentration Deposited 2024-05-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 1–1224（1224 aa）
Not recorded ZN ZINC ION × 8 MN MANGANESE (II) ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；Tacsimate Hepes
Resolution 3.40 Å R-free 0.249
9BW0 RNA Polymerase II - No ATP Deposited 2024-05-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 1–1224（1224 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；Tacsimate, Hepes pH 7.0
Resolution 3.51 Å R-free 0.246

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

View Construct and Data Evidence
UniProt name A0A6A5Q4H2_YEASX
Isoform —
PDB entities 13
Chains and sequence ranges Author chain B； PDBConstruct 1–1224； UniProt 1–1224

DNA-directed RNA polymerase II subunit RPB3

OrganismNot specified

UniProt A0A6A5Q0Z3

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 28 DNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain C； UniProt 1–318 Not recorded Tfb1 × 1 General transcription and DNA repair factor IIH subunit TFB4 × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） TATA-box-binding protein × 1 （P13393） non-template strand DNA × 1 template strand DNA × 1 DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIA large subunit × 1 （A0A6A5Q2T8） Transcription initiation factor IIA subunit 2 × 1 （A0A6A5PRZ0） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） 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

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 7ML1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7MEI Composite structure of EC+EC Deposited 2021-04-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 30-meric
Chain C 1–318（318 aa）
Chain c 1–318（318 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7MK9 Complex structure of trailing EC of EC+EC (trailing EC-focused) Deposited 2021-04-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain C 1–318（318 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7MKA Structure of EC+EC (leading EC-focused) Deposited 2021-04-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain c 1–318（318 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7ML0 RNA polymerase II pre-initiation complex (PIC1) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain C 1–318（318 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ML2 RNA polymerase II pre-initiation complex (PIC3) Deposited 2021-04-27 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain C 1–318（318 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7ML4 RNA polymerase II initially transcribing complex (ITC) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 28 PDB declaration: 31-meric
Chain C 1–318（318 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8TUG Cryo-EM structure of CPD-stalled Pol II in complex with Rad26 (engaged state) Deposited 2023-08-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric
Chain C 1–318（318 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8TVP Cryo-EM structure of CPD-stalled Pol II in complex with Rad26 (open state) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric
Chain C 1–318（318 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8TVQ Cryo-EM structure of CPD stalled 10-subunit Pol II in complex with Rad26 Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 11 PDB declaration: 14-meric
Chain C 1–318（318 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8TVS Cryo-EM structure of backtracked Pol II in complex with Rad26 Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric
Chain C 1–318（318 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
8TVV Cryo-EM structure of backtracked Pol II Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain C 1–318（318 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8TVW Cryo-EM structure of CPD-stalled Pol II (conformation 1) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain C 1–318（318 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8TVX Cryo-EM structure of CPD-stalled Pol II (Conformation 2) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain C 1–318（318 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8TVY Cryo-EM structure of CPD lesion containing RNA Polymerase II elongation complex with Rad26 and Elf1 (closed state) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: 17-meric
Chain C 1–318（318 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8U9R STRUCTURAL BASIS OF TRANSCRIPTION: RNA POLYMERASE II SUBSTRATE BINDING AND METAL COORDINATION USING A FREE-ELECTRON LASER Deposited 2023-09-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 1–318（318 aa）
Not recorded ZN ZINC ION × 8 GOL GLYCEROL × 1 MG MAGNESIUM ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；10-15 % tacsimate 100mM Hepes pH 7.5
Resolution 3.34 Å R-free 0.261
8U9X STRUCTURAL BASIS OF TRANSCRIPTION: RNA POLYMERASE II SUBSTRATE BINDING AND METAL COORDINATION AT 3.0 A OF T834P MUTANT USING A FREE-ELECTRON LASER Deposited 2023-09-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 1–318（318 aa）
Not recorded ZN ZINC ION × 8 MN MANGANESE (II) ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；10-15 % tacsimate 100mM Hepes
Resolution 3.05 Å R-free 0.307
8UMH Consensus map of PICdeltaTFIIK form2 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain C 1–318（318 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8UMI consensus map of PICdeltaTFIIK form1 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain C 1–318（318 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9BVT RNA Pol II - High Mn(+2) concentration Deposited 2024-05-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 1–318（318 aa）
Not recorded ZN ZINC ION × 8 MN MANGANESE (II) ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；Tacsimate Hepes
Resolution 3.40 Å R-free 0.249
9BW0 RNA Polymerase II - No ATP Deposited 2024-05-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 1–318（318 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；Tacsimate, Hepes pH 7.0
Resolution 3.51 Å R-free 0.246

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

View Construct and Data Evidence
UniProt name A0A6A5Q0Z3_YEASX
Isoform —
PDB entities 14
Chains and sequence ranges Author chain C； PDBConstruct 1–318； UniProt 1–318

DNA-directed RNA polymerase II subunit RPB4

OrganismNot specified

UniProt A0A6A5PTI6

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 28 DNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain D； UniProt 1–221 Not recorded Tfb1 × 1 General transcription and DNA repair factor IIH subunit TFB4 × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） TATA-box-binding protein × 1 （P13393） non-template strand DNA × 1 template strand DNA × 1 DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIA large subunit × 1 （A0A6A5Q2T8） Transcription initiation factor IIA subunit 2 × 1 （A0A6A5PRZ0） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） 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

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 7ML1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7MEI Composite structure of EC+EC Deposited 2021-04-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 30-meric
Chain D 1–221（221 aa）
Chain d 1–221（221 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7MK9 Complex structure of trailing EC of EC+EC (trailing EC-focused) Deposited 2021-04-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain D 1–221（221 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7MKA Structure of EC+EC (leading EC-focused) Deposited 2021-04-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain d 1–221（221 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7ML0 RNA polymerase II pre-initiation complex (PIC1) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain D 1–221（221 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ML2 RNA polymerase II pre-initiation complex (PIC3) Deposited 2021-04-27 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain D 1–221（221 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7ML4 RNA polymerase II initially transcribing complex (ITC) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 28 PDB declaration: 31-meric
Chain D 1–221（221 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8TUG Cryo-EM structure of CPD-stalled Pol II in complex with Rad26 (engaged state) Deposited 2023-08-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric
Chain D 1–221（221 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8TVP Cryo-EM structure of CPD-stalled Pol II in complex with Rad26 (open state) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric
Chain D 1–221（221 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8TVS Cryo-EM structure of backtracked Pol II in complex with Rad26 Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric
Chain D 1–221（221 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
8TVV Cryo-EM structure of backtracked Pol II Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain D 1–221（221 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8TVW Cryo-EM structure of CPD-stalled Pol II (conformation 1) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain D 1–221（221 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8TVX Cryo-EM structure of CPD-stalled Pol II (Conformation 2) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain D 1–221（221 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8TVY Cryo-EM structure of CPD lesion containing RNA Polymerase II elongation complex with Rad26 and Elf1 (closed state) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: 17-meric
Chain D 1–221（221 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8U9R STRUCTURAL BASIS OF TRANSCRIPTION: RNA POLYMERASE II SUBSTRATE BINDING AND METAL COORDINATION USING A FREE-ELECTRON LASER Deposited 2023-09-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 1–221（221 aa）
Not recorded ZN ZINC ION × 8 GOL GLYCEROL × 1 MG MAGNESIUM ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；10-15 % tacsimate 100mM Hepes pH 7.5
Resolution 3.34 Å R-free 0.261
8U9X STRUCTURAL BASIS OF TRANSCRIPTION: RNA POLYMERASE II SUBSTRATE BINDING AND METAL COORDINATION AT 3.0 A OF T834P MUTANT USING A FREE-ELECTRON LASER Deposited 2023-09-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 1–221（221 aa）
Not recorded ZN ZINC ION × 8 MN MANGANESE (II) ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；10-15 % tacsimate 100mM Hepes
Resolution 3.05 Å R-free 0.307
8UMH Consensus map of PICdeltaTFIIK form2 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain D 1–221（221 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8UMI consensus map of PICdeltaTFIIK form1 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain D 1–221（221 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9BVT RNA Pol II - High Mn(+2) concentration Deposited 2024-05-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 1–221（221 aa）
Not recorded ZN ZINC ION × 8 MN MANGANESE (II) ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；Tacsimate Hepes
Resolution 3.40 Å R-free 0.249
9BW0 RNA Polymerase II - No ATP Deposited 2024-05-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 1–221（221 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；Tacsimate, Hepes pH 7.0
Resolution 3.51 Å R-free 0.246

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

View Construct and Data Evidence
UniProt name A0A6A5PTI6_YEASX
Isoform —
PDB entities 15
Chains and sequence ranges Author chain D； PDBConstruct 1–221； UniProt 1–221

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

OrganismNot specified

UniProt A0A6A5Q456

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 28 DNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain E； UniProt 1–215 Not recorded Tfb1 × 1 General transcription and DNA repair factor IIH subunit TFB4 × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） TATA-box-binding protein × 1 （P13393） non-template strand DNA × 1 template strand DNA × 1 DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIA large subunit × 1 （A0A6A5Q2T8） Transcription initiation factor IIA subunit 2 × 1 （A0A6A5PRZ0） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） 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

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 7ML1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7MEI Composite structure of EC+EC Deposited 2021-04-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 30-meric
Chain E 1–215（215 aa）
Chain e 1–215（215 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7MK9 Complex structure of trailing EC of EC+EC (trailing EC-focused) Deposited 2021-04-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain E 1–215（215 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7MKA Structure of EC+EC (leading EC-focused) Deposited 2021-04-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain e 1–215（215 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7ML0 RNA polymerase II pre-initiation complex (PIC1) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain E 1–215（215 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ML2 RNA polymerase II pre-initiation complex (PIC3) Deposited 2021-04-27 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain E 1–215（215 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7ML4 RNA polymerase II initially transcribing complex (ITC) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 28 PDB declaration: 31-meric
Chain E 1–215（215 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8TUG Cryo-EM structure of CPD-stalled Pol II in complex with Rad26 (engaged state) Deposited 2023-08-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric
Chain E 1–215（215 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8TVP Cryo-EM structure of CPD-stalled Pol II in complex with Rad26 (open state) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric
Chain E 1–215（215 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8TVQ Cryo-EM structure of CPD stalled 10-subunit Pol II in complex with Rad26 Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 11 PDB declaration: 14-meric
Chain E 1–215（215 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8TVS Cryo-EM structure of backtracked Pol II in complex with Rad26 Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric
Chain E 1–215（215 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
8TVV Cryo-EM structure of backtracked Pol II Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain E 1–215（215 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8TVW Cryo-EM structure of CPD-stalled Pol II (conformation 1) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain E 1–215（215 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8TVX Cryo-EM structure of CPD-stalled Pol II (Conformation 2) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain E 1–215（215 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8TVY Cryo-EM structure of CPD lesion containing RNA Polymerase II elongation complex with Rad26 and Elf1 (closed state) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: 17-meric
Chain E 1–215（215 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8U9R STRUCTURAL BASIS OF TRANSCRIPTION: RNA POLYMERASE II SUBSTRATE BINDING AND METAL COORDINATION USING A FREE-ELECTRON LASER Deposited 2023-09-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain E 1–215（215 aa）
Not recorded ZN ZINC ION × 8 GOL GLYCEROL × 1 MG MAGNESIUM ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；10-15 % tacsimate 100mM Hepes pH 7.5
Resolution 3.34 Å R-free 0.261
8U9X STRUCTURAL BASIS OF TRANSCRIPTION: RNA POLYMERASE II SUBSTRATE BINDING AND METAL COORDINATION AT 3.0 A OF T834P MUTANT USING A FREE-ELECTRON LASER Deposited 2023-09-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain E 1–215（215 aa）
Not recorded ZN ZINC ION × 8 MN MANGANESE (II) ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；10-15 % tacsimate 100mM Hepes
Resolution 3.05 Å R-free 0.307
8UMH Consensus map of PICdeltaTFIIK form2 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain E 1–215（215 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8UMI consensus map of PICdeltaTFIIK form1 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain E 1–215（215 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9BVT RNA Pol II - High Mn(+2) concentration Deposited 2024-05-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain E 1–215（215 aa）
Not recorded ZN ZINC ION × 8 MN MANGANESE (II) ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；Tacsimate Hepes
Resolution 3.40 Å R-free 0.249
9BW0 RNA Polymerase II - No ATP Deposited 2024-05-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain E 1–215（215 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；Tacsimate, Hepes pH 7.0
Resolution 3.51 Å R-free 0.246

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

View Construct and Data Evidence
UniProt name A0A6A5Q456_YEASX
Isoform —
PDB entities 16
Chains and sequence ranges Author chain E； PDBConstruct 1–215； UniProt 1–215

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

OrganismNot specified

UniProt A0A6L0ZRI7

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 28 DNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain F； UniProt 1–155 Not recorded Tfb1 × 1 General transcription and DNA repair factor IIH subunit TFB4 × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） TATA-box-binding protein × 1 （P13393） non-template strand DNA × 1 template strand DNA × 1 DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIA large subunit × 1 （A0A6A5Q2T8） Transcription initiation factor IIA subunit 2 × 1 （A0A6A5PRZ0） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） 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

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 7ML1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7MK9 Complex structure of trailing EC of EC+EC (trailing EC-focused) Deposited 2021-04-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7MKA Structure of EC+EC (leading EC-focused) Deposited 2021-04-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain f 1–155（155 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7ML0 RNA polymerase II pre-initiation complex (PIC1) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ML2 RNA polymerase II pre-initiation complex (PIC3) Deposited 2021-04-27 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7ML4 RNA polymerase II initially transcribing complex (ITC) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 28 PDB declaration: 31-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å

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

View Construct and Data Evidence
UniProt name A0A6L0ZRI7_YEASX
Isoform —
PDB entities 17
Chains and sequence ranges Author chain F； PDBConstruct 1–155； UniProt 1–155

DNA-directed RNA polymerase II subunit RPB7

OrganismNot specified

UniProt A0A6A5Q270

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 28 DNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain G； UniProt 1–171 Not recorded Tfb1 × 1 General transcription and DNA repair factor IIH subunit TFB4 × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） TATA-box-binding protein × 1 （P13393） non-template strand DNA × 1 template strand DNA × 1 DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIA large subunit × 1 （A0A6A5Q2T8） Transcription initiation factor IIA subunit 2 × 1 （A0A6A5PRZ0） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） 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

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 7ML1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7MEI Composite structure of EC+EC Deposited 2021-04-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 30-meric
Chain G 1–171（171 aa）
Chain g 1–171（171 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7MK9 Complex structure of trailing EC of EC+EC (trailing EC-focused) Deposited 2021-04-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7MKA Structure of EC+EC (leading EC-focused) Deposited 2021-04-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain g 1–171（171 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7ML0 RNA polymerase II pre-initiation complex (PIC1) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ML2 RNA polymerase II pre-initiation complex (PIC3) Deposited 2021-04-27 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7ML4 RNA polymerase II initially transcribing complex (ITC) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 28 PDB declaration: 31-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8TUG Cryo-EM structure of CPD-stalled Pol II in complex with Rad26 (engaged state) Deposited 2023-08-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8TVP Cryo-EM structure of CPD-stalled Pol II in complex with Rad26 (open state) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8TVS Cryo-EM structure of backtracked Pol II in complex with Rad26 Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
8TVV Cryo-EM structure of backtracked Pol II Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8TVW Cryo-EM structure of CPD-stalled Pol II (conformation 1) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8TVX Cryo-EM structure of CPD-stalled Pol II (Conformation 2) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8TVY Cryo-EM structure of CPD lesion containing RNA Polymerase II elongation complex with Rad26 and Elf1 (closed state) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: 17-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8U9R STRUCTURAL BASIS OF TRANSCRIPTION: RNA POLYMERASE II SUBSTRATE BINDING AND METAL COORDINATION USING A FREE-ELECTRON LASER Deposited 2023-09-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 8 GOL GLYCEROL × 1 MG MAGNESIUM ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；10-15 % tacsimate 100mM Hepes pH 7.5
Resolution 3.34 Å R-free 0.261
8U9X STRUCTURAL BASIS OF TRANSCRIPTION: RNA POLYMERASE II SUBSTRATE BINDING AND METAL COORDINATION AT 3.0 A OF T834P MUTANT USING A FREE-ELECTRON LASER Deposited 2023-09-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 8 MN MANGANESE (II) ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；10-15 % tacsimate 100mM Hepes
Resolution 3.05 Å R-free 0.307
8UMH Consensus map of PICdeltaTFIIK form2 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8UMI consensus map of PICdeltaTFIIK form1 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain G 1–171（171 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9BVT RNA Pol II - High Mn(+2) concentration Deposited 2024-05-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 8 MN MANGANESE (II) ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；Tacsimate Hepes
Resolution 3.40 Å R-free 0.249
9BW0 RNA Polymerase II - No ATP Deposited 2024-05-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；Tacsimate, Hepes pH 7.0
Resolution 3.51 Å R-free 0.246

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

View Construct and Data Evidence
UniProt name A0A6A5Q270_YEASX
Isoform —
PDB entities 18
Chains and sequence ranges Author chain G； PDBConstruct 1–171； UniProt 1–171

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

OrganismNot specified

UniProt A0A6A5Q8C2

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 28 DNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain H； UniProt 1–146 Not recorded Tfb1 × 1 General transcription and DNA repair factor IIH subunit TFB4 × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） TATA-box-binding protein × 1 （P13393） non-template strand DNA × 1 template strand DNA × 1 DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIA large subunit × 1 （A0A6A5Q2T8） Transcription initiation factor IIA subunit 2 × 1 （A0A6A5PRZ0） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） 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

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 7ML1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7MEI Composite structure of EC+EC Deposited 2021-04-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 30-meric
Chain H 1–146（146 aa）
Chain h 1–146（146 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7MK9 Complex structure of trailing EC of EC+EC (trailing EC-focused) Deposited 2021-04-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain H 1–146（146 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7MKA Structure of EC+EC (leading EC-focused) Deposited 2021-04-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain h 1–146（146 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7ML0 RNA polymerase II pre-initiation complex (PIC1) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain H 1–146（146 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ML2 RNA polymerase II pre-initiation complex (PIC3) Deposited 2021-04-27 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain H 1–146（146 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7ML4 RNA polymerase II initially transcribing complex (ITC) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 28 PDB declaration: 31-meric
Chain H 1–146（146 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8TUG Cryo-EM structure of CPD-stalled Pol II in complex with Rad26 (engaged state) Deposited 2023-08-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric
Chain H 1–146（146 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8TVP Cryo-EM structure of CPD-stalled Pol II in complex with Rad26 (open state) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric
Chain H 1–146（146 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8TVQ Cryo-EM structure of CPD stalled 10-subunit Pol II in complex with Rad26 Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 11 PDB declaration: 14-meric
Chain H 1–146（146 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8TVS Cryo-EM structure of backtracked Pol II in complex with Rad26 Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric
Chain H 1–146（146 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
8TVV Cryo-EM structure of backtracked Pol II Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain H 1–146（146 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8TVW Cryo-EM structure of CPD-stalled Pol II (conformation 1) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain H 1–146（146 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8TVX Cryo-EM structure of CPD-stalled Pol II (Conformation 2) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain H 1–146（146 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8TVY Cryo-EM structure of CPD lesion containing RNA Polymerase II elongation complex with Rad26 and Elf1 (closed state) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: 17-meric
Chain H 1–146（146 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8U9R STRUCTURAL BASIS OF TRANSCRIPTION: RNA POLYMERASE II SUBSTRATE BINDING AND METAL COORDINATION USING A FREE-ELECTRON LASER Deposited 2023-09-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain H 1–146（146 aa）
Not recorded ZN ZINC ION × 8 GOL GLYCEROL × 1 MG MAGNESIUM ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；10-15 % tacsimate 100mM Hepes pH 7.5
Resolution 3.34 Å R-free 0.261
8U9X STRUCTURAL BASIS OF TRANSCRIPTION: RNA POLYMERASE II SUBSTRATE BINDING AND METAL COORDINATION AT 3.0 A OF T834P MUTANT USING A FREE-ELECTRON LASER Deposited 2023-09-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain H 1–146（146 aa）
Not recorded ZN ZINC ION × 8 MN MANGANESE (II) ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；10-15 % tacsimate 100mM Hepes
Resolution 3.05 Å R-free 0.307
8UMH Consensus map of PICdeltaTFIIK form2 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain H 1–146（146 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8UMI consensus map of PICdeltaTFIIK form1 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain H 1–146（146 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9BVT RNA Pol II - High Mn(+2) concentration Deposited 2024-05-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain H 1–146（146 aa）
Not recorded ZN ZINC ION × 8 MN MANGANESE (II) ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；Tacsimate Hepes
Resolution 3.40 Å R-free 0.249
9BW0 RNA Polymerase II - No ATP Deposited 2024-05-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain H 1–146（146 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；Tacsimate, Hepes pH 7.0
Resolution 3.51 Å R-free 0.246

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

View Construct and Data Evidence
UniProt name A0A6A5Q8C2_YEASX
Isoform —
PDB entities 19
Chains and sequence ranges Author chain H； PDBConstruct 1–146； UniProt 1–146

DNA-directed RNA polymerase II subunit RPB9

OrganismNot specified

UniProt A0A7I9EWC2

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 28 DNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain I； UniProt 1–122 Not recorded Tfb1 × 1 General transcription and DNA repair factor IIH subunit TFB4 × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） TATA-box-binding protein × 1 （P13393） non-template strand DNA × 1 template strand DNA × 1 DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIA large subunit × 1 （A0A6A5Q2T8） Transcription initiation factor IIA subunit 2 × 1 （A0A6A5PRZ0） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） 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

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 7ML1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7MEI Composite structure of EC+EC Deposited 2021-04-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 30-meric
Chain I 1–122（122 aa）
Chain i 1–122（122 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7MK9 Complex structure of trailing EC of EC+EC (trailing EC-focused) Deposited 2021-04-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain I 1–122（122 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7MKA Structure of EC+EC (leading EC-focused) Deposited 2021-04-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain i 1–122（122 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7ML0 RNA polymerase II pre-initiation complex (PIC1) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain I 1–122（122 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ML2 RNA polymerase II pre-initiation complex (PIC3) Deposited 2021-04-27 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain I 1–122（122 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7ML4 RNA polymerase II initially transcribing complex (ITC) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 28 PDB declaration: 31-meric
Chain I 1–122（122 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8TUG Cryo-EM structure of CPD-stalled Pol II in complex with Rad26 (engaged state) Deposited 2023-08-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric
Chain I 1–122（122 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8TVP Cryo-EM structure of CPD-stalled Pol II in complex with Rad26 (open state) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric
Chain I 1–122（122 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8TVQ Cryo-EM structure of CPD stalled 10-subunit Pol II in complex with Rad26 Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 11 PDB declaration: 14-meric
Chain I 1–122（122 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8TVS Cryo-EM structure of backtracked Pol II in complex with Rad26 Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric
Chain I 1–122（122 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
8TVV Cryo-EM structure of backtracked Pol II Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain I 1–122（122 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8TVW Cryo-EM structure of CPD-stalled Pol II (conformation 1) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain I 1–122（122 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8TVX Cryo-EM structure of CPD-stalled Pol II (Conformation 2) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain I 1–122（122 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8TVY Cryo-EM structure of CPD lesion containing RNA Polymerase II elongation complex with Rad26 and Elf1 (closed state) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: 17-meric
Chain I 1–122（122 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8U9R STRUCTURAL BASIS OF TRANSCRIPTION: RNA POLYMERASE II SUBSTRATE BINDING AND METAL COORDINATION USING A FREE-ELECTRON LASER Deposited 2023-09-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain I 1–122（122 aa）
Not recorded ZN ZINC ION × 8 GOL GLYCEROL × 1 MG MAGNESIUM ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；10-15 % tacsimate 100mM Hepes pH 7.5
Resolution 3.34 Å R-free 0.261
8U9X STRUCTURAL BASIS OF TRANSCRIPTION: RNA POLYMERASE II SUBSTRATE BINDING AND METAL COORDINATION AT 3.0 A OF T834P MUTANT USING A FREE-ELECTRON LASER Deposited 2023-09-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain I 1–122（122 aa）
Not recorded ZN ZINC ION × 8 MN MANGANESE (II) ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；10-15 % tacsimate 100mM Hepes
Resolution 3.05 Å R-free 0.307
8UMH Consensus map of PICdeltaTFIIK form2 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain I 1–122（122 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8UMI consensus map of PICdeltaTFIIK form1 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain I 1–122（122 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9BVT RNA Pol II - High Mn(+2) concentration Deposited 2024-05-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain I 1–122（122 aa）
Not recorded ZN ZINC ION × 8 MN MANGANESE (II) ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；Tacsimate Hepes
Resolution 3.40 Å R-free 0.249
9BW0 RNA Polymerase II - No ATP Deposited 2024-05-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain I 1–122（122 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；Tacsimate, Hepes pH 7.0
Resolution 3.51 Å R-free 0.246

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

View Construct and Data Evidence
UniProt name A0A7I9EWC2_YEASX
Isoform —
PDB entities 20
Chains and sequence ranges Author chain I； PDBConstruct 1–122； UniProt 1–122

DNA-directed RNA polymerases II subunit RPABC5

OrganismNot specified

UniProt A0A6A5Q7Q6

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 28 DNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain J； UniProt 1–70 Not recorded Tfb1 × 1 General transcription and DNA repair factor IIH subunit TFB4 × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） TATA-box-binding protein × 1 （P13393） non-template strand DNA × 1 template strand DNA × 1 DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIA large subunit × 1 （A0A6A5Q2T8） Transcription initiation factor IIA subunit 2 × 1 （A0A6A5PRZ0） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） 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

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 7ML1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7MEI Composite structure of EC+EC Deposited 2021-04-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 30-meric
Chain J 1–70（70 aa）
Chain j 1–70（70 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7MK9 Complex structure of trailing EC of EC+EC (trailing EC-focused) Deposited 2021-04-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain J 1–70（70 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7MKA Structure of EC+EC (leading EC-focused) Deposited 2021-04-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain j 1–70（70 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7ML0 RNA polymerase II pre-initiation complex (PIC1) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain J 1–70（70 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ML2 RNA polymerase II pre-initiation complex (PIC3) Deposited 2021-04-27 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain J 1–70（70 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7ML4 RNA polymerase II initially transcribing complex (ITC) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 28 PDB declaration: 31-meric
Chain J 1–70（70 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8TUG Cryo-EM structure of CPD-stalled Pol II in complex with Rad26 (engaged state) Deposited 2023-08-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric
Chain J 1–70（70 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8TVP Cryo-EM structure of CPD-stalled Pol II in complex with Rad26 (open state) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric
Chain J 1–70（70 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8TVQ Cryo-EM structure of CPD stalled 10-subunit Pol II in complex with Rad26 Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 11 PDB declaration: 14-meric
Chain J 1–70（70 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8TVS Cryo-EM structure of backtracked Pol II in complex with Rad26 Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric
Chain J 1–70（70 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
8TVV Cryo-EM structure of backtracked Pol II Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain J 1–70（70 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8TVW Cryo-EM structure of CPD-stalled Pol II (conformation 1) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain J 1–70（70 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8TVX Cryo-EM structure of CPD-stalled Pol II (Conformation 2) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain J 1–70（70 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8TVY Cryo-EM structure of CPD lesion containing RNA Polymerase II elongation complex with Rad26 and Elf1 (closed state) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: 17-meric
Chain J 1–70（70 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8U9R STRUCTURAL BASIS OF TRANSCRIPTION: RNA POLYMERASE II SUBSTRATE BINDING AND METAL COORDINATION USING A FREE-ELECTRON LASER Deposited 2023-09-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain J 1–70（70 aa）
Not recorded ZN ZINC ION × 8 GOL GLYCEROL × 1 MG MAGNESIUM ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；10-15 % tacsimate 100mM Hepes pH 7.5
Resolution 3.34 Å R-free 0.261
8U9X STRUCTURAL BASIS OF TRANSCRIPTION: RNA POLYMERASE II SUBSTRATE BINDING AND METAL COORDINATION AT 3.0 A OF T834P MUTANT USING A FREE-ELECTRON LASER Deposited 2023-09-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain J 1–70（70 aa）
Not recorded ZN ZINC ION × 8 MN MANGANESE (II) ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；10-15 % tacsimate 100mM Hepes
Resolution 3.05 Å R-free 0.307
8UMH Consensus map of PICdeltaTFIIK form2 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain J 1–70（70 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8UMI consensus map of PICdeltaTFIIK form1 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain J 1–70（70 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9BVT RNA Pol II - High Mn(+2) concentration Deposited 2024-05-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain J 1–70（70 aa）
Not recorded ZN ZINC ION × 8 MN MANGANESE (II) ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；Tacsimate Hepes
Resolution 3.40 Å R-free 0.249
9BW0 RNA Polymerase II - No ATP Deposited 2024-05-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain J 1–70（70 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；Tacsimate, Hepes pH 7.0
Resolution 3.51 Å R-free 0.246

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

View Construct and Data Evidence
UniProt name A0A6A5Q7Q6_YEASX
Isoform —
PDB entities 21
Chains and sequence ranges Author chain J； PDBConstruct 1–70； UniProt 1–70

DNA-directed RNA polymerase II subunit RPB11

OrganismNot specified

UniProt A0A6A5Q7A1

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 28 DNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain K； UniProt 1–120 Not recorded Tfb1 × 1 General transcription and DNA repair factor IIH subunit TFB4 × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） TATA-box-binding protein × 1 （P13393） non-template strand DNA × 1 template strand DNA × 1 DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIA large subunit × 1 （A0A6A5Q2T8） Transcription initiation factor IIA subunit 2 × 1 （A0A6A5PRZ0） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） 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

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 7ML1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7MEI Composite structure of EC+EC Deposited 2021-04-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 30-meric
Chain K 1–120（120 aa）
Chain k 1–120（120 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7MK9 Complex structure of trailing EC of EC+EC (trailing EC-focused) Deposited 2021-04-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain K 1–120（120 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7MKA Structure of EC+EC (leading EC-focused) Deposited 2021-04-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain k 1–120（120 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7ML0 RNA polymerase II pre-initiation complex (PIC1) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain K 1–120（120 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ML2 RNA polymerase II pre-initiation complex (PIC3) Deposited 2021-04-27 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain K 1–120（120 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7ML4 RNA polymerase II initially transcribing complex (ITC) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 28 PDB declaration: 31-meric
Chain K 1–120（120 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8TUG Cryo-EM structure of CPD-stalled Pol II in complex with Rad26 (engaged state) Deposited 2023-08-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric
Chain K 1–120（120 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8TVP Cryo-EM structure of CPD-stalled Pol II in complex with Rad26 (open state) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric
Chain K 1–120（120 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8TVQ Cryo-EM structure of CPD stalled 10-subunit Pol II in complex with Rad26 Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 11 PDB declaration: 14-meric
Chain K 1–120（120 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8TVS Cryo-EM structure of backtracked Pol II in complex with Rad26 Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric
Chain K 1–120（120 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
8TVV Cryo-EM structure of backtracked Pol II Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain K 1–120（120 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8TVW Cryo-EM structure of CPD-stalled Pol II (conformation 1) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain K 1–120（120 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8TVX Cryo-EM structure of CPD-stalled Pol II (Conformation 2) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain K 1–120（120 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8TVY Cryo-EM structure of CPD lesion containing RNA Polymerase II elongation complex with Rad26 and Elf1 (closed state) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: 17-meric
Chain K 1–120（120 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8U9R STRUCTURAL BASIS OF TRANSCRIPTION: RNA POLYMERASE II SUBSTRATE BINDING AND METAL COORDINATION USING A FREE-ELECTRON LASER Deposited 2023-09-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain K 1–120（120 aa）
Not recorded ZN ZINC ION × 8 GOL GLYCEROL × 1 MG MAGNESIUM ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；10-15 % tacsimate 100mM Hepes pH 7.5
Resolution 3.34 Å R-free 0.261
8U9X STRUCTURAL BASIS OF TRANSCRIPTION: RNA POLYMERASE II SUBSTRATE BINDING AND METAL COORDINATION AT 3.0 A OF T834P MUTANT USING A FREE-ELECTRON LASER Deposited 2023-09-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain K 1–120（120 aa）
Not recorded ZN ZINC ION × 8 MN MANGANESE (II) ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；10-15 % tacsimate 100mM Hepes
Resolution 3.05 Å R-free 0.307
8UMH Consensus map of PICdeltaTFIIK form2 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain K 1–120（120 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8UMI consensus map of PICdeltaTFIIK form1 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain K 1–120（120 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9BVT RNA Pol II - High Mn(+2) concentration Deposited 2024-05-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain K 1–120（120 aa）
Not recorded ZN ZINC ION × 8 MN MANGANESE (II) ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；Tacsimate Hepes
Resolution 3.40 Å R-free 0.249
9BW0 RNA Polymerase II - No ATP Deposited 2024-05-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain K 1–120（120 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；Tacsimate, Hepes pH 7.0
Resolution 3.51 Å R-free 0.246

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

View Construct and Data Evidence
UniProt name A0A6A5Q7A1_YEASX
Isoform —
PDB entities 22
Chains and sequence ranges Author chain K； PDBConstruct 1–120； UniProt 1–120

DNA-directed RNA polymerases II subunit RPABC4

OrganismNot specified

UniProt A0A6A5PY05

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 28 DNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain L； UniProt 1–70 Not recorded Tfb1 × 1 General transcription and DNA repair factor IIH subunit TFB4 × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） TATA-box-binding protein × 1 （P13393） non-template strand DNA × 1 template strand DNA × 1 DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIA large subunit × 1 （A0A6A5Q2T8） Transcription initiation factor IIA subunit 2 × 1 （A0A6A5PRZ0） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） 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

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 7ML1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7MEI Composite structure of EC+EC Deposited 2021-04-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 30-meric
Chain L 1–70（70 aa）
Chain l 1–70（70 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7MK9 Complex structure of trailing EC of EC+EC (trailing EC-focused) Deposited 2021-04-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain L 1–70（70 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7MKA Structure of EC+EC (leading EC-focused) Deposited 2021-04-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain l 1–70（70 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7ML0 RNA polymerase II pre-initiation complex (PIC1) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain L 1–70（70 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ML2 RNA polymerase II pre-initiation complex (PIC3) Deposited 2021-04-27 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain L 1–70（70 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7ML4 RNA polymerase II initially transcribing complex (ITC) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 28 PDB declaration: 31-meric
Chain L 1–70（70 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8TUG Cryo-EM structure of CPD-stalled Pol II in complex with Rad26 (engaged state) Deposited 2023-08-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric
Chain L 1–70（70 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8TVP Cryo-EM structure of CPD-stalled Pol II in complex with Rad26 (open state) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric
Chain L 1–70（70 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8TVQ Cryo-EM structure of CPD stalled 10-subunit Pol II in complex with Rad26 Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 11 PDB declaration: 14-meric
Chain L 1–70（70 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8TVS Cryo-EM structure of backtracked Pol II in complex with Rad26 Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric
Chain L 1–70（70 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
8TVV Cryo-EM structure of backtracked Pol II Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain L 1–70（70 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8TVW Cryo-EM structure of CPD-stalled Pol II (conformation 1) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain L 1–70（70 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8TVX Cryo-EM structure of CPD-stalled Pol II (Conformation 2) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain L 1–70（70 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8TVY Cryo-EM structure of CPD lesion containing RNA Polymerase II elongation complex with Rad26 and Elf1 (closed state) Deposited 2023-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: 17-meric
Chain L 1–70（70 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8U9R STRUCTURAL BASIS OF TRANSCRIPTION: RNA POLYMERASE II SUBSTRATE BINDING AND METAL COORDINATION USING A FREE-ELECTRON LASER Deposited 2023-09-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain L 1–70（70 aa）
Not recorded ZN ZINC ION × 8 GOL GLYCEROL × 1 MG MAGNESIUM ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；10-15 % tacsimate 100mM Hepes pH 7.5
Resolution 3.34 Å R-free 0.261
8U9X STRUCTURAL BASIS OF TRANSCRIPTION: RNA POLYMERASE II SUBSTRATE BINDING AND METAL COORDINATION AT 3.0 A OF T834P MUTANT USING A FREE-ELECTRON LASER Deposited 2023-09-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain L 1–70（70 aa）
Not recorded ZN ZINC ION × 8 MN MANGANESE (II) ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；10-15 % tacsimate 100mM Hepes
Resolution 3.05 Å R-free 0.307
8UMH Consensus map of PICdeltaTFIIK form2 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain L 1–70（70 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8UMI consensus map of PICdeltaTFIIK form1 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain L 1–70（70 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9BVT RNA Pol II - High Mn(+2) concentration Deposited 2024-05-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain L 1–70（70 aa）
Not recorded ZN ZINC ION × 8 MN MANGANESE (II) ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；Tacsimate Hepes
Resolution 3.40 Å R-free 0.249
9BW0 RNA Polymerase II - No ATP Deposited 2024-05-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain L 1–70（70 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；Tacsimate, Hepes pH 7.0
Resolution 3.51 Å R-free 0.246

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

View Construct and Data Evidence
UniProt name A0A6A5PY05_YEASX
Isoform —
PDB entities 23
Chains and sequence ranges Author chain L； PDBConstruct 1–70； UniProt 1–70

Transcription initiation factor IIB

OrganismNot specified

UniProt P29055

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 28 DNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain M； UniProt 1–345 Not recorded Tfb1 × 1 General transcription and DNA repair factor IIH subunit TFB4 × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） TATA-box-binding protein × 1 （P13393） non-template strand DNA × 1 template strand DNA × 1 DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIA large subunit × 1 （A0A6A5Q2T8） Transcription initiation factor IIA subunit 2 × 1 （A0A6A5PRZ0） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） 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

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 7ML1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3K7A Crystal Structure of an RNA polymerase II-TFIIB complex Deposited 2009-10-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain M 1–345（345 aa）
Not recorded ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；295 K；1.2 M sodium/potassium phosphate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 3.80 Å R-free 0.313
4BBR Structure of RNA polymerase II-TFIIB complex Deposited 2012-09-27 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain M 1–345（345 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.40 Å R-free 0.211
4BBS Structure of an initially transcribing RNA polymerase II-TFIIB complex Deposited 2012-09-27 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain M 1–345（345 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.60 Å R-free 0.225
4V1N Architecture of the RNA polymerase II-Mediator core transcription initiation complex Deposited 2014-09-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: nonadecameric
Chain M 1–345（345 aa）
Chain Q 1–734（734 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer 25 MM HEPES-KOH PH 7.5, 180 MM POTASSIUM ACETATE, 5 % GLYCEROL, 5 MM DTT；pH 7.5；25 MM HEPES-KOH PH 7.5, 180 MM POTASSIUM ACETATE, 5 % GLYCEROL, 5 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；GRIDS WERE GLOW- DISCHARGED FOR 20 S BEFORE DEPOSITION OF 4 MICROLITERS SAMPLE AND INCUBATED FOR 30 S. GRIDS WERE WASHED TWICE WITH 4 MICROLITERS DISTILLED WATER, BLOTTED, AND VITRIFIED BY PLUNGING INTO LIQUID ETHANE WITH A MANUAL PLUNGER.
Resolution 7.80 Å
4V1O Architecture of the RNA polymerase II-Mediator core transcription initiation complex Deposited 2014-09-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain M 1–345（345 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer 25 MM HEPES-KOH PH 7.5, 180 MM POTASSIUM ACETATE, 5 % GLYCEROL, 5 MM DTT；pH 7.5；25 MM HEPES-KOH PH 7.5, 180 MM POTASSIUM ACETATE, 5 % GLYCEROL, 5 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；GRIDS WERE GLOW- DISCHARGED FOR 20 S BEFORE DEPOSITION OF 4 MICROLITERS SAMPLE AND INCUBATED FOR 30 S. GRIDS WERE WASHED TWICE WITH 4 MICROLITERS DISTILLED WATER, BLOTTED, AND VITRIFIED BY PLUNGING INTO LIQUID ETHANE WITH A MANUAL PLUNGER.
Resolution 9.70 Å
5FMF the P-lobe of RNA polymerase II pre-initiation complex Deposited 2015-11-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain P 1–345（345 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer 20 MM HEPES (PH7.6), 5 MM DTT, 2 MM MG(OAC)2,AND 40 MM KOAC；pH 7.6；20 MM HEPES (PH7.6), 5 MM DTT, 2 MM MG(OAC)2,AND 40 MM KOAC
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 120, INSTRUMENT- FEI VITROBOT MARK III,
Resolution 6.00 Å
5FYW Transcription initiation complex structures elucidate DNA opening (OC) Deposited 2016-03-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain M 1–345（345 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer 25 MM HEPES-KOH PH 7.5, 150 MM POTASSIUM ACETATE, 2 MM MGCL2, 5 MM DTT；pH 7.5；25 MM HEPES-KOH PH 7.5, 150 MM POTASSIUM ACETATE, 2 MM MGCL2, 5 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；CRYOGEN - ETHANE. INSTRUMENT - FEI VITROBOT MARK IV. QUANTIFOIL R 3.5- 1 HOLEY CARBON GRIDS WERE GLOW-DISCHARGED BEFORE DEPOSITION OF 4.5 MICROLITERS OF SAMPLE. GRIDS WERE THEN BLOTTED FOR 8.5 S AND PLUNGE- FROZEN IN LIQUID ETHANE.
Resolution 4.35 Å
5FZ5 Transcription initiation complex structures elucidate DNA opening (CC) Deposited 2016-03-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain M 1–345（345 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer 25 MM HEPES-KOH PH 7.5, 150 MM POTASSIUM ACETATE, 2 MM MGCL2, 5 MM DTT；pH 7.5；25 MM HEPES-KOH PH 7.5, 150 MM POTASSIUM ACETATE, 2 MM MGCL2, 5 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE
Resolution 8.80 Å
5OQJ STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH Deposited 2017-08-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain M 1–345（345 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；GRIDS WERE BLOTTED FOR 8 S AND PLUNGE-FROZEN IN LIQUID ETHANE.
Resolution 4.70 Å
5OQM STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH AND CORE MEDIATOR Deposited 2017-08-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 44 PDB declaration: 46-meric
Chain M 1–345（345 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 8 s and plunge-frozen in liquid ethane.
Resolution 5.80 Å
5SVA Mediator-RNA Polymerase II Pre-Initiation Complex Deposited 2016-08-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric
Chain c 1–345（345 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 15.30 Å
6GYK Structure of a yeast closed complex (core CC1) Deposited 2018-06-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain M 1–345（345 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
6GYL Structure of a yeast closed complex with distorted DNA (core CCdist) Deposited 2018-06-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain M 1–345（345 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
6GYM Structure of a yeast closed complex with distorted DNA (CCdist) Deposited 2018-06-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain M 1–345（345 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 16 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.70 Å
7ML0 RNA polymerase II pre-initiation complex (PIC1) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain M 1–345（345 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ML2 RNA polymerase II pre-initiation complex (PIC3) Deposited 2021-04-27 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain M 1–345（345 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7ML4 RNA polymerase II initially transcribing complex (ITC) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 28 PDB declaration: 31-meric
Chain M 1–345（345 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7O4I Yeast RNA polymerase II transcription pre-initiation complex with initial transcription bubble Deposited 2021-04-06 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain M 1–345（345 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7O4J Yeast RNA polymerase II transcription pre-initiation complex (consensus) Deposited 2021-04-06 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain M 1–345（345 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7O72 Yeast RNA polymerase II transcription pre-initiation complex with closed promoter DNA Deposited 2021-04-12 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain M 1–345（345 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7O73 Yeast RNA polymerase II transcription pre-initiation complex with closed distorted promoter DNA Deposited 2021-04-12 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain M 1–345（345 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7O75 Yeast RNA polymerase II transcription pre-initiation complex with open promoter DNA Deposited 2021-04-13 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain M 1–345（345 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7UI9 Core Mediator-PICearly (Copy A) Deposited 2022-03-28 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain M 1–345（345 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7UIF Mediator-PIC Early (Core B) Deposited 2022-03-29 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain M 1–345（345 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
7UIO Mediator-PIC Early (Composite Model) Deposited 2022-03-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 78 PDB declaration: 80-meric
Chain AM 1–345（345 aa）
Chain BM 1–345（345 aa）
Not recorded ZN ZINC ION × 4 THR THREONINE × 1 ALA ALANINE × 1 ASP ASPARTIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7ZS9 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome (complex A) Deposited 2022-05-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain M 1–345（345 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7ZSA Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP (complex B) Deposited 2022-05-06 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain M 1–345（345 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7ZSB Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP, complex C Deposited 2022-05-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain M 1–345（345 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.60 Å
8CEN Yeast RNA polymerase II transcription pre-initiation complex with core Mediator Deposited 2023-02-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 44 PDB declaration: 46-meric
Chain M 1–345（345 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8CEO Yeast RNA polymerase II transcription pre-initiation complex with core Mediator and the +1 nucleosome Deposited 2023-02-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 52 PDB declaration: 54-meric
Chain M 1–345（345 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8UMH Consensus map of PICdeltaTFIIK form2 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain M 1–345（345 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8UMI consensus map of PICdeltaTFIIK form1 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain M 1–345（345 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8UOQ Composite map of PIC_delta_TFIIK form2 Deposited 2023-10-20 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain M 1–345（345 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8UOT Composite map of PICdeltaTFIIK form1 Deposited 2023-10-20 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain M 1–345（345 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å

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

View Construct and Data Evidence
UniProt name TF2B_YEAST
Isoform —
PDB entities 24
Chains and sequence ranges Author chain M； PDBConstruct 1–345； UniProt 1–345

Transcription initiation factor IIF subunit alpha

OrganismNot specified

UniProt P41895

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 28 DNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain Q； UniProt 1–735 Not recorded Tfb1 × 1 General transcription and DNA repair factor IIH subunit TFB4 × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） TATA-box-binding protein × 1 （P13393） non-template strand DNA × 1 template strand DNA × 1 DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIA large subunit × 1 （A0A6A5Q2T8） Transcription initiation factor IIA subunit 2 × 1 （A0A6A5PRZ0） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） 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

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 7ML1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5FYW Transcription initiation complex structures elucidate DNA opening (OC) Deposited 2016-03-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain Q 1–735（735 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer 25 MM HEPES-KOH PH 7.5, 150 MM POTASSIUM ACETATE, 2 MM MGCL2, 5 MM DTT；pH 7.5；25 MM HEPES-KOH PH 7.5, 150 MM POTASSIUM ACETATE, 2 MM MGCL2, 5 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；CRYOGEN - ETHANE. INSTRUMENT - FEI VITROBOT MARK IV. QUANTIFOIL R 3.5- 1 HOLEY CARBON GRIDS WERE GLOW-DISCHARGED BEFORE DEPOSITION OF 4.5 MICROLITERS OF SAMPLE. GRIDS WERE THEN BLOTTED FOR 8.5 S AND PLUNGE- FROZEN IN LIQUID ETHANE.
Resolution 4.35 Å
5FZ5 Transcription initiation complex structures elucidate DNA opening (CC) Deposited 2016-03-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain Q 1–735（735 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer 25 MM HEPES-KOH PH 7.5, 150 MM POTASSIUM ACETATE, 2 MM MGCL2, 5 MM DTT；pH 7.5；25 MM HEPES-KOH PH 7.5, 150 MM POTASSIUM ACETATE, 2 MM MGCL2, 5 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE
Resolution 8.80 Å
5OQJ STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH Deposited 2017-08-11 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain Q 1–735（735 aa）
Mutation：;Residues indicated as UNK are of uncertain amino acid register and may deviate from the given register by few amino acids. For details about modelling of the subunits refer to the associated publication. Residues indicated as UNK with the chain identifier Z are part of an assembly between the clutch domains of Tfb2 and Ssl2 but could not be assigned to any of the two proteins with confidence since domain swapping/beta-strand exchange may occur. To account for this uncertainty, a theoretical chain Z was introduced for this residue range but not assigned to any of the PIC components. Submission based on experimental data from EMDB EMD-3846. ; ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；GRIDS WERE BLOTTED FOR 8 S AND PLUNGE-FROZEN IN LIQUID ETHANE.
Resolution 4.70 Å
5OQM STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH AND CORE MEDIATOR Deposited 2017-08-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 44 PDB declaration: 46-meric
Chain Q 1–403（403 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 8 s and plunge-frozen in liquid ethane.
Resolution 5.80 Å
5SVA Mediator-RNA Polymerase II Pre-Initiation Complex Deposited 2016-08-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric
Chain f 1–735（735 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 15.30 Å
6GYK Structure of a yeast closed complex (core CC1) Deposited 2018-06-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain Q 1–735（735 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
6GYL Structure of a yeast closed complex with distorted DNA (core CCdist) Deposited 2018-06-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain Q 1–735（735 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
6GYM Structure of a yeast closed complex with distorted DNA (CCdist) Deposited 2018-06-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain Q 1–735（735 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 16 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.70 Å
7MEI Composite structure of EC+EC Deposited 2021-04-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 30-meric
Chain Q 1–735（735 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7MK9 Complex structure of trailing EC of EC+EC (trailing EC-focused) Deposited 2021-04-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain Q 1–735（735 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7ML0 RNA polymerase II pre-initiation complex (PIC1) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain Q 1–735（735 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ML2 RNA polymerase II pre-initiation complex (PIC3) Deposited 2021-04-27 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain Q 1–735（735 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7ML4 RNA polymerase II initially transcribing complex (ITC) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 28 PDB declaration: 31-meric
Chain Q 1–735（735 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7O4I Yeast RNA polymerase II transcription pre-initiation complex with initial transcription bubble Deposited 2021-04-06 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain Q 1–735（735 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7O4J Yeast RNA polymerase II transcription pre-initiation complex (consensus) Deposited 2021-04-06 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain Q 1–735（735 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7O72 Yeast RNA polymerase II transcription pre-initiation complex with closed promoter DNA Deposited 2021-04-12 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain Q 1–735（735 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7O73 Yeast RNA polymerase II transcription pre-initiation complex with closed distorted promoter DNA Deposited 2021-04-12 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain Q 1–735（735 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7O75 Yeast RNA polymerase II transcription pre-initiation complex with open promoter DNA Deposited 2021-04-13 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain Q 1–735（735 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7UI9 Core Mediator-PICearly (Copy A) Deposited 2022-03-28 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain P 1–735（735 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7UIF Mediator-PIC Early (Core B) Deposited 2022-03-29 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain P 1–735（735 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
7UIO Mediator-PIC Early (Composite Model) Deposited 2022-03-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 78 PDB declaration: 80-meric
Chain AP 1–735（735 aa）
Chain BP 1–735（735 aa）
Not recorded ZN ZINC ION × 4 THR THREONINE × 1 ALA ALANINE × 1 ASP ASPARTIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7ZS9 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome (complex A) Deposited 2022-05-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain Q 1–735（735 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7ZSA Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP (complex B) Deposited 2022-05-06 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain Q 1–735（735 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7ZSB Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP, complex C Deposited 2022-05-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain Q 1–735（735 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.60 Å
8UMH Consensus map of PICdeltaTFIIK form2 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain Q 1–735（735 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8UMI consensus map of PICdeltaTFIIK form1 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain Q 1–735（735 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8UOQ Composite map of PIC_delta_TFIIK form2 Deposited 2023-10-20 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain Q 1–735（735 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8UOT Composite map of PICdeltaTFIIK form1 Deposited 2023-10-20 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain Q 1–735（735 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å

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

View Construct and Data Evidence
UniProt name T2FA_YEAST
Isoform —
PDB entities 25
Chains and sequence ranges Author chain Q； PDBConstruct 1–735； UniProt 1–735

Transcription initiation factor IIF subunit beta

OrganismNot specified

UniProt A0A6A5PZ00

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 28 DNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain R； UniProt 1–400 Not recorded Tfb1 × 1 General transcription and DNA repair factor IIH subunit TFB4 × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） TATA-box-binding protein × 1 （P13393） non-template strand DNA × 1 template strand DNA × 1 DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIA large subunit × 1 （A0A6A5Q2T8） Transcription initiation factor IIA subunit 2 × 1 （A0A6A5PRZ0） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） 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

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 7ML1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7MEI Composite structure of EC+EC Deposited 2021-04-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 30-meric
Chain M 1–400（400 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7MK9 Complex structure of trailing EC of EC+EC (trailing EC-focused) Deposited 2021-04-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain M 1–400（400 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7ML0 RNA polymerase II pre-initiation complex (PIC1) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain R 1–400（400 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ML2 RNA polymerase II pre-initiation complex (PIC3) Deposited 2021-04-27 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain R 1–400（400 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7ML4 RNA polymerase II initially transcribing complex (ITC) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 28 PDB declaration: 31-meric
Chain R 1–400（400 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8UMH Consensus map of PICdeltaTFIIK form2 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain P 1–400（400 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8UMI consensus map of PICdeltaTFIIK form1 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain P 1–400（400 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å

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

View Construct and Data Evidence
UniProt name A0A6A5PZ00_YEASX
Isoform —
PDB entities 26
Chains and sequence ranges Author chain R； PDBConstruct 1–400； UniProt 1–400

Transcription initiation factor IIA large subunit

OrganismNot specified

UniProt A0A6A5Q2T8

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 × 28 DNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain U； UniProt 1–286 Not recorded Tfb1 × 1 General transcription and DNA repair factor IIH subunit TFB4 × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） TATA-box-binding protein × 1 （P13393） non-template strand DNA × 1 template strand DNA × 1 DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIA subunit 2 × 1 （A0A6A5PRZ0） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） 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

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 7ML1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7ML2 RNA polymerase II pre-initiation complex (PIC3) Deposited 2021-04-27 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain U 1–286（286 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7ML4 RNA polymerase II initially transcribing complex (ITC) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 28 PDB declaration: 31-meric
Chain U 1–286（286 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
7OHA nucleosome with TBP and TFIIA bound at SHL +2 Deposited 2021-05-09 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain L 1–286（286 aa）
Mutation：residues 95-209 are deleted No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 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 U 1–286（286 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain U 1–286（286 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain U 1–286（286 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å

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

View Construct and Data Evidence
UniProt name A0A6A5Q2T8_YEASX
Isoform —
PDB entities 27
Chains and sequence ranges Author chain U； PDBConstruct 1–286； UniProt 1–286

Transcription initiation factor IIA subunit 2

OrganismNot specified

UniProt A0A6A5PRZ0

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 × 28 DNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain V； UniProt 1–122 Not recorded Tfb1 × 1 General transcription and DNA repair factor IIH subunit TFB4 × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） TATA-box-binding protein × 1 （P13393） non-template strand DNA × 1 template strand DNA × 1 DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIA large subunit × 1 （A0A6A5Q2T8） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） 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

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 7ML1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7ML2 RNA polymerase II pre-initiation complex (PIC3) Deposited 2021-04-27 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain V 1–122（122 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7ML4 RNA polymerase II initially transcribing complex (ITC) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 28 PDB declaration: 31-meric
Chain V 1–122（122 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7OH9 Nucleosome with TBP and TFIIA bound at SHL -6 Deposited 2021-05-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain M 1–122（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7OHA nucleosome with TBP and TFIIA bound at SHL +2 Deposited 2021-05-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain M 1–122（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
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 V 1–122（122 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 V 1–122（122 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain V 1–122（122 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8UMI consensus map of PICdeltaTFIIK form1 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain V 1–122（122 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A6A5PRZ0_YEASX
Isoform —
PDB entities 28
Chains and sequence ranges Author chain V； PDBConstruct 1–122； UniProt 1–122

Transcription initiation factor IIE subunit alpha

OrganismNot specified

UniProt A0A6A5PTU5

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 28 DNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain W； UniProt 1–482 Not recorded Tfb1 × 1 General transcription and DNA repair factor IIH subunit TFB4 × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） TATA-box-binding protein × 1 （P13393） non-template strand DNA × 1 template strand DNA × 1 DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIA large subunit × 1 （A0A6A5Q2T8） Transcription initiation factor IIA subunit 2 × 1 （A0A6A5PRZ0） Transcription initiation factor IIE subunit beta × 1 （A0A6A5PS93） 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

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 7ML1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7ML0 RNA polymerase II pre-initiation complex (PIC1) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain W 1–482（482 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ML2 RNA polymerase II pre-initiation complex (PIC3) Deposited 2021-04-27 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain W 1–482（482 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7ML4 RNA polymerase II initially transcribing complex (ITC) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 28 PDB declaration: 31-meric
Chain W 1–482（482 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8UMH Consensus map of PICdeltaTFIIK form2 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain W 1–482（482 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8UMI consensus map of PICdeltaTFIIK form1 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain W 1–482（482 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å

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

View Construct and Data Evidence
UniProt name A0A6A5PTU5_YEASX
Isoform —
PDB entities 29
Chains and sequence ranges Author chain W； PDBConstruct 1–482； UniProt 1–482

Transcription initiation factor IIE subunit beta

OrganismNot specified

UniProt A0A6A5PS93

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 28 DNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain X； UniProt 1–328 Not recorded Tfb1 × 1 General transcription and DNA repair factor IIH subunit TFB4 × 1 General transcription and DNA repair factor IIH helicase subunit XPD × 1 （A0A6A5Q1C1） General transcription and DNA repair factor IIH subunit SSL1 × 1 RNA polymerase II transcription factor B subunit 2 × 1 （A0A6A5Q2X3） General transcription and DNA repair factor IIH subunit TFB5 × 1 （Q3E7C1） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （Q00578） BJ4_G0050160.mRNA.1.CDS.1 × 1 （A0A7I9BTI9） TATA-box-binding protein × 1 （P13393） non-template strand DNA × 1 template strand DNA × 1 DNA-directed RNA polymerase subunit × 1 （A0A6A5Q1P2） DNA-directed RNA polymerase subunit beta × 1 （A0A6A5Q4H2） DNA-directed RNA polymerase II subunit RPB3 × 1 （A0A6A5Q0Z3） DNA-directed RNA polymerase II subunit RPB4 × 1 （A0A6A5PTI6） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （A0A6A5Q456） DNA-directed RNA polymerases I,II,and III subunit RPABC2 × 1 （A0A6L0ZRI7） DNA-directed RNA polymerase II subunit RPB7 × 1 （A0A6A5Q270） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A6A5Q8C2） DNA-directed RNA polymerase II subunit RPB9 × 1 （A0A7I9EWC2） DNA-directed RNA polymerases II subunit RPABC5 × 1 （A0A6A5Q7Q6） DNA-directed RNA polymerase II subunit RPB11 × 1 （A0A6A5Q7A1） DNA-directed RNA polymerases II subunit RPABC4 × 1 （A0A6A5PY05） Transcription initiation factor IIB × 1 （P29055） Transcription initiation factor IIF subunit alpha × 1 （P41895） Transcription initiation factor IIF subunit beta × 1 （A0A6A5PZ00） Transcription initiation factor IIA large subunit × 1 （A0A6A5Q2T8） Transcription initiation factor IIA subunit 2 × 1 （A0A6A5PRZ0） Transcription initiation factor IIE subunit alpha × 1 （A0A6A5PTU5） 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

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 7ML1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7ML0 RNA polymerase II pre-initiation complex (PIC1) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain X 1–328（328 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ML2 RNA polymerase II pre-initiation complex (PIC3) Deposited 2021-04-27 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain X 1–328（328 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7ML4 RNA polymerase II initially transcribing complex (ITC) Deposited 2021-04-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 28 PDB declaration: 31-meric
Chain X 1–328（328 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8UMH Consensus map of PICdeltaTFIIK form2 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain X 1–328（328 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8UMI consensus map of PICdeltaTFIIK form1 Deposited 2023-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain X 1–328（328 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å

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

View Construct and Data Evidence
UniProt name A0A6A5PS93_YEASX
Isoform —
PDB entities 30
Chains and sequence ranges Author chain X； PDBConstruct 1–328； UniProt 1–328

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

SAXS scattering curve SAXS Profile

SAXS profile for 7ml1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7ml1
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id7ml1
Deposition date deposition_date2021-04-27
Structure title titleRNA polymerase II pre-initiation complex (PIC2)
Keywords keywordsPIC, TFIIH, transcription, ITC, RNA polymerase II; TRANSCRIPTION
Experimental Method methodELECTRON MICROSCOPY
▼

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

Radius of gyration Rg (Guinier) rg_guinier80.38 Å
Radius of gyration Rg (electron density) rg_electron80.72 Å
Forward intensity I(0) i012646200000.00
Molecular weight molecular_weight921380.0 kDa
Excluded volume excluded_volume1138800 ų
Envelope volume envelope_volume1923200 ų
Hydration-shell volume shell_volume200180 ų
Envelope diameter envelope_diameter285.7 Å
Shell Rg shell_rg78.66 Å
Envelope Rg envelope_rg78.24 Å
Shape Rg shape_rg80.79 Å
Total Rg total_rg80.47 Å
Total atoms total_atoms64538
Residues n_residues8311
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

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

Maximum dimension Dmax dmax275.2 Å
Rg (real space) rg_real83.89 Å
Rg uncertainty (real space) rg_real_error1.29 Å
I(0) (real space) i0_real1.2650e+10
I(0) uncertainty (real space) i0_real_error2.3320e+08
Rg (reciprocal space) rg_reciprocal79.56 Å
I(0) (reciprocal space) i0_reciprocal12620000000.0000
Solution quality estimate total_estimate0.8785
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary86.9 Å
Skewness Skewness skewness0.499
Kurtosis Kurtosis kurtosis-0.231
Angular range angular_range— – 0.0950 Å−1
Current regularization parameter α current_alpha1.3170
Highest regularization parameter α highest_alpha825200000.0000
Real-space data points n_real_points20
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.886; Stabil: 0.877; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.153
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (33)

▼

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id7ml1001
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id7ml1A01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology274 — Enzyme I; Chain A, domain 2
Homologous superfamily homologous superfamily100 — RNA polymerase Rpb1, domain 3
Domain ID domain_id7ml1A02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily140 —
Domain ID domain_id7ml1M01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily10 — Cyclin-like
▶

8. Citations (1)

▶

9. Files and Curves (10)