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5iyc

Human core-PIC in the initial transcribing state

Method: ELECTRON MICROSCOPY Dmax: 196.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-directed RNA polymerase II subunit RPB1

OrganismNot specified

UniProt P24928

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 × 21 DNA 2 PDB declaration: 23-meric（23） Consistent with all polymer counts Chain A； UniProt 1–1970 Not recorded DNA-directed RNA polymerase II subunit RPB2 × 1 （P30876） DNA-directed RNA polymerase II subunit RPB3 × 1 （P19387） DNA-directed RNA polymerase II subunit RPB4 × 1 （O15514） DNA-directed RNA polymerase II subunit RPB5 × 1 （P19388） DNA-directed RNA polymerase II subunit RPB6 × 1 （P61218） DNA-directed RNA polymerase II subunit RPB7 × 1 （P62487） DNA-directed RNA polymerase II subunit RPB8 × 1 （P52434） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36954） DNA-directed RNA polymerase II subunit RPB10 × 1 （P62875） DNA-directed RNA polymerase II subunit RPB11-a × 1 （P52435） DNA-directed RNA polymerase II subunit RPB12 × 1 （P53803） Transcription initiation factor IIB × 1 （Q00403） Transcription initiation factor IIA subunit 1 × 1 （P52655） Transcription initiation factor IIA subunit 2 × 1 （P52657） TATA-box-binding protein × 1 （P20226） General transcription factor IIE subunit 1 × 1 （P29083） Transcription initiation factor IIE subunit beta × 1 （P29084） General transcription factor IIF subunit 1 × 1 （P35269） General transcription factor IIF subunit 2 × 1 （P13984） Transcription elongation factor A protein 1 × 1 （P23193） SCP-X × 1 SCP-Y × 1 MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV). Resolution 3.90 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 5IYC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2GHQ CTD-specific phosphatase Scp1 in complex with peptide C-terminal domain of RNA polymerase II Deposited 2006-03-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1795–1803（9 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；(1)0.5M Ammonium sulfate, 0.2M Lithium sulfate, 100mM HEPES 7.5 (2) 1M sodium tartrate, 100mM Tris pH 8.5 , pH 7.5 - 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.05 Å R-free 0.248
2GHQ CTD-specific phosphatase Scp1 in complex with peptide C-terminal domain of RNA polymerase II Deposited 2006-03-27 Different construct Different mutation/modification 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 1795–1803（9 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；(1)0.5M Ammonium sulfate, 0.2M Lithium sulfate, 100mM HEPES 7.5 (2) 1M sodium tartrate, 100mM Tris pH 8.5 , pH 7.5 - 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.05 Å R-free 0.248
2GHT CTD-specific phosphatase Scp1 in complex with peptide from C-terminal domain of RNA polymerase II Deposited 2006-03-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1796–1803（8 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；(1) 0.5M Ammonium sulfate, 0.2M Lithium sulfate, 100mM HEPES 7.5 (2) 2M sodium tartrate, 100mM Tris pH 8.5, pH 7.5 - 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.80 Å R-free 0.232
2GHT CTD-specific phosphatase Scp1 in complex with peptide from C-terminal domain of RNA polymerase II Deposited 2006-03-27 Different construct Different mutation/modification 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 1796–1803（8 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；(1) 0.5M Ammonium sulfate, 0.2M Lithium sulfate, 100mM HEPES 7.5 (2) 2M sodium tartrate, 100mM Tris pH 8.5, pH 7.5 - 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.80 Å R-free 0.232
2LTO TDRD3 complex Deposited 2012-05-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1804–1816（13 aa） Fragment：UNP residues 1804-1816
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 8；293.15 K；Ionic strength (raw mmCIF value) 150；Pressure ambient
NMR sample composition 1.7 mM [U-99% 13C; U-99% 15N] protein_1, 50 mM sodium phosphate, 10 mM beta-mercaptoethanol, 150 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
4JXT CID of human RPRD1A in complex with a phosphorylated peptide from RPB1-CTD Deposited 2013-03-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1612–1630（19 aa） Fragment：UNP residues 1612-1630
Non-standard monomer：Yes (specific site not provided by mmCIF) UNX UNKNOWN LIGAND × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；20% PEG-4000, 10% isopropanol, 0.1M HEPES., pH 7.5, vapor diffusion, temperature 291K
Resolution 1.90 Å R-free 0.237
5IY6 Human holo-PIC in the closed state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain A 1–1970（1970 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.20 Å
5IY7 Human holo-PIC in the open state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain A 1–1970（1970 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 8.60 Å
5IY8 Human holo-PIC in the initial transcribing state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain A 1–1970（1970 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.90 Å
5IY9 Human holo-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric
Chain A 1–1970（1970 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 6.30 Å
5IYA Human core-PIC in the closed state Deposited 2016-03-24 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain A 1–1970（1970 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 5.40 Å
5IYB Human core-PIC in the open state Deposited 2016-03-24 Parsed fields agree Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain A 1–1970（1970 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
5IYD Human core-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain A 1–1970（1970 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
6DRD RNA Pol II(G) Deposited 2018-06-11 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain A 1–1970（1970 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6G0R Crystal Structure of the first bromodomain of human BRD4 in complex with an acetylated POLR2A peptide (K775ac/K778ac) Deposited 2018-03-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 772–782（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；20.0 % PEG 6K 10.0 % EtGly 0.1 M HEPES pH 7.0 0.1 M MgCl2
Resolution 1.25 Å R-free 0.175
6O9L Human holo-PIC in the closed state Deposited 2019-03-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 31 PDB declaration: 33-meric
Chain A 1–1970（1970 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
6XRE Structure of the p53/RNA polymerase II assembly Deposited 2020-07-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain A 1–1970（1970 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；The assembled p53/Pol II co-complex was applied directly on the grid for 10 sec followed by 5.5 sec of blotting. The sample grid was then washed with 3.5% trehalose in 0.1 M KCl/HEM buffer (20 mM HEPES, 0.2 mM EDTA, 2 mM MgCl2 at pH 7.9) for 10 sec, blotted for 5.5 sec, and finally frozen in liquid ethane.
Resolution 4.60 Å
7EGB TFIID-based holo PIC on SCP promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain o 1–1970（1970 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7EGC p53-bound TFIID-based holo PIC on HDM2 promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain o 1–1970（1970 aa）
Not recorded ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7LBM Structure of the human Mediator-bound transcription pre-initiation complex Deposited 2021-01-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 54 PDB declaration: 56-meric
Chain A 1–1970（1970 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7YCX The structure of INTAC-PEC complex Deposited 2022-07-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain 1 1–1699（1699 aa）
Chain 1 1704–1856（153 aa）
Chain 1 1865–1970（106 aa）
Not recorded ZN ZINC ION × 10 MN MANGANESE (II) ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.18 Å
8XRJ RNA polymerase II elongation complex with upstream nucleosome extracted from human nuclei Deposited 2024-01-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain A 1–1970（1970 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8XRM RNA polymerase II elongation complex with DSIF, SPT6, and ELOF1 transcribing genomic DNA extracted from human nuclei Deposited 2024-01-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: 19-meric
Chain A 1–1970（1970 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
8XSO RNA polymerase II elongation complex transcribing genomic DNA extracted from human nuclei Deposited 2024-01-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain A 1–1970（1970 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8XVS RNA polymerase II elongation complex with downstream nucleosome extracted from human nuclei Deposited 2024-01-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain A 1–1970（1970 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 4.10 Å
9B9L RPRD1B C-terminal interacting domain bound to a pThr4 CTD peptide Deposited 2024-04-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1616–1630（15 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Co-crystallization of CID with CTD peptide occurred in a reservoir solution of 20-32% PEG3350 and 0.1M lithium sulfate. 1:3 molar ratio of protein to peptide was used
Resolution 2.50 Å R-free 0.347
9EHZ Cryo-EM structure of Human RNA polymerase II Elongation Complex in an Intermediate Translocation State Deposited 2024-11-25 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 1–1970（1970 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
9EI1 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the absence of nucleotide Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain A 1–1970（1970 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9EI2 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to an apo RECQL5 helicase (RECQL5 IRI Module focused-classified) Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1970（1970 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9EI3 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the presence of AMPPNP Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain A 1–1970（1970 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9EI4 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the presence of ADP Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain A 1–1970（1970 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9HM8 NMR solution structure of RPRD2 CTD-interacting domain and pS2,7 RNAPII CTD peptide. Deposited 2024-12-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1612–1622（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 8；293.15 K；Ionic strength (raw mmCIF value) 100；Pressure 1
NMR sample composition 0.4 mM [U-100% 13C; U-100% 15N] RPRD2 CID, 1 mM pS2pS7 CTD, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
9IA7 NMR solution structure of RPRD2 CTD-interacting domain and pT4 RNAPII CTD peptide. Deposited 2025-02-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1612–1623（12 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 8；293.15 K；Ionic strength (raw mmCIF value) 100；Pressure 1
NMR sample composition 0.5 mM [U-100% 13C; U-100% 15N] RPRD2 CID, 1.5 mM pT4 CTD, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
9QPX BRCA1 BRCT tandem repeat with RNA polymerase II pSer5-CTD peptide Deposited 2025-03-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1615–1628（14 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；0.1M PCB buffer (sodium propionate, sodium cacodylate, BIS-TRIS propane in the molar ratios 2:1:2) pH 6, 25%PEG 1500
Resolution 3.00 Å R-free 0.312
9QPX BRCA1 BRCT tandem repeat with RNA polymerase II pSer5-CTD peptide Deposited 2025-03-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1615–1628（14 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；0.1M PCB buffer (sodium propionate, sodium cacodylate, BIS-TRIS propane in the molar ratios 2:1:2) pH 6, 25%PEG 1500
Resolution 3.00 Å R-free 0.312
9QPX BRCA1 BRCT tandem repeat with RNA polymerase II pSer5-CTD peptide Deposited 2025-03-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 1615–1628（14 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；0.1M PCB buffer (sodium propionate, sodium cacodylate, BIS-TRIS propane in the molar ratios 2:1:2) pH 6, 25%PEG 1500
Resolution 3.00 Å R-free 0.312
9VD9 Cryo-EM structure of the human DSS1-INTAC-PEC complex Deposited 2025-06-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 35 PDB declaration: 38-meric
Chain 1 1–1970（1970 aa）
Chain m 1618–1631（14 aa）
Not recorded ZN ZINC ION × 10 MN MANGANESE (II) ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å

33 other PDB entries and 37 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPB1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–1970； UniProt 1–1970

DNA-directed RNA polymerase II subunit RPB2

OrganismNot specified

UniProt P30876

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 × 21 DNA 2 PDB declaration: 23-meric（23） Consistent with all polymer counts Chain B； UniProt 1–1174 Not recorded DNA-directed RNA polymerase II subunit RPB1 × 1 （P24928） DNA-directed RNA polymerase II subunit RPB3 × 1 （P19387） DNA-directed RNA polymerase II subunit RPB4 × 1 （O15514） DNA-directed RNA polymerase II subunit RPB5 × 1 （P19388） DNA-directed RNA polymerase II subunit RPB6 × 1 （P61218） DNA-directed RNA polymerase II subunit RPB7 × 1 （P62487） DNA-directed RNA polymerase II subunit RPB8 × 1 （P52434） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36954） DNA-directed RNA polymerase II subunit RPB10 × 1 （P62875） DNA-directed RNA polymerase II subunit RPB11-a × 1 （P52435） DNA-directed RNA polymerase II subunit RPB12 × 1 （P53803） Transcription initiation factor IIB × 1 （Q00403） Transcription initiation factor IIA subunit 1 × 1 （P52655） Transcription initiation factor IIA subunit 2 × 1 （P52657） TATA-box-binding protein × 1 （P20226） General transcription factor IIE subunit 1 × 1 （P29083） Transcription initiation factor IIE subunit beta × 1 （P29084） General transcription factor IIF subunit 1 × 1 （P35269） General transcription factor IIF subunit 2 × 1 （P13984） Transcription elongation factor A protein 1 × 1 （P23193） SCP-X × 1 SCP-Y × 1 MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV). Resolution 3.90 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 5IYC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5IY6 Human holo-PIC in the closed state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain B 1–1174（1174 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.20 Å
5IY7 Human holo-PIC in the open state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain B 1–1174（1174 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 8.60 Å
5IY8 Human holo-PIC in the initial transcribing state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain B 1–1174（1174 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.90 Å
5IY9 Human holo-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric
Chain B 1–1174（1174 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 6.30 Å
5IYA Human core-PIC in the closed state Deposited 2016-03-24 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain B 1–1174（1174 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 5.40 Å
5IYB Human core-PIC in the open state Deposited 2016-03-24 Parsed fields agree Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain B 1–1174（1174 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
5IYD Human core-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain B 1–1174（1174 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
6DRD RNA Pol II(G) Deposited 2018-06-11 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain B 1–1174（1174 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6O9L Human holo-PIC in the closed state Deposited 2019-03-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 31 PDB declaration: 33-meric
Chain B 1–1174（1174 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
6XRE Structure of the p53/RNA polymerase II assembly Deposited 2020-07-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain B 1–1174（1174 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；The assembled p53/Pol II co-complex was applied directly on the grid for 10 sec followed by 5.5 sec of blotting. The sample grid was then washed with 3.5% trehalose in 0.1 M KCl/HEM buffer (20 mM HEPES, 0.2 mM EDTA, 2 mM MgCl2 at pH 7.9) for 10 sec, blotted for 5.5 sec, and finally frozen in liquid ethane.
Resolution 4.60 Å
7LBM Structure of the human Mediator-bound transcription pre-initiation complex Deposited 2021-01-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 54 PDB declaration: 56-meric
Chain B 1–1174（1174 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
8XRJ RNA polymerase II elongation complex with upstream nucleosome extracted from human nuclei Deposited 2024-01-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain B 1–1174（1174 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8XRM RNA polymerase II elongation complex with DSIF, SPT6, and ELOF1 transcribing genomic DNA extracted from human nuclei Deposited 2024-01-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: 19-meric
Chain B 1–1174（1174 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
8XSO RNA polymerase II elongation complex transcribing genomic DNA extracted from human nuclei Deposited 2024-01-09 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 1–1174（1174 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8XVS RNA polymerase II elongation complex with downstream nucleosome extracted from human nuclei Deposited 2024-01-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain B 1–1174（1174 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 4.10 Å
9EHZ Cryo-EM structure of Human RNA polymerase II Elongation Complex in an Intermediate Translocation State Deposited 2024-11-25 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 1–1174（1174 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
9EI1 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the absence of nucleotide Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain B 1–1174（1174 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9EI3 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the presence of AMPPNP Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain B 1–1174（1174 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9EI4 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the presence of ADP Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain B 1–1174（1174 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9VD9 Cryo-EM structure of the human DSS1-INTAC-PEC complex Deposited 2025-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 35 PDB declaration: 38-meric
Chain 2 1–1174（1174 aa）
Not recorded ZN ZINC ION × 10 MN MANGANESE (II) ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å

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

View Construct and Data Evidence
UniProt name RPB2_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–1174； UniProt 1–1174

DNA-directed RNA polymerase II subunit RPB3

OrganismNot specified

UniProt P19387

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 × 21 DNA 2 PDB declaration: 23-meric（23） Consistent with all polymer counts Chain C； UniProt 1–275 Not recorded DNA-directed RNA polymerase II subunit RPB1 × 1 （P24928） DNA-directed RNA polymerase II subunit RPB2 × 1 （P30876） DNA-directed RNA polymerase II subunit RPB4 × 1 （O15514） DNA-directed RNA polymerase II subunit RPB5 × 1 （P19388） DNA-directed RNA polymerase II subunit RPB6 × 1 （P61218） DNA-directed RNA polymerase II subunit RPB7 × 1 （P62487） DNA-directed RNA polymerase II subunit RPB8 × 1 （P52434） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36954） DNA-directed RNA polymerase II subunit RPB10 × 1 （P62875） DNA-directed RNA polymerase II subunit RPB11-a × 1 （P52435） DNA-directed RNA polymerase II subunit RPB12 × 1 （P53803） Transcription initiation factor IIB × 1 （Q00403） Transcription initiation factor IIA subunit 1 × 1 （P52655） Transcription initiation factor IIA subunit 2 × 1 （P52657） TATA-box-binding protein × 1 （P20226） General transcription factor IIE subunit 1 × 1 （P29083） Transcription initiation factor IIE subunit beta × 1 （P29084） General transcription factor IIF subunit 1 × 1 （P35269） General transcription factor IIF subunit 2 × 1 （P13984） Transcription elongation factor A protein 1 × 1 （P23193） SCP-X × 1 SCP-Y × 1 MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV). Resolution 3.90 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 5IYC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5IY6 Human holo-PIC in the closed state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain C 1–275（275 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.20 Å
5IY7 Human holo-PIC in the open state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain C 1–275（275 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 8.60 Å
5IY8 Human holo-PIC in the initial transcribing state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain C 1–275（275 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.90 Å
5IY9 Human holo-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric
Chain C 1–275（275 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 6.30 Å
5IYA Human core-PIC in the closed state Deposited 2016-03-24 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain C 1–275（275 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 5.40 Å
5IYB Human core-PIC in the open state Deposited 2016-03-24 Parsed fields agree Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain C 1–275（275 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
5IYD Human core-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain C 1–275（275 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
6DRD RNA Pol II(G) Deposited 2018-06-11 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain C 1–275（275 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6O9L Human holo-PIC in the closed state Deposited 2019-03-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 31 PDB declaration: 33-meric
Chain C 1–275（275 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
6XRE Structure of the p53/RNA polymerase II assembly Deposited 2020-07-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain C 1–275（275 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；The assembled p53/Pol II co-complex was applied directly on the grid for 10 sec followed by 5.5 sec of blotting. The sample grid was then washed with 3.5% trehalose in 0.1 M KCl/HEM buffer (20 mM HEPES, 0.2 mM EDTA, 2 mM MgCl2 at pH 7.9) for 10 sec, blotted for 5.5 sec, and finally frozen in liquid ethane.
Resolution 4.60 Å
7LBM Structure of the human Mediator-bound transcription pre-initiation complex Deposited 2021-01-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 54 PDB declaration: 56-meric
Chain C 1–275（275 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
8XRJ RNA polymerase II elongation complex with upstream nucleosome extracted from human nuclei Deposited 2024-01-07 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 C 1–275（275 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8XRM RNA polymerase II elongation complex with DSIF, SPT6, and ELOF1 transcribing genomic DNA extracted from human nuclei Deposited 2024-01-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: 19-meric
Chain C 1–275（275 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
8XSO RNA polymerase II elongation complex transcribing genomic DNA extracted from human nuclei Deposited 2024-01-09 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 1–275（275 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8XVS RNA polymerase II elongation complex with downstream nucleosome extracted from human nuclei Deposited 2024-01-15 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 C 1–275（275 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 4.10 Å
9EHZ Cryo-EM structure of Human RNA polymerase II Elongation Complex in an Intermediate Translocation State Deposited 2024-11-25 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 1–275（275 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
9EI1 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the absence of nucleotide Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain C 1–275（275 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9EI3 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the presence of AMPPNP Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain C 1–275（275 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9EI4 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the presence of ADP Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain C 1–275（275 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9VD9 Cryo-EM structure of the human DSS1-INTAC-PEC complex Deposited 2025-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 35 PDB declaration: 38-meric
Chain 3 1–275（275 aa）
Not recorded ZN ZINC ION × 10 MN MANGANESE (II) ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å

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

View Construct and Data Evidence
UniProt name RPB3_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–275； UniProt 1–275

DNA-directed RNA polymerase II subunit RPB4

OrganismNot specified

UniProt O15514

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 × 21 DNA 2 PDB declaration: 23-meric（23） Consistent with all polymer counts Chain D； UniProt 1–142 Not recorded DNA-directed RNA polymerase II subunit RPB1 × 1 （P24928） DNA-directed RNA polymerase II subunit RPB2 × 1 （P30876） DNA-directed RNA polymerase II subunit RPB3 × 1 （P19387） DNA-directed RNA polymerase II subunit RPB5 × 1 （P19388） DNA-directed RNA polymerase II subunit RPB6 × 1 （P61218） DNA-directed RNA polymerase II subunit RPB7 × 1 （P62487） DNA-directed RNA polymerase II subunit RPB8 × 1 （P52434） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36954） DNA-directed RNA polymerase II subunit RPB10 × 1 （P62875） DNA-directed RNA polymerase II subunit RPB11-a × 1 （P52435） DNA-directed RNA polymerase II subunit RPB12 × 1 （P53803） Transcription initiation factor IIB × 1 （Q00403） Transcription initiation factor IIA subunit 1 × 1 （P52655） Transcription initiation factor IIA subunit 2 × 1 （P52657） TATA-box-binding protein × 1 （P20226） General transcription factor IIE subunit 1 × 1 （P29083） Transcription initiation factor IIE subunit beta × 1 （P29084） General transcription factor IIF subunit 1 × 1 （P35269） General transcription factor IIF subunit 2 × 1 （P13984） Transcription elongation factor A protein 1 × 1 （P23193） SCP-X × 1 SCP-Y × 1 MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV). Resolution 3.90 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 5IYC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2C35 Subunits Rpb4 and Rpb7 of human RNA polymerase II Deposited 2005-10-04 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–142（142 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.4；291 K；VAPOUR DIFFUSION AT 18C USING EQUAL VOLUMES OF PROTEIN AT 15MG/ML IN 20MM PIPES PH 6.8, 100MM NACL, 15% GLYCEROL, PRECIPITANT CONTAINING 100MM PIPES PH 7.4, 25% PEG (MW4000), 15% GLYCEROL.
Resolution 2.70 Å R-free 0.266
2C35 Subunits Rpb4 and Rpb7 of human RNA polymerase II Deposited 2005-10-04 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–142（142 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.4；291 K；VAPOUR DIFFUSION AT 18C USING EQUAL VOLUMES OF PROTEIN AT 15MG/ML IN 20MM PIPES PH 6.8, 100MM NACL, 15% GLYCEROL, PRECIPITANT CONTAINING 100MM PIPES PH 7.4, 25% PEG (MW4000), 15% GLYCEROL.
Resolution 2.70 Å R-free 0.266
2C35 Subunits Rpb4 and Rpb7 of human RNA polymerase II Deposited 2005-10-04 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–142（142 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.4；291 K；VAPOUR DIFFUSION AT 18C USING EQUAL VOLUMES OF PROTEIN AT 15MG/ML IN 20MM PIPES PH 6.8, 100MM NACL, 15% GLYCEROL, PRECIPITANT CONTAINING 100MM PIPES PH 7.4, 25% PEG (MW4000), 15% GLYCEROL.
Resolution 2.70 Å R-free 0.266
2C35 Subunits Rpb4 and Rpb7 of human RNA polymerase II Deposited 2005-10-04 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 1–142（142 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.4；291 K；VAPOUR DIFFUSION AT 18C USING EQUAL VOLUMES OF PROTEIN AT 15MG/ML IN 20MM PIPES PH 6.8, 100MM NACL, 15% GLYCEROL, PRECIPITANT CONTAINING 100MM PIPES PH 7.4, 25% PEG (MW4000), 15% GLYCEROL.
Resolution 2.70 Å R-free 0.266
5IY6 Human holo-PIC in the closed state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain D 1–142（142 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.20 Å
5IY7 Human holo-PIC in the open state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain D 1–142（142 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 8.60 Å
5IY8 Human holo-PIC in the initial transcribing state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain D 1–142（142 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.90 Å
5IY9 Human holo-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric
Chain D 1–142（142 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 6.30 Å
5IYA Human core-PIC in the closed state Deposited 2016-03-24 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain D 1–142（142 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 5.40 Å
5IYB Human core-PIC in the open state Deposited 2016-03-24 Parsed fields agree Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain D 1–142（142 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
5IYD Human core-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain D 1–142（142 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
6DRD RNA Pol II(G) Deposited 2018-06-11 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain D 1–142（142 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6O9L Human holo-PIC in the closed state Deposited 2019-03-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 31 PDB declaration: 33-meric
Chain D 1–142（142 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
6XRE Structure of the p53/RNA polymerase II assembly Deposited 2020-07-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain D 1–142（142 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；The assembled p53/Pol II co-complex was applied directly on the grid for 10 sec followed by 5.5 sec of blotting. The sample grid was then washed with 3.5% trehalose in 0.1 M KCl/HEM buffer (20 mM HEPES, 0.2 mM EDTA, 2 mM MgCl2 at pH 7.9) for 10 sec, blotted for 5.5 sec, and finally frozen in liquid ethane.
Resolution 4.60 Å
7LBM Structure of the human Mediator-bound transcription pre-initiation complex Deposited 2021-01-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 54 PDB declaration: 56-meric
Chain D 1–142（142 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
8XRJ RNA polymerase II elongation complex with upstream nucleosome extracted from human nuclei Deposited 2024-01-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain D 1–142（142 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8XRM RNA polymerase II elongation complex with DSIF, SPT6, and ELOF1 transcribing genomic DNA extracted from human nuclei Deposited 2024-01-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: 19-meric
Chain D 1–142（142 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
8XSO RNA polymerase II elongation complex transcribing genomic DNA extracted from human nuclei Deposited 2024-01-09 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 1–142（142 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8XVS RNA polymerase II elongation complex with downstream nucleosome extracted from human nuclei Deposited 2024-01-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain D 1–142（142 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 4.10 Å
9EHZ Cryo-EM structure of Human RNA polymerase II Elongation Complex in an Intermediate Translocation State Deposited 2024-11-25 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 1–142（142 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
9EI1 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the absence of nucleotide Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain D 1–142（142 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9EI3 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the presence of AMPPNP Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain D 1–142（142 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9EI4 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the presence of ADP Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain D 1–142（142 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9VD9 Cryo-EM structure of the human DSS1-INTAC-PEC complex Deposited 2025-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 35 PDB declaration: 38-meric
Chain l 1–142（142 aa）
Not recorded ZN ZINC ION × 10 MN MANGANESE (II) ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å

21 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPB4_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain D； PDBConstruct 1–142； UniProt 1–142

DNA-directed RNA polymerase II subunit RPB5

OrganismNot specified

UniProt P19388

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 × 21 DNA 2 PDB declaration: 23-meric（23） Consistent with all polymer counts Chain E； UniProt 1–210 Not recorded DNA-directed RNA polymerase II subunit RPB1 × 1 （P24928） DNA-directed RNA polymerase II subunit RPB2 × 1 （P30876） DNA-directed RNA polymerase II subunit RPB3 × 1 （P19387） DNA-directed RNA polymerase II subunit RPB4 × 1 （O15514） DNA-directed RNA polymerase II subunit RPB6 × 1 （P61218） DNA-directed RNA polymerase II subunit RPB7 × 1 （P62487） DNA-directed RNA polymerase II subunit RPB8 × 1 （P52434） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36954） DNA-directed RNA polymerase II subunit RPB10 × 1 （P62875） DNA-directed RNA polymerase II subunit RPB11-a × 1 （P52435） DNA-directed RNA polymerase II subunit RPB12 × 1 （P53803） Transcription initiation factor IIB × 1 （Q00403） Transcription initiation factor IIA subunit 1 × 1 （P52655） Transcription initiation factor IIA subunit 2 × 1 （P52657） TATA-box-binding protein × 1 （P20226） General transcription factor IIE subunit 1 × 1 （P29083） Transcription initiation factor IIE subunit beta × 1 （P29084） General transcription factor IIF subunit 1 × 1 （P35269） General transcription factor IIF subunit 2 × 1 （P13984） Transcription elongation factor A protein 1 × 1 （P23193） SCP-X × 1 SCP-Y × 1 MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV). Resolution 3.90 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 5IYC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5IY6 Human holo-PIC in the closed state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain E 1–210（210 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.20 Å
5IY7 Human holo-PIC in the open state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain E 1–210（210 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 8.60 Å
5IY8 Human holo-PIC in the initial transcribing state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain E 1–210（210 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.90 Å
5IY9 Human holo-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric
Chain E 1–210（210 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 6.30 Å
5IYA Human core-PIC in the closed state Deposited 2016-03-24 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain E 1–210（210 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 5.40 Å
5IYB Human core-PIC in the open state Deposited 2016-03-24 Parsed fields agree Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain E 1–210（210 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
5IYD Human core-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain E 1–210（210 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
6DRD RNA Pol II(G) Deposited 2018-06-11 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain E 1–210（210 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6O9L Human holo-PIC in the closed state Deposited 2019-03-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 31 PDB declaration: 33-meric
Chain E 1–210（210 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
6XRE Structure of the p53/RNA polymerase II assembly Deposited 2020-07-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain E 1–210（210 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；The assembled p53/Pol II co-complex was applied directly on the grid for 10 sec followed by 5.5 sec of blotting. The sample grid was then washed with 3.5% trehalose in 0.1 M KCl/HEM buffer (20 mM HEPES, 0.2 mM EDTA, 2 mM MgCl2 at pH 7.9) for 10 sec, blotted for 5.5 sec, and finally frozen in liquid ethane.
Resolution 4.60 Å
7A6H Cryo-EM structure of human apo RNA Polymerase III Deposited 2020-08-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain E 1–210（210 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Wait time 10 s Blot force 4 Blot time 4 s
Resolution 3.30 Å
7AE1 Cryo-EM structure of human RNA Polymerase III elongation complex 1 Deposited 2020-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain E 1–210（210 aa）
Not recorded ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Wait time 10 s Blot force 4 Blot time 4 s
Resolution 2.80 Å
7AE3 Cryo-EM structure of human RNA Polymerase III elongation complex 3 Deposited 2020-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain E 1–210（210 aa）
Not recorded ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Wait time 10 s Blot force 4 Blot time 4 s
Resolution 3.10 Å
7AEA Cryo-EM structure of human RNA Polymerase III elongation complex 2 Deposited 2020-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain E 1–210（210 aa）
Not recorded ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Wait time 10 s Blot force 4 Blot time 4 s
Resolution 3.40 Å
7AST Apo Human RNA Polymerase III Deposited 2020-10-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain F 1–210（210 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7D58 cryo-EM structure of human RNA polymerase III in elongating state Deposited 2020-09-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain E 1–210（210 aa）
Not recorded ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7D59 cryo-EM structure of human RNA polymerase III in apo state Deposited 2020-09-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain E 1–210（210 aa）
Not recorded ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7DN3 Structure of Human RNA Polymerase III elongation complex Deposited 2020-12-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain E 1–210（210 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 6 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7DU2 RNA polymerase III EC complex in post-translocation state Deposited 2021-01-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain E 1–210（210 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 6 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.35 Å
7FJI human Pol III elongation complex Deposited 2021-08-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain E 1–210（210 aa）
Not recorded ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
Resolution 3.60 Å
7FJJ human Pol III pre-termination complex Deposited 2021-08-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain E 1–210（210 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
Resolution 3.60 Å
7LBM Structure of the human Mediator-bound transcription pre-initiation complex Deposited 2021-01-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 54 PDB declaration: 56-meric
Chain E 1–210（210 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7OB9 Cryo-EM structure of human RNA Polymerase I in elongation state Deposited 2021-04-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain E 1–210（210 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 3, blot time 0 s, wait time 0 s
Resolution 2.70 Å
7OBA Cryo-EM structure of human RNA Polymerase I in complex with RRN3 Deposited 2021-04-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain E 1–210（210 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 3, blot time 0 s, wait time 0 s
Resolution 3.10 Å
7OBB Cryo-EM structure of human RNA Polymerase I Open Complex Deposited 2021-04-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain E 1–210（210 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 3, blot time 0 s, wait time 0 s
Resolution 3.30 Å
7VBA Structure of the pre state human RNA Polymerase I Elongation Complex Deposited 2021-08-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain E 1–210（210 aa）
Not recorded ZN ZINC ION × 5 MG MAGNESIUM ION × 1 2TM 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.89 Å
7VBB Structure of the post state human RNA Polymerase I Elongation Complex Deposited 2021-08-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain E 1–210（210 aa）
Not recorded ZN ZINC ION × 5 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.81 Å
7VBC Back track state of human RNA Polymerase I Elongation Complex Deposited 2021-08-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain E 1–210（210 aa）
Not recorded ZN ZINC ION × 5 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.01 Å
8A43 Human RNA polymerase I Deposited 2022-06-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain E 1–210（210 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.09 Å
8ITY human RNA polymerase III pre-initiation complex closed DNA 1 Deposited 2023-03-23 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain E 1–210（210 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
8IUE RNA polymerase III pre-initiation complex melting complex 1 Deposited 2023-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain E 1–210（210 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.10 Å
8IUH RNA polymerase III pre-initiation complex open complex 1 Deposited 2023-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain E 1–210（210 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.40 Å
8XRJ RNA polymerase II elongation complex with upstream nucleosome extracted from human nuclei Deposited 2024-01-07 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 E 1–210（210 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8XRM RNA polymerase II elongation complex with DSIF, SPT6, and ELOF1 transcribing genomic DNA extracted from human nuclei Deposited 2024-01-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: 19-meric
Chain E 1–210（210 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
8XSO RNA polymerase II elongation complex transcribing genomic DNA extracted from human nuclei Deposited 2024-01-09 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 1–210（210 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8XVS RNA polymerase II elongation complex with downstream nucleosome extracted from human nuclei Deposited 2024-01-15 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 E 1–210（210 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 4.10 Å
9EHZ Cryo-EM structure of Human RNA polymerase II Elongation Complex in an Intermediate Translocation State Deposited 2024-11-25 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 1–210（210 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
9EI1 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the absence of nucleotide Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain E 1–210（210 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9EI3 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the presence of AMPPNP Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain E 1–210（210 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9EI4 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the presence of ADP Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain E 1–210（210 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9FSO Human RNA Polymerase III Class III Open Pre-initiation Complex 1 (OC1) Deposited 2024-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain M 1–210（210 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.28 Å
9FSP RNA Polymerase III Class III Open Pre-initation Complex 2 (OC2) Deposited 2024-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain M 1–210（210 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
9FSQ RNA Polymerase III Class III Melting Pre-Initiation Complex (MC) Deposited 2024-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain M 1–210（210 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.51 Å
9FSR RNA Polymerase III Class III Open Mini Pre-initiation Complex 1 (OC1-mini) Deposited 2024-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain M 1–210（210 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.76 Å
9FSS RNA Polymerase III Class III Open Mini Pre-Initiation complex 2 (OC2-mini) Deposited 2024-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain M 1–210（210 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.14 Å
9K2G Human RNA Polymerase III de novo transcribing complex 13 (TC13) Deposited 2024-10-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric
Chain E 1–210（210 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.00 Å
9K36 Human RNA Polymerase III de novo transcribing complex 12 (TC12) Deposited 2024-10-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric
Chain E 1–210（210 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.90 Å
9K38 Human RNA Polymerase III de novo transcribing complex 6 (TC6) Deposited 2024-10-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric
Chain E 1–210（210 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.10 Å
9K39 Human RNA Polymerase III de novo transcribing complex 8 (TC8) Deposited 2024-10-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric
Chain E 1–210（210 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.80 Å
9K3B Human RNA Polymerase III de novo transcribing complex 10 overall (TC10-overall) Deposited 2024-10-18 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 E 1–210（210 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.80 Å
9K3U Human RNA Polymerase III de novo transcribing complex 5 (TC5) Deposited 2024-10-20 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 E 1–210（210 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.00 Å
9K3V Human RNA Polymerase III de novo transcribing complex 4 (TC4) Deposited 2024-10-20 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 E 1–210（210 aa）
Not recorded ZN ZINC ION × 7 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.50 Å
9LKT Human RNA Polymerase III de novo transcribing complex 10 (TC10) Deposited 2025-01-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric
Chain E 1–210（210 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.50 Å
9LXN Human RNA Polymerase III de novo transcribing complex 5 (TC5)(without 3'dATP) Deposited 2025-02-18 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 E 1–210（210 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.30 Å
9LXO Human RNA Polymerase III de novo transcribing complex 6 (TC6)(without 3'dATP) Deposited 2025-02-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric
Chain E 1–210（210 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.60 Å
9VD9 Cryo-EM structure of the human DSS1-INTAC-PEC complex Deposited 2025-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 35 PDB declaration: 38-meric
Chain 4 1–210（210 aa）
Not recorded ZN ZINC ION × 10 MN MANGANESE (II) ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å

56 other PDB entries and 56 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPAB1_HUMAN
Isoform —
PDB entities 5
Chains and sequence ranges Author chain E； PDBConstruct 1–210； UniProt 1–210

DNA-directed RNA polymerase II subunit RPB6

OrganismNot specified

UniProt P61218

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 × 21 DNA 2 PDB declaration: 23-meric（23） Consistent with all polymer counts Chain F； UniProt 1–127 Not recorded DNA-directed RNA polymerase II subunit RPB1 × 1 （P24928） DNA-directed RNA polymerase II subunit RPB2 × 1 （P30876） DNA-directed RNA polymerase II subunit RPB3 × 1 （P19387） DNA-directed RNA polymerase II subunit RPB4 × 1 （O15514） DNA-directed RNA polymerase II subunit RPB5 × 1 （P19388） DNA-directed RNA polymerase II subunit RPB7 × 1 （P62487） DNA-directed RNA polymerase II subunit RPB8 × 1 （P52434） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36954） DNA-directed RNA polymerase II subunit RPB10 × 1 （P62875） DNA-directed RNA polymerase II subunit RPB11-a × 1 （P52435） DNA-directed RNA polymerase II subunit RPB12 × 1 （P53803） Transcription initiation factor IIB × 1 （Q00403） Transcription initiation factor IIA subunit 1 × 1 （P52655） Transcription initiation factor IIA subunit 2 × 1 （P52657） TATA-box-binding protein × 1 （P20226） General transcription factor IIE subunit 1 × 1 （P29083） Transcription initiation factor IIE subunit beta × 1 （P29084） General transcription factor IIF subunit 1 × 1 （P35269） General transcription factor IIF subunit 2 × 1 （P13984） Transcription elongation factor A protein 1 × 1 （P23193） SCP-X × 1 SCP-Y × 1 MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV). Resolution 3.90 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 5IYC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5IY6 Human holo-PIC in the closed state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain F 1–127（127 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.20 Å
5IY7 Human holo-PIC in the open state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain F 1–127（127 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 8.60 Å
5IY8 Human holo-PIC in the initial transcribing state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain F 1–127（127 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.90 Å
5IY9 Human holo-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric
Chain F 1–127（127 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 6.30 Å
5IYA Human core-PIC in the closed state Deposited 2016-03-24 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain F 1–127（127 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 5.40 Å
5IYB Human core-PIC in the open state Deposited 2016-03-24 Parsed fields agree Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain F 1–127（127 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
5IYD Human core-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain F 1–127（127 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
6DRD RNA Pol II(G) Deposited 2018-06-11 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain F 1–127（127 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6O9L Human holo-PIC in the closed state Deposited 2019-03-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 31 PDB declaration: 33-meric
Chain F 1–127（127 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
6XRE Structure of the p53/RNA polymerase II assembly Deposited 2020-07-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain F 1–127（127 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；The assembled p53/Pol II co-complex was applied directly on the grid for 10 sec followed by 5.5 sec of blotting. The sample grid was then washed with 3.5% trehalose in 0.1 M KCl/HEM buffer (20 mM HEPES, 0.2 mM EDTA, 2 mM MgCl2 at pH 7.9) for 10 sec, blotted for 5.5 sec, and finally frozen in liquid ethane.
Resolution 4.60 Å
7A6H Cryo-EM structure of human apo RNA Polymerase III Deposited 2020-08-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain F 1–127（127 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Wait time 10 s Blot force 4 Blot time 4 s
Resolution 3.30 Å
7AE1 Cryo-EM structure of human RNA Polymerase III elongation complex 1 Deposited 2020-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain F 1–127（127 aa）
Not recorded ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Wait time 10 s Blot force 4 Blot time 4 s
Resolution 2.80 Å
7AE3 Cryo-EM structure of human RNA Polymerase III elongation complex 3 Deposited 2020-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain F 1–127（127 aa）
Not recorded ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Wait time 10 s Blot force 4 Blot time 4 s
Resolution 3.10 Å
7AEA Cryo-EM structure of human RNA Polymerase III elongation complex 2 Deposited 2020-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain F 1–127（127 aa）
Not recorded ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Wait time 10 s Blot force 4 Blot time 4 s
Resolution 3.40 Å
7AST Apo Human RNA Polymerase III Deposited 2020-10-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain E 1–127（127 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7D58 cryo-EM structure of human RNA polymerase III in elongating state Deposited 2020-09-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain F 1–127（127 aa）
Not recorded ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7D59 cryo-EM structure of human RNA polymerase III in apo state Deposited 2020-09-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain F 1–127（127 aa）
Not recorded ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7DN3 Structure of Human RNA Polymerase III elongation complex Deposited 2020-12-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain F 1–127（127 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 6 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7DTH Solution structure of RPB6, common subunit of RNA polymerases I, II, and III Deposited 2021-01-05 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–127（127 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 25；Pressure 1
NMR sample composition 2.0 mM [U-100% 13C; U-100% 15N] RPB6, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 2.0 mM [U-100% 13C; U-100% 15N] RPB6, 100% D2O | 100% D2O
Resolution not provided
7DTI Solution structure of the complex between RNA polymerase subunit RPB6 and TFIIH p62 PH domain Deposited 2021-01-05 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–127（127 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 25；Pressure 1
NMR sample composition 0.38 mM [U-100% 13C; U-100% 15N] RPB6, 0.38 mM TFIIH p62, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.38 mM [U-100% 13C; U-100% 15N] RPB6, 0.38 mM TFIIH p62, 100% D2O | 100% D2O
NMR sample composition 0.38 mM [U-100% 13C; U-100% 15N] TFIIH p62, 0.38 mM RPB6, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.38 mM [U-100% 13C; U-100% 15N] TFIIH p62, 0.38 mM RPB6, 100% D2O | 100% D2O
Resolution not provided
7DU2 RNA polymerase III EC complex in post-translocation state Deposited 2021-01-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain F 1–127（127 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 6 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.35 Å
7FJI human Pol III elongation complex Deposited 2021-08-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain F 1–127（127 aa）
Not recorded ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
Resolution 3.60 Å
7FJJ human Pol III pre-termination complex Deposited 2021-08-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain F 1–127（127 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
Resolution 3.60 Å
7LBM Structure of the human Mediator-bound transcription pre-initiation complex Deposited 2021-01-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 54 PDB declaration: 56-meric
Chain F 1–127（127 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7OB9 Cryo-EM structure of human RNA Polymerase I in elongation state Deposited 2021-04-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain F 1–127（127 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 3, blot time 0 s, wait time 0 s
Resolution 2.70 Å
7OBA Cryo-EM structure of human RNA Polymerase I in complex with RRN3 Deposited 2021-04-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain F 1–127（127 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 3, blot time 0 s, wait time 0 s
Resolution 3.10 Å
7OBB Cryo-EM structure of human RNA Polymerase I Open Complex Deposited 2021-04-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain F 1–127（127 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 3, blot time 0 s, wait time 0 s
Resolution 3.30 Å
7VBA Structure of the pre state human RNA Polymerase I Elongation Complex Deposited 2021-08-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain F 1–127（127 aa）
Not recorded ZN ZINC ION × 5 MG MAGNESIUM ION × 1 2TM 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.89 Å
7VBB Structure of the post state human RNA Polymerase I Elongation Complex Deposited 2021-08-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain F 1–127（127 aa）
Not recorded ZN ZINC ION × 5 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.81 Å
7VBC Back track state of human RNA Polymerase I Elongation Complex Deposited 2021-08-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain F 1–127（127 aa）
Not recorded ZN ZINC ION × 5 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.01 Å
8A43 Human RNA polymerase I Deposited 2022-06-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain F 1–127（127 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.09 Å
8ITY human RNA polymerase III pre-initiation complex closed DNA 1 Deposited 2023-03-23 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain F 1–127（127 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
8IUE RNA polymerase III pre-initiation complex melting complex 1 Deposited 2023-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain F 1–127（127 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.10 Å
8IUH RNA polymerase III pre-initiation complex open complex 1 Deposited 2023-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain F 1–127（127 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.40 Å
8XRJ RNA polymerase II elongation complex with upstream nucleosome extracted from human nuclei Deposited 2024-01-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain F 1–127（127 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8XRM RNA polymerase II elongation complex with DSIF, SPT6, and ELOF1 transcribing genomic DNA extracted from human nuclei Deposited 2024-01-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: 19-meric
Chain F 1–127（127 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
8XSO RNA polymerase II elongation complex transcribing genomic DNA extracted from human nuclei Deposited 2024-01-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
Chain F 1–127（127 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8XVS RNA polymerase II elongation complex with downstream nucleosome extracted from human nuclei Deposited 2024-01-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain F 1–127（127 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 4.10 Å
9EHZ Cryo-EM structure of Human RNA polymerase II Elongation Complex in an Intermediate Translocation State Deposited 2024-11-25 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 1–127（127 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
9EI1 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the absence of nucleotide Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain F 1–127（127 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9EI3 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the presence of AMPPNP Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain F 1–127（127 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9EI4 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the presence of ADP Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain F 1–127（127 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9FSO Human RNA Polymerase III Class III Open Pre-initiation Complex 1 (OC1) Deposited 2024-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain N 1–127（127 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.28 Å
9FSP RNA Polymerase III Class III Open Pre-initation Complex 2 (OC2) Deposited 2024-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain N 1–127（127 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
9FSQ RNA Polymerase III Class III Melting Pre-Initiation Complex (MC) Deposited 2024-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain N 1–127（127 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.51 Å
9FSR RNA Polymerase III Class III Open Mini Pre-initiation Complex 1 (OC1-mini) Deposited 2024-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain N 1–127（127 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.76 Å
9FSS RNA Polymerase III Class III Open Mini Pre-Initiation complex 2 (OC2-mini) Deposited 2024-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain N 1–127（127 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.14 Å
9K2G Human RNA Polymerase III de novo transcribing complex 13 (TC13) Deposited 2024-10-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric
Chain F 1–127（127 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.00 Å
9K36 Human RNA Polymerase III de novo transcribing complex 12 (TC12) Deposited 2024-10-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric
Chain F 1–127（127 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.90 Å
9K38 Human RNA Polymerase III de novo transcribing complex 6 (TC6) Deposited 2024-10-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric
Chain F 1–127（127 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.10 Å
9K39 Human RNA Polymerase III de novo transcribing complex 8 (TC8) Deposited 2024-10-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric
Chain F 1–127（127 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.80 Å
9K3B Human RNA Polymerase III de novo transcribing complex 10 overall (TC10-overall) Deposited 2024-10-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain F 1–127（127 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.80 Å
9K3U Human RNA Polymerase III de novo transcribing complex 5 (TC5) Deposited 2024-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain F 1–127（127 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.00 Å
9K3V Human RNA Polymerase III de novo transcribing complex 4 (TC4) Deposited 2024-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain F 1–127（127 aa）
Not recorded ZN ZINC ION × 7 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.50 Å
9LKT Human RNA Polymerase III de novo transcribing complex 10 (TC10) Deposited 2025-01-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric
Chain F 1–127（127 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.50 Å
9LXN Human RNA Polymerase III de novo transcribing complex 5 (TC5)(without 3'dATP) Deposited 2025-02-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain F 1–127（127 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.30 Å
9LXO Human RNA Polymerase III de novo transcribing complex 6 (TC6)(without 3'dATP) Deposited 2025-02-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric
Chain F 1–127（127 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.60 Å
9VD9 Cryo-EM structure of the human DSS1-INTAC-PEC complex Deposited 2025-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 35 PDB declaration: 38-meric
Chain 5 1–127（127 aa）
Not recorded ZN ZINC ION × 10 MN MANGANESE (II) ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å

58 other PDB entries and 58 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPAB2_HUMAN
Isoform —
PDB entities 6
Chains and sequence ranges Author chain F； PDBConstruct 1–127； UniProt 1–127

DNA-directed RNA polymerase II subunit RPB7

OrganismNot specified

UniProt P62487

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 × 21 DNA 2 PDB declaration: 23-meric（23） Consistent with all polymer counts Chain G； UniProt 1–172 Not recorded DNA-directed RNA polymerase II subunit RPB1 × 1 （P24928） DNA-directed RNA polymerase II subunit RPB2 × 1 （P30876） DNA-directed RNA polymerase II subunit RPB3 × 1 （P19387） DNA-directed RNA polymerase II subunit RPB4 × 1 （O15514） DNA-directed RNA polymerase II subunit RPB5 × 1 （P19388） DNA-directed RNA polymerase II subunit RPB6 × 1 （P61218） DNA-directed RNA polymerase II subunit RPB8 × 1 （P52434） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36954） DNA-directed RNA polymerase II subunit RPB10 × 1 （P62875） DNA-directed RNA polymerase II subunit RPB11-a × 1 （P52435） DNA-directed RNA polymerase II subunit RPB12 × 1 （P53803） Transcription initiation factor IIB × 1 （Q00403） Transcription initiation factor IIA subunit 1 × 1 （P52655） Transcription initiation factor IIA subunit 2 × 1 （P52657） TATA-box-binding protein × 1 （P20226） General transcription factor IIE subunit 1 × 1 （P29083） Transcription initiation factor IIE subunit beta × 1 （P29084） General transcription factor IIF subunit 1 × 1 （P35269） General transcription factor IIF subunit 2 × 1 （P13984） Transcription elongation factor A protein 1 × 1 （P23193） SCP-X × 1 SCP-Y × 1 MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV). Resolution 3.90 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 5IYC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2C35 Subunits Rpb4 and Rpb7 of human RNA polymerase II Deposited 2005-10-04 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 1–172（172 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.4；291 K；VAPOUR DIFFUSION AT 18C USING EQUAL VOLUMES OF PROTEIN AT 15MG/ML IN 20MM PIPES PH 6.8, 100MM NACL, 15% GLYCEROL, PRECIPITANT CONTAINING 100MM PIPES PH 7.4, 25% PEG (MW4000), 15% GLYCEROL.
Resolution 2.70 Å R-free 0.266
2C35 Subunits Rpb4 and Rpb7 of human RNA polymerase II Deposited 2005-10-04 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 1–172（172 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.4；291 K；VAPOUR DIFFUSION AT 18C USING EQUAL VOLUMES OF PROTEIN AT 15MG/ML IN 20MM PIPES PH 6.8, 100MM NACL, 15% GLYCEROL, PRECIPITANT CONTAINING 100MM PIPES PH 7.4, 25% PEG (MW4000), 15% GLYCEROL.
Resolution 2.70 Å R-free 0.266
2C35 Subunits Rpb4 and Rpb7 of human RNA polymerase II Deposited 2005-10-04 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–172（172 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.4；291 K；VAPOUR DIFFUSION AT 18C USING EQUAL VOLUMES OF PROTEIN AT 15MG/ML IN 20MM PIPES PH 6.8, 100MM NACL, 15% GLYCEROL, PRECIPITANT CONTAINING 100MM PIPES PH 7.4, 25% PEG (MW4000), 15% GLYCEROL.
Resolution 2.70 Å R-free 0.266
2C35 Subunits Rpb4 and Rpb7 of human RNA polymerase II Deposited 2005-10-04 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–172（172 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.4；291 K；VAPOUR DIFFUSION AT 18C USING EQUAL VOLUMES OF PROTEIN AT 15MG/ML IN 20MM PIPES PH 6.8, 100MM NACL, 15% GLYCEROL, PRECIPITANT CONTAINING 100MM PIPES PH 7.4, 25% PEG (MW4000), 15% GLYCEROL.
Resolution 2.70 Å R-free 0.266
5IY6 Human holo-PIC in the closed state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain G 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.20 Å
5IY7 Human holo-PIC in the open state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain G 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 8.60 Å
5IY8 Human holo-PIC in the initial transcribing state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain G 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.90 Å
5IY9 Human holo-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric
Chain G 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 6.30 Å
5IYA Human core-PIC in the closed state Deposited 2016-03-24 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain G 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 5.40 Å
5IYB Human core-PIC in the open state Deposited 2016-03-24 Parsed fields agree Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain G 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
5IYD Human core-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain G 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
6DRD RNA Pol II(G) Deposited 2018-06-11 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain G 1–172（172 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6O9L Human holo-PIC in the closed state Deposited 2019-03-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 31 PDB declaration: 33-meric
Chain G 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
6XRE Structure of the p53/RNA polymerase II assembly Deposited 2020-07-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain G 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；The assembled p53/Pol II co-complex was applied directly on the grid for 10 sec followed by 5.5 sec of blotting. The sample grid was then washed with 3.5% trehalose in 0.1 M KCl/HEM buffer (20 mM HEPES, 0.2 mM EDTA, 2 mM MgCl2 at pH 7.9) for 10 sec, blotted for 5.5 sec, and finally frozen in liquid ethane.
Resolution 4.60 Å
7LBM Structure of the human Mediator-bound transcription pre-initiation complex Deposited 2021-01-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 54 PDB declaration: 56-meric
Chain G 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
8XRJ RNA polymerase II elongation complex with upstream nucleosome extracted from human nuclei Deposited 2024-01-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain G 1–172（172 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8XRM RNA polymerase II elongation complex with DSIF, SPT6, and ELOF1 transcribing genomic DNA extracted from human nuclei Deposited 2024-01-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: 19-meric
Chain G 1–172（172 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
8XSO RNA polymerase II elongation complex transcribing genomic DNA extracted from human nuclei Deposited 2024-01-09 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 1–172（172 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8XVS RNA polymerase II elongation complex with downstream nucleosome extracted from human nuclei Deposited 2024-01-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain G 1–172（172 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 4.10 Å
9EHZ Cryo-EM structure of Human RNA polymerase II Elongation Complex in an Intermediate Translocation State Deposited 2024-11-25 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 1–172（172 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
9EI1 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the absence of nucleotide Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain G 1–172（172 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9EI3 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the presence of AMPPNP Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain G 1–172（172 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9EI4 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the presence of ADP Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain G 1–172（172 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9VD9 Cryo-EM structure of the human DSS1-INTAC-PEC complex Deposited 2025-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 35 PDB declaration: 38-meric
Chain k 1–172（172 aa）
Not recorded ZN ZINC ION × 10 MN MANGANESE (II) ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å

21 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPB7_HUMAN
Isoform —
PDB entities 7
Chains and sequence ranges Author chain G； PDBConstruct 1–172； UniProt 1–172

DNA-directed RNA polymerase II subunit RPB8

OrganismNot specified

UniProt P52434

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 × 21 DNA 2 PDB declaration: 23-meric（23） Consistent with all polymer counts Chain H； UniProt 1–150 Not recorded DNA-directed RNA polymerase II subunit RPB1 × 1 （P24928） DNA-directed RNA polymerase II subunit RPB2 × 1 （P30876） DNA-directed RNA polymerase II subunit RPB3 × 1 （P19387） DNA-directed RNA polymerase II subunit RPB4 × 1 （O15514） DNA-directed RNA polymerase II subunit RPB5 × 1 （P19388） DNA-directed RNA polymerase II subunit RPB6 × 1 （P61218） DNA-directed RNA polymerase II subunit RPB7 × 1 （P62487） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36954） DNA-directed RNA polymerase II subunit RPB10 × 1 （P62875） DNA-directed RNA polymerase II subunit RPB11-a × 1 （P52435） DNA-directed RNA polymerase II subunit RPB12 × 1 （P53803） Transcription initiation factor IIB × 1 （Q00403） Transcription initiation factor IIA subunit 1 × 1 （P52655） Transcription initiation factor IIA subunit 2 × 1 （P52657） TATA-box-binding protein × 1 （P20226） General transcription factor IIE subunit 1 × 1 （P29083） Transcription initiation factor IIE subunit beta × 1 （P29084） General transcription factor IIF subunit 1 × 1 （P35269） General transcription factor IIF subunit 2 × 1 （P13984） Transcription elongation factor A protein 1 × 1 （P23193） SCP-X × 1 SCP-Y × 1 MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV). Resolution 3.90 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 5IYC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2F3I Solution Structure of a Subunit of RNA Polymerase II Deposited 2005-11-21 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–150（150 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.3；303 K；Ionic strength (raw mmCIF value) 50mM；Pressure ambient
NMR sample composition 0.5mM RNA Polymerase II Subunit U-15N,13C | 20mM potassium phosphate buffer, 10mM DTT; 90% H2O, 10% D2O
Resolution not provided
5IY6 Human holo-PIC in the closed state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain H 1–150（150 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.20 Å
5IY7 Human holo-PIC in the open state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain H 1–150（150 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 8.60 Å
5IY8 Human holo-PIC in the initial transcribing state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain H 1–150（150 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.90 Å
5IY9 Human holo-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric
Chain H 1–150（150 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 6.30 Å
5IYA Human core-PIC in the closed state Deposited 2016-03-24 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain H 1–150（150 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 5.40 Å
5IYB Human core-PIC in the open state Deposited 2016-03-24 Parsed fields agree Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain H 1–150（150 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
5IYD Human core-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain H 1–150（150 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
6DRD RNA Pol II(G) Deposited 2018-06-11 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain H 1–150（150 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6O9L Human holo-PIC in the closed state Deposited 2019-03-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 31 PDB declaration: 33-meric
Chain H 1–150（150 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
6XRE Structure of the p53/RNA polymerase II assembly Deposited 2020-07-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain H 1–150（150 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；The assembled p53/Pol II co-complex was applied directly on the grid for 10 sec followed by 5.5 sec of blotting. The sample grid was then washed with 3.5% trehalose in 0.1 M KCl/HEM buffer (20 mM HEPES, 0.2 mM EDTA, 2 mM MgCl2 at pH 7.9) for 10 sec, blotted for 5.5 sec, and finally frozen in liquid ethane.
Resolution 4.60 Å
7A6H Cryo-EM structure of human apo RNA Polymerase III Deposited 2020-08-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain H 1–150（150 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Wait time 10 s Blot force 4 Blot time 4 s
Resolution 3.30 Å
7AE1 Cryo-EM structure of human RNA Polymerase III elongation complex 1 Deposited 2020-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain H 1–150（150 aa）
Not recorded ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Wait time 10 s Blot force 4 Blot time 4 s
Resolution 2.80 Å
7AE3 Cryo-EM structure of human RNA Polymerase III elongation complex 3 Deposited 2020-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain H 1–150（150 aa）
Not recorded ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Wait time 10 s Blot force 4 Blot time 4 s
Resolution 3.10 Å
7AEA Cryo-EM structure of human RNA Polymerase III elongation complex 2 Deposited 2020-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain H 1–150（150 aa）
Not recorded ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Wait time 10 s Blot force 4 Blot time 4 s
Resolution 3.40 Å
7AST Apo Human RNA Polymerase III Deposited 2020-10-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain D 1–150（150 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7D58 cryo-EM structure of human RNA polymerase III in elongating state Deposited 2020-09-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain H 1–150（150 aa）
Not recorded ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7D59 cryo-EM structure of human RNA polymerase III in apo state Deposited 2020-09-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain H 1–150（150 aa）
Not recorded ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7DN3 Structure of Human RNA Polymerase III elongation complex Deposited 2020-12-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain H 1–150（150 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 6 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7DU2 RNA polymerase III EC complex in post-translocation state Deposited 2021-01-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain H 1–150（150 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 6 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.35 Å
7FJI human Pol III elongation complex Deposited 2021-08-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain H 1–150（150 aa）
Not recorded ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
Resolution 3.60 Å
7FJJ human Pol III pre-termination complex Deposited 2021-08-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain H 1–150（150 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
Resolution 3.60 Å
7LBM Structure of the human Mediator-bound transcription pre-initiation complex Deposited 2021-01-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 54 PDB declaration: 56-meric
Chain H 1–150（150 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7OB9 Cryo-EM structure of human RNA Polymerase I in elongation state Deposited 2021-04-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain H 1–150（150 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 3, blot time 0 s, wait time 0 s
Resolution 2.70 Å
7OBA Cryo-EM structure of human RNA Polymerase I in complex with RRN3 Deposited 2021-04-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain H 1–150（150 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 3, blot time 0 s, wait time 0 s
Resolution 3.10 Å
7OBB Cryo-EM structure of human RNA Polymerase I Open Complex Deposited 2021-04-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain H 1–150（150 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 3, blot time 0 s, wait time 0 s
Resolution 3.30 Å
7VBA Structure of the pre state human RNA Polymerase I Elongation Complex Deposited 2021-08-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain H 1–150（150 aa）
Not recorded ZN ZINC ION × 5 MG MAGNESIUM ION × 1 2TM 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.89 Å
7VBB Structure of the post state human RNA Polymerase I Elongation Complex Deposited 2021-08-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain H 1–150（150 aa）
Not recorded ZN ZINC ION × 5 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.81 Å
7VBC Back track state of human RNA Polymerase I Elongation Complex Deposited 2021-08-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain H 1–150（150 aa）
Not recorded ZN ZINC ION × 5 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.01 Å
8A43 Human RNA polymerase I Deposited 2022-06-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain H 1–150（150 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.09 Å
8ITY human RNA polymerase III pre-initiation complex closed DNA 1 Deposited 2023-03-23 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain H 1–150（150 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
8IUE RNA polymerase III pre-initiation complex melting complex 1 Deposited 2023-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain H 1–150（150 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.10 Å
8IUH RNA polymerase III pre-initiation complex open complex 1 Deposited 2023-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain H 1–150（150 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.40 Å
8XRJ RNA polymerase II elongation complex with upstream nucleosome extracted from human nuclei Deposited 2024-01-07 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 H 1–150（150 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8XRM RNA polymerase II elongation complex with DSIF, SPT6, and ELOF1 transcribing genomic DNA extracted from human nuclei Deposited 2024-01-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: 19-meric
Chain H 1–150（150 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
8XSO RNA polymerase II elongation complex transcribing genomic DNA extracted from human nuclei Deposited 2024-01-09 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 1–150（150 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8XVS RNA polymerase II elongation complex with downstream nucleosome extracted from human nuclei Deposited 2024-01-15 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 H 1–150（150 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 4.10 Å
9EHZ Cryo-EM structure of Human RNA polymerase II Elongation Complex in an Intermediate Translocation State Deposited 2024-11-25 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 1–150（150 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
9EI1 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the absence of nucleotide Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain H 1–150（150 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9EI3 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the presence of AMPPNP Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain H 1–150（150 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9EI4 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the presence of ADP Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain H 1–150（150 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9FSO Human RNA Polymerase III Class III Open Pre-initiation Complex 1 (OC1) Deposited 2024-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain O 1–150（150 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.28 Å
9FSP RNA Polymerase III Class III Open Pre-initation Complex 2 (OC2) Deposited 2024-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain O 1–150（150 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
9FSQ RNA Polymerase III Class III Melting Pre-Initiation Complex (MC) Deposited 2024-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain O 1–150（150 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.51 Å
9FSR RNA Polymerase III Class III Open Mini Pre-initiation Complex 1 (OC1-mini) Deposited 2024-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain O 1–150（150 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.76 Å
9FSS RNA Polymerase III Class III Open Mini Pre-Initiation complex 2 (OC2-mini) Deposited 2024-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain O 1–150（150 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.14 Å
9K2G Human RNA Polymerase III de novo transcribing complex 13 (TC13) Deposited 2024-10-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric
Chain H 1–150（150 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.00 Å
9K36 Human RNA Polymerase III de novo transcribing complex 12 (TC12) Deposited 2024-10-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric
Chain H 1–150（150 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.90 Å
9K38 Human RNA Polymerase III de novo transcribing complex 6 (TC6) Deposited 2024-10-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric
Chain H 1–150（150 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.10 Å
9K39 Human RNA Polymerase III de novo transcribing complex 8 (TC8) Deposited 2024-10-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric
Chain H 1–150（150 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.80 Å
9K3B Human RNA Polymerase III de novo transcribing complex 10 overall (TC10-overall) Deposited 2024-10-18 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 H 1–150（150 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.80 Å
9K3U Human RNA Polymerase III de novo transcribing complex 5 (TC5) Deposited 2024-10-20 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 H 1–150（150 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.00 Å
9K3V Human RNA Polymerase III de novo transcribing complex 4 (TC4) Deposited 2024-10-20 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 H 1–150（150 aa）
Not recorded ZN ZINC ION × 7 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.50 Å
9LKT Human RNA Polymerase III de novo transcribing complex 10 (TC10) Deposited 2025-01-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric
Chain H 1–150（150 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.50 Å
9LXN Human RNA Polymerase III de novo transcribing complex 5 (TC5)(without 3'dATP) Deposited 2025-02-18 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 H 1–150（150 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.30 Å
9LXO Human RNA Polymerase III de novo transcribing complex 6 (TC6)(without 3'dATP) Deposited 2025-02-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric
Chain H 1–150（150 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.60 Å
9VD9 Cryo-EM structure of the human DSS1-INTAC-PEC complex Deposited 2025-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 35 PDB declaration: 38-meric
Chain 6 1–150（150 aa）
Not recorded ZN ZINC ION × 10 MN MANGANESE (II) ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å

57 other PDB entries and 57 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPAB3_HUMAN
Isoform —
PDB entities 8
Chains and sequence ranges Author chain H； PDBConstruct 1–150； UniProt 1–150

DNA-directed RNA polymerase II subunit RPB9

OrganismNot specified

UniProt P36954

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 × 21 DNA 2 PDB declaration: 23-meric（23） Consistent with all polymer counts Chain I； UniProt 1–125 Not recorded DNA-directed RNA polymerase II subunit RPB1 × 1 （P24928） DNA-directed RNA polymerase II subunit RPB2 × 1 （P30876） DNA-directed RNA polymerase II subunit RPB3 × 1 （P19387） DNA-directed RNA polymerase II subunit RPB4 × 1 （O15514） DNA-directed RNA polymerase II subunit RPB5 × 1 （P19388） DNA-directed RNA polymerase II subunit RPB6 × 1 （P61218） DNA-directed RNA polymerase II subunit RPB7 × 1 （P62487） DNA-directed RNA polymerase II subunit RPB8 × 1 （P52434） DNA-directed RNA polymerase II subunit RPB10 × 1 （P62875） DNA-directed RNA polymerase II subunit RPB11-a × 1 （P52435） DNA-directed RNA polymerase II subunit RPB12 × 1 （P53803） Transcription initiation factor IIB × 1 （Q00403） Transcription initiation factor IIA subunit 1 × 1 （P52655） Transcription initiation factor IIA subunit 2 × 1 （P52657） TATA-box-binding protein × 1 （P20226） General transcription factor IIE subunit 1 × 1 （P29083） Transcription initiation factor IIE subunit beta × 1 （P29084） General transcription factor IIF subunit 1 × 1 （P35269） General transcription factor IIF subunit 2 × 1 （P13984） Transcription elongation factor A protein 1 × 1 （P23193） SCP-X × 1 SCP-Y × 1 MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV). Resolution 3.90 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 5IYC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5IY6 Human holo-PIC in the closed state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain I 1–125（125 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.20 Å
5IY7 Human holo-PIC in the open state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain I 1–125（125 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 8.60 Å
5IY8 Human holo-PIC in the initial transcribing state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain I 1–125（125 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.90 Å
5IY9 Human holo-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric
Chain I 1–125（125 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 6.30 Å
5IYA Human core-PIC in the closed state Deposited 2016-03-24 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain I 1–125（125 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 5.40 Å
5IYB Human core-PIC in the open state Deposited 2016-03-24 Parsed fields agree Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain I 1–125（125 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
5IYD Human core-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain I 1–125（125 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
6DRD RNA Pol II(G) Deposited 2018-06-11 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain I 1–125（125 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6O9L Human holo-PIC in the closed state Deposited 2019-03-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 31 PDB declaration: 33-meric
Chain I 1–125（125 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
6XRE Structure of the p53/RNA polymerase II assembly Deposited 2020-07-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain I 1–125（125 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；The assembled p53/Pol II co-complex was applied directly on the grid for 10 sec followed by 5.5 sec of blotting. The sample grid was then washed with 3.5% trehalose in 0.1 M KCl/HEM buffer (20 mM HEPES, 0.2 mM EDTA, 2 mM MgCl2 at pH 7.9) for 10 sec, blotted for 5.5 sec, and finally frozen in liquid ethane.
Resolution 4.60 Å
7LBM Structure of the human Mediator-bound transcription pre-initiation complex Deposited 2021-01-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 54 PDB declaration: 56-meric
Chain I 1–125（125 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
8XRJ RNA polymerase II elongation complex with upstream nucleosome extracted from human nuclei Deposited 2024-01-07 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 I 1–125（125 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8XRM RNA polymerase II elongation complex with DSIF, SPT6, and ELOF1 transcribing genomic DNA extracted from human nuclei Deposited 2024-01-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: 19-meric
Chain I 1–125（125 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
8XSO RNA polymerase II elongation complex transcribing genomic DNA extracted from human nuclei Deposited 2024-01-09 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 1–125（125 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8XVS RNA polymerase II elongation complex with downstream nucleosome extracted from human nuclei Deposited 2024-01-15 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 I 1–125（125 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 4.10 Å
9EHZ Cryo-EM structure of Human RNA polymerase II Elongation Complex in an Intermediate Translocation State Deposited 2024-11-25 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 1–125（125 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
9EI1 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the absence of nucleotide Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain I 1–125（125 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9EI3 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the presence of AMPPNP Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain I 1–125（125 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9EI4 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the presence of ADP Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain I 1–125（125 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9VD9 Cryo-EM structure of the human DSS1-INTAC-PEC complex Deposited 2025-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 35 PDB declaration: 38-meric
Chain 7 1–125（125 aa）
Not recorded ZN ZINC ION × 10 MN MANGANESE (II) ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å

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

View Construct and Data Evidence
UniProt name RPB9_HUMAN
Isoform —
PDB entities 9
Chains and sequence ranges Author chain I； PDBConstruct 1–125； UniProt 1–125

DNA-directed RNA polymerase II subunit RPB10

OrganismNot specified

UniProt P62875

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 × 21 DNA 2 PDB declaration: 23-meric（23） Consistent with all polymer counts Chain J； UniProt 1–67 Not recorded DNA-directed RNA polymerase II subunit RPB1 × 1 （P24928） DNA-directed RNA polymerase II subunit RPB2 × 1 （P30876） DNA-directed RNA polymerase II subunit RPB3 × 1 （P19387） DNA-directed RNA polymerase II subunit RPB4 × 1 （O15514） DNA-directed RNA polymerase II subunit RPB5 × 1 （P19388） DNA-directed RNA polymerase II subunit RPB6 × 1 （P61218） DNA-directed RNA polymerase II subunit RPB7 × 1 （P62487） DNA-directed RNA polymerase II subunit RPB8 × 1 （P52434） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36954） DNA-directed RNA polymerase II subunit RPB11-a × 1 （P52435） DNA-directed RNA polymerase II subunit RPB12 × 1 （P53803） Transcription initiation factor IIB × 1 （Q00403） Transcription initiation factor IIA subunit 1 × 1 （P52655） Transcription initiation factor IIA subunit 2 × 1 （P52657） TATA-box-binding protein × 1 （P20226） General transcription factor IIE subunit 1 × 1 （P29083） Transcription initiation factor IIE subunit beta × 1 （P29084） General transcription factor IIF subunit 1 × 1 （P35269） General transcription factor IIF subunit 2 × 1 （P13984） Transcription elongation factor A protein 1 × 1 （P23193） SCP-X × 1 SCP-Y × 1 MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV). Resolution 3.90 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 5IYC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5IY6 Human holo-PIC in the closed state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain J 1–67（67 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.20 Å
5IY7 Human holo-PIC in the open state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain J 1–67（67 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 8.60 Å
5IY8 Human holo-PIC in the initial transcribing state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain J 1–67（67 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.90 Å
5IY9 Human holo-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric
Chain J 1–67（67 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 6.30 Å
5IYA Human core-PIC in the closed state Deposited 2016-03-24 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain J 1–67（67 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 5.40 Å
5IYB Human core-PIC in the open state Deposited 2016-03-24 Parsed fields agree Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain J 1–67（67 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
5IYD Human core-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain J 1–67（67 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
6DRD RNA Pol II(G) Deposited 2018-06-11 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain J 1–67（67 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6O9L Human holo-PIC in the closed state Deposited 2019-03-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 31 PDB declaration: 33-meric
Chain J 1–67（67 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
6XRE Structure of the p53/RNA polymerase II assembly Deposited 2020-07-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain J 1–67（67 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；The assembled p53/Pol II co-complex was applied directly on the grid for 10 sec followed by 5.5 sec of blotting. The sample grid was then washed with 3.5% trehalose in 0.1 M KCl/HEM buffer (20 mM HEPES, 0.2 mM EDTA, 2 mM MgCl2 at pH 7.9) for 10 sec, blotted for 5.5 sec, and finally frozen in liquid ethane.
Resolution 4.60 Å
7A6H Cryo-EM structure of human apo RNA Polymerase III Deposited 2020-08-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain J 1–67（67 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Wait time 10 s Blot force 4 Blot time 4 s
Resolution 3.30 Å
7AE1 Cryo-EM structure of human RNA Polymerase III elongation complex 1 Deposited 2020-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain J 1–67（67 aa）
Not recorded ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Wait time 10 s Blot force 4 Blot time 4 s
Resolution 2.80 Å
7AE3 Cryo-EM structure of human RNA Polymerase III elongation complex 3 Deposited 2020-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain J 1–67（67 aa）
Not recorded ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Wait time 10 s Blot force 4 Blot time 4 s
Resolution 3.10 Å
7AEA Cryo-EM structure of human RNA Polymerase III elongation complex 2 Deposited 2020-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain J 1–67（67 aa）
Not recorded ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Wait time 10 s Blot force 4 Blot time 4 s
Resolution 3.40 Å
7AST Apo Human RNA Polymerase III Deposited 2020-10-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain B 1–67（67 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7DN3 Structure of Human RNA Polymerase III elongation complex Deposited 2020-12-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain J 1–67（67 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 6 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7DU2 RNA polymerase III EC complex in post-translocation state Deposited 2021-01-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain J 1–67（67 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 6 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.35 Å
7FJI human Pol III elongation complex Deposited 2021-08-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain J 1–67（67 aa）
Not recorded ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
Resolution 3.60 Å
7FJJ human Pol III pre-termination complex Deposited 2021-08-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain J 1–67（67 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
Resolution 3.60 Å
7LBM Structure of the human Mediator-bound transcription pre-initiation complex Deposited 2021-01-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 54 PDB declaration: 56-meric
Chain J 1–67（67 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7OB9 Cryo-EM structure of human RNA Polymerase I in elongation state Deposited 2021-04-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain J 1–67（67 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 3, blot time 0 s, wait time 0 s
Resolution 2.70 Å
7OBA Cryo-EM structure of human RNA Polymerase I in complex with RRN3 Deposited 2021-04-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain J 1–67（67 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 3, blot time 0 s, wait time 0 s
Resolution 3.10 Å
7OBB Cryo-EM structure of human RNA Polymerase I Open Complex Deposited 2021-04-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain J 1–67（67 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 3, blot time 0 s, wait time 0 s
Resolution 3.30 Å
7VBA Structure of the pre state human RNA Polymerase I Elongation Complex Deposited 2021-08-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain J 1–67（67 aa）
Not recorded ZN ZINC ION × 5 MG MAGNESIUM ION × 1 2TM 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.89 Å
7VBB Structure of the post state human RNA Polymerase I Elongation Complex Deposited 2021-08-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain J 1–67（67 aa）
Not recorded ZN ZINC ION × 5 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.81 Å
7VBC Back track state of human RNA Polymerase I Elongation Complex Deposited 2021-08-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain J 1–67（67 aa）
Not recorded ZN ZINC ION × 5 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.01 Å
8A43 Human RNA polymerase I Deposited 2022-06-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain J 1–67（67 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.09 Å
8ITY human RNA polymerase III pre-initiation complex closed DNA 1 Deposited 2023-03-23 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain J 1–67（67 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
8IUE RNA polymerase III pre-initiation complex melting complex 1 Deposited 2023-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain J 1–67（67 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.10 Å
8IUH RNA polymerase III pre-initiation complex open complex 1 Deposited 2023-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain J 1–67（67 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.40 Å
8XRJ RNA polymerase II elongation complex with upstream nucleosome extracted from human nuclei Deposited 2024-01-07 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 J 1–67（67 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8XRM RNA polymerase II elongation complex with DSIF, SPT6, and ELOF1 transcribing genomic DNA extracted from human nuclei Deposited 2024-01-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: 19-meric
Chain J 1–67（67 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
8XSO RNA polymerase II elongation complex transcribing genomic DNA extracted from human nuclei Deposited 2024-01-09 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 1–67（67 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8XVS RNA polymerase II elongation complex with downstream nucleosome extracted from human nuclei Deposited 2024-01-15 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 J 1–67（67 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 4.10 Å
9EHZ Cryo-EM structure of Human RNA polymerase II Elongation Complex in an Intermediate Translocation State Deposited 2024-11-25 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 1–67（67 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
9EI1 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the absence of nucleotide Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain J 1–67（67 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9EI3 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the presence of AMPPNP Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain J 1–67（67 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9EI4 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the presence of ADP Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain J 1–67（67 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9FSO Human RNA Polymerase III Class III Open Pre-initiation Complex 1 (OC1) Deposited 2024-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain Q 1–67（67 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.28 Å
9FSP RNA Polymerase III Class III Open Pre-initation Complex 2 (OC2) Deposited 2024-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain Q 1–67（67 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
9FSQ RNA Polymerase III Class III Melting Pre-Initiation Complex (MC) Deposited 2024-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain Q 1–67（67 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.51 Å
9FSR RNA Polymerase III Class III Open Mini Pre-initiation Complex 1 (OC1-mini) Deposited 2024-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain Q 1–67（67 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.76 Å
9FSS RNA Polymerase III Class III Open Mini Pre-Initiation complex 2 (OC2-mini) Deposited 2024-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain Q 1–67（67 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.14 Å
9K2G Human RNA Polymerase III de novo transcribing complex 13 (TC13) Deposited 2024-10-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric
Chain J 1–67（67 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.00 Å
9K36 Human RNA Polymerase III de novo transcribing complex 12 (TC12) Deposited 2024-10-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric
Chain J 1–67（67 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.90 Å
9K38 Human RNA Polymerase III de novo transcribing complex 6 (TC6) Deposited 2024-10-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric
Chain J 1–67（67 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.10 Å
9K39 Human RNA Polymerase III de novo transcribing complex 8 (TC8) Deposited 2024-10-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric
Chain J 1–67（67 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.80 Å
9K3B Human RNA Polymerase III de novo transcribing complex 10 overall (TC10-overall) Deposited 2024-10-18 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 J 1–67（67 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.80 Å
9K3U Human RNA Polymerase III de novo transcribing complex 5 (TC5) Deposited 2024-10-20 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 J 1–67（67 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.00 Å
9K3V Human RNA Polymerase III de novo transcribing complex 4 (TC4) Deposited 2024-10-20 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 J 1–67（67 aa）
Not recorded ZN ZINC ION × 7 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.50 Å
9LKT Human RNA Polymerase III de novo transcribing complex 10 (TC10) Deposited 2025-01-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric
Chain J 1–67（67 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.50 Å
9LXN Human RNA Polymerase III de novo transcribing complex 5 (TC5)(without 3'dATP) Deposited 2025-02-18 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 J 1–67（67 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.30 Å
9LXO Human RNA Polymerase III de novo transcribing complex 6 (TC6)(without 3'dATP) Deposited 2025-02-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric
Chain J 1–67（67 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.60 Å
9VD9 Cryo-EM structure of the human DSS1-INTAC-PEC complex Deposited 2025-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 35 PDB declaration: 38-meric
Chain 8 1–67（67 aa）
Not recorded ZN ZINC ION × 10 MN MANGANESE (II) ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å

54 other PDB entries and 54 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPAB5_HUMAN
Isoform —
PDB entities 10
Chains and sequence ranges Author chain J； PDBConstruct 1–67； UniProt 1–67

DNA-directed RNA polymerase II subunit RPB11-a

OrganismNot specified

UniProt P52435

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 × 21 DNA 2 PDB declaration: 23-meric（23） Consistent with all polymer counts Chain K； UniProt 1–117 Not recorded DNA-directed RNA polymerase II subunit RPB1 × 1 （P24928） DNA-directed RNA polymerase II subunit RPB2 × 1 （P30876） DNA-directed RNA polymerase II subunit RPB3 × 1 （P19387） DNA-directed RNA polymerase II subunit RPB4 × 1 （O15514） DNA-directed RNA polymerase II subunit RPB5 × 1 （P19388） DNA-directed RNA polymerase II subunit RPB6 × 1 （P61218） DNA-directed RNA polymerase II subunit RPB7 × 1 （P62487） DNA-directed RNA polymerase II subunit RPB8 × 1 （P52434） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36954） DNA-directed RNA polymerase II subunit RPB10 × 1 （P62875） DNA-directed RNA polymerase II subunit RPB12 × 1 （P53803） Transcription initiation factor IIB × 1 （Q00403） Transcription initiation factor IIA subunit 1 × 1 （P52655） Transcription initiation factor IIA subunit 2 × 1 （P52657） TATA-box-binding protein × 1 （P20226） General transcription factor IIE subunit 1 × 1 （P29083） Transcription initiation factor IIE subunit beta × 1 （P29084） General transcription factor IIF subunit 1 × 1 （P35269） General transcription factor IIF subunit 2 × 1 （P13984） Transcription elongation factor A protein 1 × 1 （P23193） SCP-X × 1 SCP-Y × 1 MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV). Resolution 3.90 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 5IYC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5IY6 Human holo-PIC in the closed state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain K 1–117（117 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.20 Å
5IY7 Human holo-PIC in the open state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain K 1–117（117 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 8.60 Å
5IY8 Human holo-PIC in the initial transcribing state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain K 1–117（117 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.90 Å
5IY9 Human holo-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric
Chain K 1–117（117 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 6.30 Å
5IYA Human core-PIC in the closed state Deposited 2016-03-24 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain K 1–117（117 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 5.40 Å
5IYB Human core-PIC in the open state Deposited 2016-03-24 Parsed fields agree Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain K 1–117（117 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
5IYD Human core-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain K 1–117（117 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
6DRD RNA Pol II(G) Deposited 2018-06-11 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain K 1–117（117 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6O9L Human holo-PIC in the closed state Deposited 2019-03-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 31 PDB declaration: 33-meric
Chain K 1–117（117 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
6XRE Structure of the p53/RNA polymerase II assembly Deposited 2020-07-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain K 1–117（117 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；The assembled p53/Pol II co-complex was applied directly on the grid for 10 sec followed by 5.5 sec of blotting. The sample grid was then washed with 3.5% trehalose in 0.1 M KCl/HEM buffer (20 mM HEPES, 0.2 mM EDTA, 2 mM MgCl2 at pH 7.9) for 10 sec, blotted for 5.5 sec, and finally frozen in liquid ethane.
Resolution 4.60 Å
7LBM Structure of the human Mediator-bound transcription pre-initiation complex Deposited 2021-01-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 54 PDB declaration: 56-meric
Chain K 1–117（117 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
8XRJ RNA polymerase II elongation complex with upstream nucleosome extracted from human nuclei Deposited 2024-01-07 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 K 1–117（117 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8XRM RNA polymerase II elongation complex with DSIF, SPT6, and ELOF1 transcribing genomic DNA extracted from human nuclei Deposited 2024-01-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: 19-meric
Chain K 1–117（117 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
8XSO RNA polymerase II elongation complex transcribing genomic DNA extracted from human nuclei Deposited 2024-01-09 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 1–117（117 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8XVS RNA polymerase II elongation complex with downstream nucleosome extracted from human nuclei Deposited 2024-01-15 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 K 1–117（117 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 4.10 Å
9EHZ Cryo-EM structure of Human RNA polymerase II Elongation Complex in an Intermediate Translocation State Deposited 2024-11-25 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 1–117（117 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
9EI1 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the absence of nucleotide Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain K 1–117（117 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9EI3 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the presence of AMPPNP Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain K 1–117（117 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9EI4 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the presence of ADP Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain K 1–117（117 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9VD9 Cryo-EM structure of the human DSS1-INTAC-PEC complex Deposited 2025-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 35 PDB declaration: 38-meric
Chain 9 1–117（117 aa）
Not recorded ZN ZINC ION × 10 MN MANGANESE (II) ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å

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

View Construct and Data Evidence
UniProt name RPB11_HUMAN
Isoform —
PDB entities 11
Chains and sequence ranges Author chain K； PDBConstruct 1–117； UniProt 1–117

DNA-directed RNA polymerase II subunit RPB12

OrganismNot specified

UniProt P53803

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 × 21 DNA 2 PDB declaration: 23-meric（23） Consistent with all polymer counts Chain L； UniProt 1–58 Not recorded DNA-directed RNA polymerase II subunit RPB1 × 1 （P24928） DNA-directed RNA polymerase II subunit RPB2 × 1 （P30876） DNA-directed RNA polymerase II subunit RPB3 × 1 （P19387） DNA-directed RNA polymerase II subunit RPB4 × 1 （O15514） DNA-directed RNA polymerase II subunit RPB5 × 1 （P19388） DNA-directed RNA polymerase II subunit RPB6 × 1 （P61218） DNA-directed RNA polymerase II subunit RPB7 × 1 （P62487） DNA-directed RNA polymerase II subunit RPB8 × 1 （P52434） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36954） DNA-directed RNA polymerase II subunit RPB10 × 1 （P62875） DNA-directed RNA polymerase II subunit RPB11-a × 1 （P52435） Transcription initiation factor IIB × 1 （Q00403） Transcription initiation factor IIA subunit 1 × 1 （P52655） Transcription initiation factor IIA subunit 2 × 1 （P52657） TATA-box-binding protein × 1 （P20226） General transcription factor IIE subunit 1 × 1 （P29083） Transcription initiation factor IIE subunit beta × 1 （P29084） General transcription factor IIF subunit 1 × 1 （P35269） General transcription factor IIF subunit 2 × 1 （P13984） Transcription elongation factor A protein 1 × 1 （P23193） SCP-X × 1 SCP-Y × 1 MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV). Resolution 3.90 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 5IYC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5IY6 Human holo-PIC in the closed state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain L 1–58（58 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.20 Å
5IY7 Human holo-PIC in the open state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain L 1–58（58 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 8.60 Å
5IY8 Human holo-PIC in the initial transcribing state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain L 1–58（58 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.90 Å
5IY9 Human holo-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric
Chain L 1–58（58 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 6.30 Å
5IYA Human core-PIC in the closed state Deposited 2016-03-24 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain L 1–58（58 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 5.40 Å
5IYB Human core-PIC in the open state Deposited 2016-03-24 Parsed fields agree Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain L 1–58（58 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
5IYD Human core-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain L 1–58（58 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
6DRD RNA Pol II(G) Deposited 2018-06-11 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain L 1–58（58 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6O9L Human holo-PIC in the closed state Deposited 2019-03-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 31 PDB declaration: 33-meric
Chain L 1–58（58 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
6XRE Structure of the p53/RNA polymerase II assembly Deposited 2020-07-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain L 1–58（58 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；The assembled p53/Pol II co-complex was applied directly on the grid for 10 sec followed by 5.5 sec of blotting. The sample grid was then washed with 3.5% trehalose in 0.1 M KCl/HEM buffer (20 mM HEPES, 0.2 mM EDTA, 2 mM MgCl2 at pH 7.9) for 10 sec, blotted for 5.5 sec, and finally frozen in liquid ethane.
Resolution 4.60 Å
7A6H Cryo-EM structure of human apo RNA Polymerase III Deposited 2020-08-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain L 1–58（58 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Wait time 10 s Blot force 4 Blot time 4 s
Resolution 3.30 Å
7AE1 Cryo-EM structure of human RNA Polymerase III elongation complex 1 Deposited 2020-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain L 1–58（58 aa）
Not recorded ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Wait time 10 s Blot force 4 Blot time 4 s
Resolution 2.80 Å
7AE3 Cryo-EM structure of human RNA Polymerase III elongation complex 3 Deposited 2020-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain L 1–58（58 aa）
Not recorded ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Wait time 10 s Blot force 4 Blot time 4 s
Resolution 3.10 Å
7AEA Cryo-EM structure of human RNA Polymerase III elongation complex 2 Deposited 2020-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain L 1–58（58 aa）
Not recorded ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Wait time 10 s Blot force 4 Blot time 4 s
Resolution 3.40 Å
7AST Apo Human RNA Polymerase III Deposited 2020-10-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain C 1–58（58 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7D58 cryo-EM structure of human RNA polymerase III in elongating state Deposited 2020-09-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain L 1–58（58 aa）
Not recorded ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7D59 cryo-EM structure of human RNA polymerase III in apo state Deposited 2020-09-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain L 1–58（58 aa）
Not recorded ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7DN3 Structure of Human RNA Polymerase III elongation complex Deposited 2020-12-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain L 1–58（58 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 6 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7DU2 RNA polymerase III EC complex in post-translocation state Deposited 2021-01-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain L 1–58（58 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 6 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.35 Å
7FJI human Pol III elongation complex Deposited 2021-08-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain L 1–58（58 aa）
Not recorded ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
Resolution 3.60 Å
7FJJ human Pol III pre-termination complex Deposited 2021-08-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain L 1–58（58 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 7 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
Resolution 3.60 Å
7LBM Structure of the human Mediator-bound transcription pre-initiation complex Deposited 2021-01-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 54 PDB declaration: 56-meric
Chain L 1–58（58 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7OB9 Cryo-EM structure of human RNA Polymerase I in elongation state Deposited 2021-04-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain L 1–58（58 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 3, blot time 0 s, wait time 0 s
Resolution 2.70 Å
7OBA Cryo-EM structure of human RNA Polymerase I in complex with RRN3 Deposited 2021-04-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain L 1–58（58 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 3, blot time 0 s, wait time 0 s
Resolution 3.10 Å
7OBB Cryo-EM structure of human RNA Polymerase I Open Complex Deposited 2021-04-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain L 1–58（58 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 3, blot time 0 s, wait time 0 s
Resolution 3.30 Å
7VBA Structure of the pre state human RNA Polymerase I Elongation Complex Deposited 2021-08-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain L 1–58（58 aa）
Not recorded ZN ZINC ION × 5 MG MAGNESIUM ION × 1 2TM 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.89 Å
7VBB Structure of the post state human RNA Polymerase I Elongation Complex Deposited 2021-08-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain L 1–58（58 aa）
Not recorded ZN ZINC ION × 5 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.81 Å
7VBC Back track state of human RNA Polymerase I Elongation Complex Deposited 2021-08-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain L 1–58（58 aa）
Not recorded ZN ZINC ION × 5 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.01 Å
8A43 Human RNA polymerase I Deposited 2022-06-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain L 1–58（58 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.09 Å
8ITY human RNA polymerase III pre-initiation complex closed DNA 1 Deposited 2023-03-23 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain L 1–58（58 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
8IUE RNA polymerase III pre-initiation complex melting complex 1 Deposited 2023-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain L 1–58（58 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.10 Å
8IUH RNA polymerase III pre-initiation complex open complex 1 Deposited 2023-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain L 1–58（58 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.40 Å
8XRJ RNA polymerase II elongation complex with upstream nucleosome extracted from human nuclei Deposited 2024-01-07 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 L 1–58（58 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8XRM RNA polymerase II elongation complex with DSIF, SPT6, and ELOF1 transcribing genomic DNA extracted from human nuclei Deposited 2024-01-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: 19-meric
Chain L 1–58（58 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
8XSO RNA polymerase II elongation complex transcribing genomic DNA extracted from human nuclei Deposited 2024-01-09 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 1–58（58 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8XVS RNA polymerase II elongation complex with downstream nucleosome extracted from human nuclei Deposited 2024-01-15 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 L 1–58（58 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 4.10 Å
9EHZ Cryo-EM structure of Human RNA polymerase II Elongation Complex in an Intermediate Translocation State Deposited 2024-11-25 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 1–58（58 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
9EI1 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the absence of nucleotide Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain L 1–58（58 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9EI3 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the presence of AMPPNP Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain L 1–58（58 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9EI4 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the presence of ADP Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain L 1–58（58 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9FSO Human RNA Polymerase III Class III Open Pre-initiation Complex 1 (OC1) Deposited 2024-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain P 1–58（58 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.28 Å
9FSP RNA Polymerase III Class III Open Pre-initation Complex 2 (OC2) Deposited 2024-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain P 1–58（58 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
9FSQ RNA Polymerase III Class III Melting Pre-Initiation Complex (MC) Deposited 2024-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain P 1–58（58 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.51 Å
9FSR RNA Polymerase III Class III Open Mini Pre-initiation Complex 1 (OC1-mini) Deposited 2024-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain P 1–58（58 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.76 Å
9FSS RNA Polymerase III Class III Open Mini Pre-Initiation complex 2 (OC2-mini) Deposited 2024-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain P 1–58（58 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.14 Å
9K2G Human RNA Polymerase III de novo transcribing complex 13 (TC13) Deposited 2024-10-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric
Chain L 1–58（58 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.00 Å
9K36 Human RNA Polymerase III de novo transcribing complex 12 (TC12) Deposited 2024-10-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric
Chain L 1–58（58 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.90 Å
9K38 Human RNA Polymerase III de novo transcribing complex 6 (TC6) Deposited 2024-10-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric
Chain L 1–58（58 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.10 Å
9K39 Human RNA Polymerase III de novo transcribing complex 8 (TC8) Deposited 2024-10-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric
Chain L 1–58（58 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.80 Å
9K3B Human RNA Polymerase III de novo transcribing complex 10 overall (TC10-overall) Deposited 2024-10-18 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 L 1–58（58 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.80 Å
9K3U Human RNA Polymerase III de novo transcribing complex 5 (TC5) Deposited 2024-10-20 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 L 1–58（58 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.00 Å
9K3V Human RNA Polymerase III de novo transcribing complex 4 (TC4) Deposited 2024-10-20 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 L 1–58（58 aa）
Not recorded ZN ZINC ION × 7 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.50 Å
9LKT Human RNA Polymerase III de novo transcribing complex 10 (TC10) Deposited 2025-01-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric
Chain L 1–58（58 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.50 Å
9LXN Human RNA Polymerase III de novo transcribing complex 5 (TC5)(without 3'dATP) Deposited 2025-02-18 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 L 1–58（58 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.30 Å
9LXO Human RNA Polymerase III de novo transcribing complex 6 (TC6)(without 3'dATP) Deposited 2025-02-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric
Chain L 1–58（58 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.60 Å
9VD9 Cryo-EM structure of the human DSS1-INTAC-PEC complex Deposited 2025-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 35 PDB declaration: 38-meric
Chain a 1–58（58 aa）
Not recorded ZN ZINC ION × 10 MN MANGANESE (II) ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å

56 other PDB entries and 56 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPAB4_HUMAN
Isoform —
PDB entities 12
Chains and sequence ranges Author chain L； PDBConstruct 1–58； UniProt 1–58

Transcription initiation factor IIB

Homo sapiens

UniProt Q00403

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 × 21 DNA 2 PDB declaration: 23-meric（23） Consistent with all polymer counts Chain M； UniProt 1–316 Not recorded DNA-directed RNA polymerase II subunit RPB1 × 1 （P24928） DNA-directed RNA polymerase II subunit RPB2 × 1 （P30876） DNA-directed RNA polymerase II subunit RPB3 × 1 （P19387） DNA-directed RNA polymerase II subunit RPB4 × 1 （O15514） DNA-directed RNA polymerase II subunit RPB5 × 1 （P19388） DNA-directed RNA polymerase II subunit RPB6 × 1 （P61218） DNA-directed RNA polymerase II subunit RPB7 × 1 （P62487） DNA-directed RNA polymerase II subunit RPB8 × 1 （P52434） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36954） DNA-directed RNA polymerase II subunit RPB10 × 1 （P62875） DNA-directed RNA polymerase II subunit RPB11-a × 1 （P52435） DNA-directed RNA polymerase II subunit RPB12 × 1 （P53803） Transcription initiation factor IIA subunit 1 × 1 （P52655） Transcription initiation factor IIA subunit 2 × 1 （P52657） TATA-box-binding protein × 1 （P20226） General transcription factor IIE subunit 1 × 1 （P29083） Transcription initiation factor IIE subunit beta × 1 （P29084） General transcription factor IIF subunit 1 × 1 （P35269） General transcription factor IIF subunit 2 × 1 （P13984） Transcription elongation factor A protein 1 × 1 （P23193） SCP-X × 1 SCP-Y × 1 MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV). Resolution 3.90 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 5IYC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1C9B CRYSTAL STRUCTURE OF A HUMAN TBP CORE DOMAIN-HUMAN TFIIB CORE DOMAIN COMPLEX BOUND TO AN EXTENDED, MODIFIED ADENOVIRAL MAJOR LATE PROMOTER (ADMLP) Deposited 1999-08-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain A 110–316（207 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；277 K；PEG 8000, TRIS.HCL, AMMONIUM ACETATE, MAGNESIUM CHLORIDE, POTASSIUM CHLORIDE, SODIUM CITRATE, DTT, GLYCEROL, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Resolution 2.65 Å R-free 0.260
1C9B CRYSTAL STRUCTURE OF A HUMAN TBP CORE DOMAIN-HUMAN TFIIB CORE DOMAIN COMPLEX BOUND TO AN EXTENDED, MODIFIED ADENOVIRAL MAJOR LATE PROMOTER (ADMLP) Deposited 1999-08-01 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 110–316（207 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；277 K；PEG 8000, TRIS.HCL, AMMONIUM ACETATE, MAGNESIUM CHLORIDE, POTASSIUM CHLORIDE, SODIUM CITRATE, DTT, GLYCEROL, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Resolution 2.65 Å R-free 0.260
1C9B CRYSTAL STRUCTURE OF A HUMAN TBP CORE DOMAIN-HUMAN TFIIB CORE DOMAIN COMPLEX BOUND TO AN EXTENDED, MODIFIED ADENOVIRAL MAJOR LATE PROMOTER (ADMLP) Deposited 1999-08-01 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 110–316（207 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；277 K；PEG 8000, TRIS.HCL, AMMONIUM ACETATE, MAGNESIUM CHLORIDE, POTASSIUM CHLORIDE, SODIUM CITRATE, DTT, GLYCEROL, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Resolution 2.65 Å R-free 0.260
1C9B CRYSTAL STRUCTURE OF A HUMAN TBP CORE DOMAIN-HUMAN TFIIB CORE DOMAIN COMPLEX BOUND TO AN EXTENDED, MODIFIED ADENOVIRAL MAJOR LATE PROMOTER (ADMLP) Deposited 1999-08-01 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 110–316（207 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；277 K；PEG 8000, TRIS.HCL, AMMONIUM ACETATE, MAGNESIUM CHLORIDE, POTASSIUM CHLORIDE, SODIUM CITRATE, DTT, GLYCEROL, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Resolution 2.65 Å R-free 0.260
1C9B CRYSTAL STRUCTURE OF A HUMAN TBP CORE DOMAIN-HUMAN TFIIB CORE DOMAIN COMPLEX BOUND TO AN EXTENDED, MODIFIED ADENOVIRAL MAJOR LATE PROMOTER (ADMLP) Deposited 1999-08-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain Q 110–316（207 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；277 K；PEG 8000, TRIS.HCL, AMMONIUM ACETATE, MAGNESIUM CHLORIDE, POTASSIUM CHLORIDE, SODIUM CITRATE, DTT, GLYCEROL, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Resolution 2.65 Å R-free 0.260
1DL6 SOLUTION STRUCTURE OF HUMAN TFIIB N-TERMINAL DOMAIN Deposited 1999-12-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–59（58 aa） Fragment：N-TERMINAL DOMAIN
Not recorded ZN ZINC ION × 1 SOLUTION NMR
NMR measurement conditions pH 7；298 K；Pressure AMBIENT
NMR sample composition 3MM HTFIIB N-TERMINAL DOMAIN U-15N; 50MM PHOSPHATE; 90% H2O, 10% D2O
Resolution not provided
1RLY RDC-derived models of the zinc ribbon domain of human general transcription TFIIB (zinc bound structures) 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 monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–60（60 aa）
Not recorded ZN ZINC ION × 1 SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Pressure ambient
NMR sample composition 0.6mM TFIIB Uniform labeling with 15N: U-98% 15N, 20mM [2H4]-imidazole hydrochloride, 2.5mM ZnCl2, 5% glycerol, 20mM sodium sulfate at pH 6.5, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.6mM TFIIB Uniform labeling with 15N: U-98% 15N, 20mM [2H4]-imidazole hydrochloride, 2.5mM ZnCl2, 5% glycerol, 20mM sodium sulfate at pH 6.5, 12mg/mL of filamentous phage, Pf1, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
1RO4 RDC-derived models of the zinc ribbon domain of human general transcription factor TFIIB (zinc free structures) Deposited 2003-12-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–60（60 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Pressure ambient
NMR sample composition 0.6mM TFIIB Uniform labeling with 15N: U-98% 15N, 20mM [2H4]-imidazole hydrochloride, 5% glycerol and 20mM sodium sulfate at pH 6.5, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.6mM TFIIB Uniform labeling with 15N: U-98% 15N, 20mM [2H4]-imidazole hydrochloride, 5% glycerol and 20mM sodium sulfate at pH 6.5, 12mg/mL of filamentous phage, Pf1, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
1TFB NMR STUDIES OF HUMAN GENERAL TRANSCRIPTION FACTOR TFIIB: DYNAMICS AND INTERACTION WITH VP16 ACTIVATION DOMAIN, 20 STRUCTURES Deposited 1996-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 112–316（205 aa） Fragment：CONSTRUCT COMPRISES RESIDUES 1 - 3 AND 112 - 316 OF FULL LENGTH HUMAN TFIIB
Mutation：DEL(4 - 111) No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1VOL TFIIB (HUMAN CORE DOMAIN)/TBP (A.THALIANA)/TATA ELEMENT TERNARY COMPLEX Deposited 1996-04-29 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 113–316（204 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.70 Å R-free 0.318
2PHG Model for VP16 binding to TFIIB Deposited 2007-04-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 112–316（205 aa） Fragment：c-terminal core domain
Mutation：D111S No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.6；298 K；Ionic strength (raw mmCIF value) 100 mM；Pressure 1
NMR sample composition 0.2 mM VP16ad U-15N, 0-0.2 mM TFIIBc, 50 mM KCl, 50 mM phosphate buffer pH 5.6, 95% H2O, 5% D2O | 95% H2O/5% D2O
Resolution not provided
5IY6 Human holo-PIC in the closed state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain M 1–316（316 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.20 Å
5IY7 Human holo-PIC in the open state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain M 1–316（316 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 8.60 Å
5IY8 Human holo-PIC in the initial transcribing state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain M 1–316（316 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.90 Å
5IY9 Human holo-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric
Chain M 1–316（316 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 6.30 Å
5IYA Human core-PIC in the closed state Deposited 2016-03-24 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain M 1–316（316 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 5.40 Å
5IYB Human core-PIC in the open state Deposited 2016-03-24 Parsed fields agree Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain M 1–316（316 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
5IYD Human core-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain M 1–316（316 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
5WH1 Apo form of the C-terminal region of human Transcription Factor IIB Deposited 2017-07-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 107–316（210 aa） Fragment：C-terminal residues 107-316
Not recorded SO4 SULFATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；100 mM sodium acetate trihydrate pH 4.5, 2 M ammonium sulfate
Resolution 3.39 Å R-free 0.214
5WH1 Apo form of the C-terminal region of human Transcription Factor IIB Deposited 2017-07-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 107–316（210 aa） Fragment：C-terminal residues 107-316
Not recorded SO4 SULFATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；100 mM sodium acetate trihydrate pH 4.5, 2 M ammonium sulfate
Resolution 3.39 Å R-free 0.214
5WH1 Apo form of the C-terminal region of human Transcription Factor IIB Deposited 2017-07-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 107–316（210 aa） Fragment：C-terminal residues 107-316
Not recorded SO4 SULFATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；100 mM sodium acetate trihydrate pH 4.5, 2 M ammonium sulfate
Resolution 3.39 Å R-free 0.214
5WH1 Apo form of the C-terminal region of human Transcription Factor IIB Deposited 2017-07-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 107–316（210 aa） Fragment：C-terminal residues 107-316
Not recorded SO4 SULFATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；100 mM sodium acetate trihydrate pH 4.5, 2 M ammonium sulfate
Resolution 3.39 Å R-free 0.214
6O9L Human holo-PIC in the closed state Deposited 2019-03-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 31 PDB declaration: 33-meric
Chain M 1–316（316 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
7EDX p53-bound TFIID-based core PIC on HDM2 promoter Deposited 2021-03-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 37 PDB declaration: 39-meric
Chain R 1–316（316 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7EG7 TFIID-based core PIC on SCP promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 37 PDB declaration: 39-meric
Chain R 1–316（316 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.20 Å
7EG8 TFIID-based core PIC on PUMA promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 37 PDB declaration: 39-meric
Chain R 1–316（316 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.40 Å
7EG9 TFIID-based intermediate PIC on SCP promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 39 PDB declaration: 41-meric
Chain R 1–316（316 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7EGA TFIID-based intermediate PIC on PUMA promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 39 PDB declaration: 41-meric
Chain R 1–316（316 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
7EGB TFIID-based holo PIC on SCP promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain R 1–316（316 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7EGC p53-bound TFIID-based holo PIC on HDM2 promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain R 1–316（316 aa）
Not recorded ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7ENA TFIID-based PIC-Mediator holo-complex in pre-assembled state (pre-hPIC-MED) Deposited 2021-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 74 PDB declaration: 76-meric
Chain BA 1–316（316 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.07 Å
7ENC TFIID-based PIC-Mediator holo-complex in fully-assembled state (hPIC-MED) Deposited 2021-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 74 PDB declaration: 76-meric
Chain BA 1–316（316 aa）
Not recorded ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.13 Å
7LBM Structure of the human Mediator-bound transcription pre-initiation complex Deposited 2021-01-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 54 PDB declaration: 56-meric
Chain O 1–316（316 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7NVR Human Mediator with RNA Polymerase II Pre-initiation complex Deposited 2021-03-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 56 PDB declaration: 58-meric
Chain M 1–316（316 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 18 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7NVS RNA polymerase II core pre-initiation complex with closed promoter DNA in proximal position Deposited 2021-03-16 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 1–316（316 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7NVT RNA polymerase II core pre-initiation complex with closed promoter DNA in distal position Deposited 2021-03-16 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 1–316（316 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7NVU RNA polymerase II core pre-initiation complex with open promoter DNA Deposited 2021-03-16 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 1–316（316 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
7NVY RNA polymerase II pre-initiation complex with closed promoter DNA in proximal position Deposited 2021-03-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain M 1–316（316 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 7.30 Å
7NVZ RNA polymerase II pre-initiation complex with closed promoter DNA in distal position Deposited 2021-03-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain M 1–316（316 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 7.20 Å
7NW0 RNA polymerase II pre-initiation complex with open promoter DNA Deposited 2021-03-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain M 1–316（316 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.60 Å
7ZWC Structure of SNAPc:TBP-TFIIA-TFIIB sub-complex bound to U5 snRNA promoter Deposited 2022-05-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain M 1–316（316 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7ZWD Structure of SNAPc containing Pol II pre-initiation complex bound to U5 snRNA promoter (CC) Deposited 2022-05-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric
Chain M 1–316（316 aa）
Not recorded ZN ZINC ION × 11 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ZX7 Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter (CC) Deposited 2022-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric
Chain M 1–316（316 aa）
Not recorded ZN ZINC ION × 11 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7ZX8 Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter (OC) Deposited 2022-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric
Chain M 1–316（316 aa）
Not recorded ZN ZINC ION × 11 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ZXE Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter (OC) Deposited 2022-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain M 1–316（316 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8BVW RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W) Deposited 2022-12-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric
Chain M 1–316（316 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 4.00 Å
8BYQ RNA polymerase II pre-initiation complex with the proximal +1 nucleosome (PIC-Nuc10W) Deposited 2022-12-14 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 M 1–316（316 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 16 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8BZ1 RNA polymerase II core pre-initiation complex with the proximal +1 nucleosome (cPIC-Nuc10W) Deposited 2022-12-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain M 1–316（316 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8GXQ PIC-Mediator in complex with +1 nucleosome (T40N) in MH-binding state Deposited 2022-09-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric
Chain BA 1–316（316 aa）
Not recorded ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.04 Å
8GXS PIC-Mediator in complex with +1 nucleosome (T40N) in H-binding state Deposited 2022-09-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric
Chain BA 1–316（316 aa）
Not recorded ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.16 Å
8S51 RNA polymerase II core initially transcribing complex with an ordered RNA of 8 nt Deposited 2024-02-22 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 M 1–316（316 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8S52 RNA polymerase II core initially transcribing complex with an ordered RNA of 10 nt Deposited 2024-02-22 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 M 1–316（316 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8S5N RNA polymerase II core initially transcribing complex with an ordered RNA of 12 nt Deposited 2024-02-24 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 M 1–316（316 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8WAK Structure of transcribing complex 2 (TC2), the initially transcribing complex with Pol II positioned 2nt downstream of TSS. Deposited 2023-09-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain R 1–316（316 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.47 Å
8WAL Structure of transcribing complex 3 (TC3), the initially transcribing complex with Pol II positioned 3nt downstream of TSS. Deposited 2023-09-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain R 1–316（316 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.52 Å
8WAN Structure of transcribing complex 4 (TC4), the initially transcribing complex with Pol II positioned 4nt downstream of TSS. Deposited 2023-09-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain R 1–316（316 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.07 Å
8WAO Structure of transcribing complex 5 (TC5), the initially transcribing complex with Pol II positioned 5nt downstream of TSS. Deposited 2023-09-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain R 1–316（316 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å
8WAP Structure of transcribing complex 6 (TC6), the initially transcribing complex with Pol II positioned 6nt downstream of TSS. Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain R 1–316（316 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.85 Å
8WAQ Structure of transcribing complex 7 (TC7), the initially transcribing complex with Pol II positioned 7nt downstream of TSS. Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain R 1–316（316 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.29 Å
8WAR Structure of transcribing complex 8 (TC8), the initially transcribing complex with Pol II positioned 8nt downstream of TSS. Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain R 1–316（316 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
8WAS Structure of transcribing complex 9 (TC9), the initially transcribing complex with Pol II positioned 9nt downstream of TSS. Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain R 1–316（316 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.13 Å

54 other PDB entries and 61 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TF2B_HUMAN
Isoform —
PDB entities 13
Chains and sequence ranges Author chain M； PDBConstruct 1–316； UniProt 1–316

Transcription initiation factor IIA subunit 1

Homo sapiens

UniProt P52655

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 × 21 DNA 2 PDB declaration: 23-meric（23） Consistent with all polymer counts Chain N； UniProt 1–376 Not recorded DNA-directed RNA polymerase II subunit RPB1 × 1 （P24928） DNA-directed RNA polymerase II subunit RPB2 × 1 （P30876） DNA-directed RNA polymerase II subunit RPB3 × 1 （P19387） DNA-directed RNA polymerase II subunit RPB4 × 1 （O15514） DNA-directed RNA polymerase II subunit RPB5 × 1 （P19388） DNA-directed RNA polymerase II subunit RPB6 × 1 （P61218） DNA-directed RNA polymerase II subunit RPB7 × 1 （P62487） DNA-directed RNA polymerase II subunit RPB8 × 1 （P52434） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36954） DNA-directed RNA polymerase II subunit RPB10 × 1 （P62875） DNA-directed RNA polymerase II subunit RPB11-a × 1 （P52435） DNA-directed RNA polymerase II subunit RPB12 × 1 （P53803） Transcription initiation factor IIB × 1 （Q00403） Transcription initiation factor IIA subunit 2 × 1 （P52657） TATA-box-binding protein × 1 （P20226） General transcription factor IIE subunit 1 × 1 （P29083） Transcription initiation factor IIE subunit beta × 1 （P29084） General transcription factor IIF subunit 1 × 1 （P35269） General transcription factor IIF subunit 2 × 1 （P13984） Transcription elongation factor A protein 1 × 1 （P23193） SCP-X × 1 SCP-Y × 1 MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV). Resolution 3.90 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 5IYC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1NVP HUMAN TFIIA/TBP/DNA COMPLEX Deposited 2003-02-04 Different construct Different mutation/modification 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 B 2–58（57 aa） Fragment：N-terminal 58 amino acids
Chain C 303–376（74 aa） Fragment：c-terminal 76 amino acids
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；PEG6000, lithium nitrate, calcium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.10 Å R-free 0.247
5FUR Structure of human TFIID-IIA bound to core promoter DNA Deposited 2016-01-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 9–51（43 aa）
Chain C 330–376（47 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 10 MM HEPES, 10 MM MGCL2, 50 MM KCL, 3% TREHALOSE 1 MM DTT, 0.0125% NP-40；pH 7.9；10 MM HEPES, 10 MM MGCL2, 50 MM KCL, 3% TREHALOSE 1 MM DTT, 0.0125% NP-40
cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE
Resolution 8.50 Å
5IY6 Human holo-PIC in the closed state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain N 1–376（376 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.20 Å
5IY7 Human holo-PIC in the open state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain N 1–376（376 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 8.60 Å
5IY8 Human holo-PIC in the initial transcribing state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain N 1–376（376 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.90 Å
5IY9 Human holo-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric
Chain N 1–376（376 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 6.30 Å
5IYA Human core-PIC in the closed state Deposited 2016-03-24 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain N 1–376（376 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 5.40 Å
5IYB Human core-PIC in the open state Deposited 2016-03-24 Parsed fields agree Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain N 1–376（376 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
5IYD Human core-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain N 1–376（376 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
5M4S Transcription factor TFIIA as a single chain protein Deposited 2016-10-19 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 2–58（57 aa）
Chain A 328–376（49 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20mM Tris (8.0), 1mM DTT, 0.5mM EDTA and 25mM NaCl
Resolution 2.38 Å R-free 0.242
6O9L Human holo-PIC in the closed state Deposited 2019-03-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 31 PDB declaration: 33-meric
Chain N 1–376（376 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
7EDX p53-bound TFIID-based core PIC on HDM2 promoter Deposited 2021-03-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 37 PDB declaration: 39-meric
Chain Q 1–376（376 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7EG7 TFIID-based core PIC on SCP promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 37 PDB declaration: 39-meric
Chain Q 1–376（376 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.20 Å
7EG8 TFIID-based core PIC on PUMA promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 37 PDB declaration: 39-meric
Chain Q 1–376（376 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.40 Å
7EG9 TFIID-based intermediate PIC on SCP promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 39 PDB declaration: 41-meric
Chain Q 1–376（376 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7EGA TFIID-based intermediate PIC on PUMA promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 39 PDB declaration: 41-meric
Chain Q 1–376（376 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
7EGB TFIID-based holo PIC on SCP promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain Q 1–376（376 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7EGC p53-bound TFIID-based holo PIC on HDM2 promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain Q 1–376（376 aa）
Not recorded ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7EGD SCP promoter-bound TFIID-TFIIA in initial TBP-loading state Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric
Chain Q 1–376（376 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.75 Å
7EGI TFIID in rearranged conformation Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 22 PDB declaration: 22-meric
Chain Q 1–376（376 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.82 Å
7EGJ SCP promoter-bound TFIID-TFIIA in post TBP-loading state Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric
Chain Q 1–376（376 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.64 Å
7LBM Structure of the human Mediator-bound transcription pre-initiation complex Deposited 2021-01-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 54 PDB declaration: 56-meric
Chain M 1–376（376 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7NVR Human Mediator with RNA Polymerase II Pre-initiation complex Deposited 2021-03-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 56 PDB declaration: 58-meric
Chain U 1–376（376 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 18 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7NVS RNA polymerase II core pre-initiation complex with closed promoter DNA in proximal position Deposited 2021-03-16 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 1–376（376 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7NVT RNA polymerase II core pre-initiation complex with closed promoter DNA in distal position Deposited 2021-03-16 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 1–376（376 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7NVU RNA polymerase II core pre-initiation complex with open promoter DNA Deposited 2021-03-16 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 1–376（376 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
7NVY RNA polymerase II pre-initiation complex with closed promoter DNA in proximal position Deposited 2021-03-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain U 1–376（376 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 7.30 Å
7NVZ RNA polymerase II pre-initiation complex with closed promoter DNA in distal position Deposited 2021-03-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain U 1–376（376 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 7.20 Å
7NW0 RNA polymerase II pre-initiation complex with open promoter DNA Deposited 2021-03-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain U 1–376（376 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.60 Å
7ZWC Structure of SNAPc:TBP-TFIIA-TFIIB sub-complex bound to U5 snRNA promoter Deposited 2022-05-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain U 1–376（376 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7ZWD Structure of SNAPc containing Pol II pre-initiation complex bound to U5 snRNA promoter (CC) Deposited 2022-05-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric
Chain U 1–376（376 aa）
Not recorded ZN ZINC ION × 11 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ZX7 Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter (CC) Deposited 2022-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric
Chain U 1–376（376 aa）
Not recorded ZN ZINC ION × 11 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7ZX8 Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter (OC) Deposited 2022-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric
Chain U 1–376（376 aa）
Not recorded ZN ZINC ION × 11 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ZXE Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter (OC) Deposited 2022-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain U 1–376（376 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8BVW RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W) Deposited 2022-12-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric
Chain U 1–376（376 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 4.00 Å
8BYQ RNA polymerase II pre-initiation complex with the proximal +1 nucleosome (PIC-Nuc10W) Deposited 2022-12-14 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 U 1–376（376 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 16 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8BZ1 RNA polymerase II core pre-initiation complex with the proximal +1 nucleosome (cPIC-Nuc10W) Deposited 2022-12-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain U 1–376（376 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8GXQ PIC-Mediator in complex with +1 nucleosome (T40N) in MH-binding state Deposited 2022-09-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric
Chain DQ 1–376（376 aa）
Not recorded ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.04 Å
8GXS PIC-Mediator in complex with +1 nucleosome (T40N) in H-binding state Deposited 2022-09-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric
Chain DQ 1–376（376 aa）
Not recorded ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.16 Å
8S51 RNA polymerase II core initially transcribing complex with an ordered RNA of 8 nt Deposited 2024-02-22 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 1–376（376 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8S52 RNA polymerase II core initially transcribing complex with an ordered RNA of 10 nt Deposited 2024-02-22 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 1–376（376 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8S5N RNA polymerase II core initially transcribing complex with an ordered RNA of 12 nt Deposited 2024-02-24 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 1–376（376 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8WAK Structure of transcribing complex 2 (TC2), the initially transcribing complex with Pol II positioned 2nt downstream of TSS. Deposited 2023-09-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain Q 1–376（376 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.47 Å
8WAL Structure of transcribing complex 3 (TC3), the initially transcribing complex with Pol II positioned 3nt downstream of TSS. Deposited 2023-09-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain Q 1–376（376 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.52 Å
8WAN Structure of transcribing complex 4 (TC4), the initially transcribing complex with Pol II positioned 4nt downstream of TSS. Deposited 2023-09-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain Q 1–376（376 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.07 Å
8WAO Structure of transcribing complex 5 (TC5), the initially transcribing complex with Pol II positioned 5nt downstream of TSS. Deposited 2023-09-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain Q 1–376（376 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å
8WAP Structure of transcribing complex 6 (TC6), the initially transcribing complex with Pol II positioned 6nt downstream of TSS. Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain Q 1–376（376 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.85 Å
8WAQ Structure of transcribing complex 7 (TC7), the initially transcribing complex with Pol II positioned 7nt downstream of TSS. Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain Q 1–376（376 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.29 Å
8WAR Structure of transcribing complex 8 (TC8), the initially transcribing complex with Pol II positioned 8nt downstream of TSS. Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain Q 1–376（376 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
8WAS Structure of transcribing complex 9 (TC9), the initially transcribing complex with Pol II positioned 9nt downstream of TSS. Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain Q 1–376（376 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.13 Å

50 other PDB entries and 50 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TF2AA_HUMAN
Isoform —
PDB entities 14
Chains and sequence ranges Author chain N； PDBConstruct 1–376； UniProt 1–376

Transcription initiation factor IIA subunit 2

Homo sapiens

UniProt P52657

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 × 21 DNA 2 PDB declaration: 23-meric（23） Consistent with all polymer counts Chain O； UniProt 1–109 Not recorded DNA-directed RNA polymerase II subunit RPB1 × 1 （P24928） DNA-directed RNA polymerase II subunit RPB2 × 1 （P30876） DNA-directed RNA polymerase II subunit RPB3 × 1 （P19387） DNA-directed RNA polymerase II subunit RPB4 × 1 （O15514） DNA-directed RNA polymerase II subunit RPB5 × 1 （P19388） DNA-directed RNA polymerase II subunit RPB6 × 1 （P61218） DNA-directed RNA polymerase II subunit RPB7 × 1 （P62487） DNA-directed RNA polymerase II subunit RPB8 × 1 （P52434） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36954） DNA-directed RNA polymerase II subunit RPB10 × 1 （P62875） DNA-directed RNA polymerase II subunit RPB11-a × 1 （P52435） DNA-directed RNA polymerase II subunit RPB12 × 1 （P53803） Transcription initiation factor IIB × 1 （Q00403） Transcription initiation factor IIA subunit 1 × 1 （P52655） TATA-box-binding protein × 1 （P20226） General transcription factor IIE subunit 1 × 1 （P29083） Transcription initiation factor IIE subunit beta × 1 （P29084） General transcription factor IIF subunit 1 × 1 （P35269） General transcription factor IIF subunit 2 × 1 （P13984） Transcription elongation factor A protein 1 × 1 （P23193） SCP-X × 1 SCP-Y × 1 MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV). Resolution 3.90 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 5IYC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1NVP HUMAN TFIIA/TBP/DNA COMPLEX Deposited 2003-02-04 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 D 2–109（108 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；PEG6000, lithium nitrate, calcium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.10 Å R-free 0.247
5FUR Structure of human TFIID-IIA bound to core promoter DNA Deposited 2016-01-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 3–99（97 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 10 MM HEPES, 10 MM MGCL2, 50 MM KCL, 3% TREHALOSE 1 MM DTT, 0.0125% NP-40；pH 7.9；10 MM HEPES, 10 MM MGCL2, 50 MM KCL, 3% TREHALOSE 1 MM DTT, 0.0125% NP-40
cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE
Resolution 8.50 Å
5IY6 Human holo-PIC in the closed state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain O 1–109（109 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.20 Å
5IY7 Human holo-PIC in the open state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain O 1–109（109 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 8.60 Å
5IY8 Human holo-PIC in the initial transcribing state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain O 1–109（109 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.90 Å
5IY9 Human holo-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric
Chain O 1–109（109 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 6.30 Å
5IYA Human core-PIC in the closed state Deposited 2016-03-24 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain O 1–109（109 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 5.40 Å
5IYB Human core-PIC in the open state Deposited 2016-03-24 Parsed fields agree Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain O 1–109（109 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
5IYD Human core-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain O 1–109（109 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
5M4S Transcription factor TFIIA as a single chain protein Deposited 2016-10-19 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 2–103（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20mM Tris (8.0), 1mM DTT, 0.5mM EDTA and 25mM NaCl
Resolution 2.38 Å R-free 0.242
6MZM Human TFIID bound to promoter DNA and TFIIA Deposited 2018-11-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain X 3–99（97 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；BT 4s; BF 15N
Resolution 7.50 Å
6O9L Human holo-PIC in the closed state Deposited 2019-03-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 31 PDB declaration: 33-meric
Chain O 1–109（109 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
7EDX p53-bound TFIID-based core PIC on HDM2 promoter Deposited 2021-03-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 37 PDB declaration: 39-meric
Chain O 1–109（109 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7EG7 TFIID-based core PIC on SCP promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 37 PDB declaration: 39-meric
Chain O 1–109（109 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.20 Å
7EG8 TFIID-based core PIC on PUMA promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 37 PDB declaration: 39-meric
Chain O 1–109（109 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.40 Å
7EG9 TFIID-based intermediate PIC on SCP promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 39 PDB declaration: 41-meric
Chain O 1–109（109 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7EGA TFIID-based intermediate PIC on PUMA promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 39 PDB declaration: 41-meric
Chain O 1–109（109 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
7EGB TFIID-based holo PIC on SCP promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain O 1–109（109 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7EGC p53-bound TFIID-based holo PIC on HDM2 promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain O 1–109（109 aa）
Not recorded ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7EGD SCP promoter-bound TFIID-TFIIA in initial TBP-loading state Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric
Chain O 1–109（109 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.75 Å
7EGI TFIID in rearranged conformation Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 22 PDB declaration: 22-meric
Chain O 1–109（109 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.82 Å
7EGJ SCP promoter-bound TFIID-TFIIA in post TBP-loading state Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric
Chain O 1–109（109 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.64 Å
7ENA TFIID-based PIC-Mediator holo-complex in pre-assembled state (pre-hPIC-MED) Deposited 2021-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 74 PDB declaration: 76-meric
Chain DO 1–109（109 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.07 Å
7ENC TFIID-based PIC-Mediator holo-complex in fully-assembled state (hPIC-MED) Deposited 2021-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 74 PDB declaration: 76-meric
Chain DO 1–109（109 aa）
Not recorded ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.13 Å
7LBM Structure of the human Mediator-bound transcription pre-initiation complex Deposited 2021-01-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 54 PDB declaration: 56-meric
Chain N 1–109（109 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7NVR Human Mediator with RNA Polymerase II Pre-initiation complex Deposited 2021-03-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 56 PDB declaration: 58-meric
Chain V 1–109（109 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 18 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7NVS RNA polymerase II core pre-initiation complex with closed promoter DNA in proximal position Deposited 2021-03-16 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 V 1–109（109 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7NVT RNA polymerase II core pre-initiation complex with closed promoter DNA in distal position Deposited 2021-03-16 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 V 1–109（109 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7NVU RNA polymerase II core pre-initiation complex with open promoter DNA Deposited 2021-03-16 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 V 1–109（109 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
7NVY RNA polymerase II pre-initiation complex with closed promoter DNA in proximal position Deposited 2021-03-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain V 1–109（109 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 7.30 Å
7NVZ RNA polymerase II pre-initiation complex with closed promoter DNA in distal position Deposited 2021-03-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain V 1–109（109 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 7.20 Å
7NW0 RNA polymerase II pre-initiation complex with open promoter DNA Deposited 2021-03-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain V 1–109（109 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.60 Å
7ZWC Structure of SNAPc:TBP-TFIIA-TFIIB sub-complex bound to U5 snRNA promoter Deposited 2022-05-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain V 1–109（109 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7ZWD Structure of SNAPc containing Pol II pre-initiation complex bound to U5 snRNA promoter (CC) Deposited 2022-05-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric
Chain V 1–109（109 aa）
Not recorded ZN ZINC ION × 11 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ZX7 Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter (CC) Deposited 2022-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric
Chain V 1–109（109 aa）
Not recorded ZN ZINC ION × 11 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7ZX8 Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter (OC) Deposited 2022-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric
Chain V 1–109（109 aa）
Not recorded ZN ZINC ION × 11 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ZXE Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter (OC) Deposited 2022-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain V 1–109（109 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8BVW RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W) Deposited 2022-12-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric
Chain V 1–109（109 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 4.00 Å
8BYQ RNA polymerase II pre-initiation complex with the proximal +1 nucleosome (PIC-Nuc10W) Deposited 2022-12-14 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 V 1–109（109 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 16 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8BZ1 RNA polymerase II core pre-initiation complex with the proximal +1 nucleosome (cPIC-Nuc10W) Deposited 2022-12-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain V 1–109（109 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8GXQ PIC-Mediator in complex with +1 nucleosome (T40N) in MH-binding state Deposited 2022-09-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric
Chain DO 1–109（109 aa）
Not recorded ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.04 Å
8GXS PIC-Mediator in complex with +1 nucleosome (T40N) in H-binding state Deposited 2022-09-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric
Chain DO 1–109（109 aa）
Not recorded ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.16 Å
8S51 RNA polymerase II core initially transcribing complex with an ordered RNA of 8 nt Deposited 2024-02-22 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 V 1–109（109 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8S52 RNA polymerase II core initially transcribing complex with an ordered RNA of 10 nt Deposited 2024-02-22 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 V 1–109（109 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8S5N RNA polymerase II core initially transcribing complex with an ordered RNA of 12 nt Deposited 2024-02-24 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 V 1–109（109 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8WAK Structure of transcribing complex 2 (TC2), the initially transcribing complex with Pol II positioned 2nt downstream of TSS. Deposited 2023-09-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain O 1–109（109 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.47 Å
8WAL Structure of transcribing complex 3 (TC3), the initially transcribing complex with Pol II positioned 3nt downstream of TSS. Deposited 2023-09-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain O 1–109（109 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.52 Å
8WAN Structure of transcribing complex 4 (TC4), the initially transcribing complex with Pol II positioned 4nt downstream of TSS. Deposited 2023-09-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain O 1–109（109 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.07 Å
8WAO Structure of transcribing complex 5 (TC5), the initially transcribing complex with Pol II positioned 5nt downstream of TSS. Deposited 2023-09-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain O 1–109（109 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å
8WAP Structure of transcribing complex 6 (TC6), the initially transcribing complex with Pol II positioned 6nt downstream of TSS. Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain O 1–109（109 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.85 Å
8WAQ Structure of transcribing complex 7 (TC7), the initially transcribing complex with Pol II positioned 7nt downstream of TSS. Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain O 1–109（109 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.29 Å
8WAR Structure of transcribing complex 8 (TC8), the initially transcribing complex with Pol II positioned 8nt downstream of TSS. Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain O 1–109（109 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
8WAS Structure of transcribing complex 9 (TC9), the initially transcribing complex with Pol II positioned 9nt downstream of TSS. Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain O 1–109（109 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.13 Å

53 other PDB entries and 53 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name T2AG_HUMAN
Isoform —
PDB entities 15
Chains and sequence ranges Author chain O； PDBConstruct 1–109； UniProt 1–109

TATA-box-binding protein

Homo sapiens

UniProt P20226

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 × 21 DNA 2 PDB declaration: 23-meric（23） Consistent with all polymer counts Chain P； UniProt 1–339 Not recorded DNA-directed RNA polymerase II subunit RPB1 × 1 （P24928） DNA-directed RNA polymerase II subunit RPB2 × 1 （P30876） DNA-directed RNA polymerase II subunit RPB3 × 1 （P19387） DNA-directed RNA polymerase II subunit RPB4 × 1 （O15514） DNA-directed RNA polymerase II subunit RPB5 × 1 （P19388） DNA-directed RNA polymerase II subunit RPB6 × 1 （P61218） DNA-directed RNA polymerase II subunit RPB7 × 1 （P62487） DNA-directed RNA polymerase II subunit RPB8 × 1 （P52434） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36954） DNA-directed RNA polymerase II subunit RPB10 × 1 （P62875） DNA-directed RNA polymerase II subunit RPB11-a × 1 （P52435） DNA-directed RNA polymerase II subunit RPB12 × 1 （P53803） Transcription initiation factor IIB × 1 （Q00403） Transcription initiation factor IIA subunit 1 × 1 （P52655） Transcription initiation factor IIA subunit 2 × 1 （P52657） General transcription factor IIE subunit 1 × 1 （P29083） Transcription initiation factor IIE subunit beta × 1 （P29084） General transcription factor IIF subunit 1 × 1 （P35269） General transcription factor IIF subunit 2 × 1 （P13984） Transcription elongation factor A protein 1 × 1 （P23193） SCP-X × 1 SCP-Y × 1 MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV). Resolution 3.90 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 5IYC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1C9B CRYSTAL STRUCTURE OF A HUMAN TBP CORE DOMAIN-HUMAN TFIIB CORE DOMAIN COMPLEX BOUND TO AN EXTENDED, MODIFIED ADENOVIRAL MAJOR LATE PROMOTER (ADMLP) Deposited 1999-08-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain B 158–337（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；277 K；PEG 8000, TRIS.HCL, AMMONIUM ACETATE, MAGNESIUM CHLORIDE, POTASSIUM CHLORIDE, SODIUM CITRATE, DTT, GLYCEROL, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Resolution 2.65 Å R-free 0.260
1C9B CRYSTAL STRUCTURE OF A HUMAN TBP CORE DOMAIN-HUMAN TFIIB CORE DOMAIN COMPLEX BOUND TO AN EXTENDED, MODIFIED ADENOVIRAL MAJOR LATE PROMOTER (ADMLP) Deposited 1999-08-01 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 F 158–337（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；277 K；PEG 8000, TRIS.HCL, AMMONIUM ACETATE, MAGNESIUM CHLORIDE, POTASSIUM CHLORIDE, SODIUM CITRATE, DTT, GLYCEROL, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Resolution 2.65 Å R-free 0.260
1C9B CRYSTAL STRUCTURE OF A HUMAN TBP CORE DOMAIN-HUMAN TFIIB CORE DOMAIN COMPLEX BOUND TO AN EXTENDED, MODIFIED ADENOVIRAL MAJOR LATE PROMOTER (ADMLP) Deposited 1999-08-01 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 J 158–337（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；277 K；PEG 8000, TRIS.HCL, AMMONIUM ACETATE, MAGNESIUM CHLORIDE, POTASSIUM CHLORIDE, SODIUM CITRATE, DTT, GLYCEROL, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Resolution 2.65 Å R-free 0.260
1C9B CRYSTAL STRUCTURE OF A HUMAN TBP CORE DOMAIN-HUMAN TFIIB CORE DOMAIN COMPLEX BOUND TO AN EXTENDED, MODIFIED ADENOVIRAL MAJOR LATE PROMOTER (ADMLP) Deposited 1999-08-01 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 N 158–337（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；277 K；PEG 8000, TRIS.HCL, AMMONIUM ACETATE, MAGNESIUM CHLORIDE, POTASSIUM CHLORIDE, SODIUM CITRATE, DTT, GLYCEROL, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Resolution 2.65 Å R-free 0.260
1C9B CRYSTAL STRUCTURE OF A HUMAN TBP CORE DOMAIN-HUMAN TFIIB CORE DOMAIN COMPLEX BOUND TO AN EXTENDED, MODIFIED ADENOVIRAL MAJOR LATE PROMOTER (ADMLP) Deposited 1999-08-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain R 158–337（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；277 K；PEG 8000, TRIS.HCL, AMMONIUM ACETATE, MAGNESIUM CHLORIDE, POTASSIUM CHLORIDE, SODIUM CITRATE, DTT, GLYCEROL, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Resolution 2.65 Å R-free 0.260
1CDW HUMAN TBP CORE DOMAIN COMPLEXED WITH DNA Deposited 1996-04-11 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: trimeric
Chain A 159–337（179 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.90 Å R-free 0.258
1JFI Crystal Structure of the NC2-TBP-DNA Ternary Complex Deposited 2001-06-20 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 C 159–339（181 aa） Fragment：RESIDUES 359-539
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；PEG 4000, sodium citrate, potassium chloride, magnesium chloride, DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.62 Å R-free 0.277
1NVP HUMAN TFIIA/TBP/DNA COMPLEX Deposited 2003-02-04 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 159–339（181 aa） Fragment：C-TERMINAL 181 AMINO ACIDS
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；PEG6000, lithium nitrate, calcium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.10 Å R-free 0.247
1TGH TATA BINDING PROTEIN (TBP)/DNA COMPLEX Deposited 1996-02-13 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: trimeric
Chain A 113–297（185 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；pH 8.00
Resolution 2.90 Å R-free 0.294
4ROC Human TFIIB-related factor 2 (Brf2) and TBP bound to U6#2 promoter Deposited 2014-10-28 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 B 159–339（181 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293 K；10-20% PEG 3350, 50-100 mM MgCl2, 2 mM DTT, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.90 Å R-free 0.215
4ROD Human TFIIB-related factor 2 (Brf2) and TBP bound to TRNAU1 promoter Deposited 2014-10-28 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 B 159–339（181 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293 K；10-20% PEG 3350, 50-100 mM MgCl2, 2 mM DTT, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.70 Å R-free 0.247
4ROE Human TFIIB-related factor 2 (Brf2) and TBP bound to RPPH1 promoter Deposited 2014-10-28 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 B 159–339（181 aa）
Not recorded MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293 K；10-20% PEG 3350, 50-100 mM MgCl2, 2 mM DTT, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.20 Å R-free 0.222
5FUR Structure of human TFIID-IIA bound to core promoter DNA Deposited 2016-01-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–339（339 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 10 MM HEPES, 10 MM MGCL2, 50 MM KCL, 3% TREHALOSE 1 MM DTT, 0.0125% NP-40；pH 7.9；10 MM HEPES, 10 MM MGCL2, 50 MM KCL, 3% TREHALOSE 1 MM DTT, 0.0125% NP-40
cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE
Resolution 8.50 Å
5IY6 Human holo-PIC in the closed state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain P 1–339（339 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.20 Å
5IY7 Human holo-PIC in the open state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain P 1–339（339 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 8.60 Å
5IY8 Human holo-PIC in the initial transcribing state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain P 1–339（339 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.90 Å
5IY9 Human holo-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric
Chain P 1–339（339 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 6.30 Å
5IYA Human core-PIC in the closed state Deposited 2016-03-24 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain P 1–339（339 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 5.40 Å
5IYB Human core-PIC in the open state Deposited 2016-03-24 Parsed fields agree Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain P 1–339（339 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
5IYD Human core-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain P 1–339（339 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
5N9G TFIIIB -TBP/Brf2/DNA and SANT domain of Bdp1- Deposited 2017-02-24 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 B 159–339（181 aa） Fragment：UNP residues 159-339
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；10-16% PEG 8000, 150-200 mM KCl, 100 mM MES pH 6.5, 10-15 mM MgCl2, 1 mM TCEP
Resolution 2.70 Å R-free 0.234
5N9G TFIIIB -TBP/Brf2/DNA and SANT domain of Bdp1- Deposited 2017-02-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain G 159–339（181 aa） Fragment：UNP residues 159-339
Not recorded NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；10-16% PEG 8000, 150-200 mM KCl, 100 mM MES pH 6.5, 10-15 mM MgCl2, 1 mM TCEP
Resolution 2.70 Å R-free 0.234
6MZD Human TFIID Lobe A canonical Deposited 2018-11-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain T 1–339（339 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；BT 4s; BF 15N
Resolution 9.80 Å
6MZL Human TFIID canonical state Deposited 2018-11-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 22 PDB declaration: 22-meric
Chain T 1–339（339 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；BT 4s; BF 15N
Resolution 23.00 Å
6MZM Human TFIID bound to promoter DNA and TFIIA Deposited 2018-11-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain T 1–339（339 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；BT 4s; BF 15N
Resolution 7.50 Å
6O9L Human holo-PIC in the closed state Deposited 2019-03-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 31 PDB declaration: 33-meric
Chain P 1–339（339 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
7EDX p53-bound TFIID-based core PIC on HDM2 promoter Deposited 2021-03-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 37 PDB declaration: 39-meric
Chain P 1–339（339 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7EG7 TFIID-based core PIC on SCP promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 37 PDB declaration: 39-meric
Chain P 1–339（339 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.20 Å
7EG8 TFIID-based core PIC on PUMA promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 37 PDB declaration: 39-meric
Chain P 1–339（339 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.40 Å
7EG9 TFIID-based intermediate PIC on SCP promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 39 PDB declaration: 41-meric
Chain P 1–339（339 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7EGA TFIID-based intermediate PIC on PUMA promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 39 PDB declaration: 41-meric
Chain P 1–339（339 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
7EGB TFIID-based holo PIC on SCP promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain P 1–339（339 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7EGC p53-bound TFIID-based holo PIC on HDM2 promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain P 1–339（339 aa）
Not recorded ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7EGD SCP promoter-bound TFIID-TFIIA in initial TBP-loading state Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric
Chain P 1–339（339 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.75 Å
7EGE TFIID in canonical conformation Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain P 1–339（339 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.00 Å
7EGF TFIID lobe A subcomplex Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain P 1–339（339 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.16 Å
7EGI TFIID in rearranged conformation Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 22 PDB declaration: 22-meric
Chain P 1–339（339 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.82 Å
7EGJ SCP promoter-bound TFIID-TFIIA in post TBP-loading state Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric
Chain P 1–339（339 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.64 Å
7ENA TFIID-based PIC-Mediator holo-complex in pre-assembled state (pre-hPIC-MED) Deposited 2021-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 74 PDB declaration: 76-meric
Chain DP 1–339（339 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.07 Å
7ENC TFIID-based PIC-Mediator holo-complex in fully-assembled state (hPIC-MED) Deposited 2021-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 74 PDB declaration: 76-meric
Chain DP 1–339（339 aa）
Not recorded ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.13 Å
7LBM Structure of the human Mediator-bound transcription pre-initiation complex Deposited 2021-01-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 54 PDB declaration: 56-meric
Chain P 1–339（339 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7NVR Human Mediator with RNA Polymerase II Pre-initiation complex Deposited 2021-03-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 56 PDB declaration: 58-meric
Chain O 1–339（339 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 18 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7NVS RNA polymerase II core pre-initiation complex with closed promoter DNA in proximal position Deposited 2021-03-16 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 1–339（339 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7NVT RNA polymerase II core pre-initiation complex with closed promoter DNA in distal position Deposited 2021-03-16 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 1–339（339 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7NVU RNA polymerase II core pre-initiation complex with open promoter DNA Deposited 2021-03-16 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 1–339（339 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
7NVY RNA polymerase II pre-initiation complex with closed promoter DNA in proximal position Deposited 2021-03-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain O 1–339（339 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 7.30 Å
7NVZ RNA polymerase II pre-initiation complex with closed promoter DNA in distal position Deposited 2021-03-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain O 1–339（339 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 7.20 Å
7NW0 RNA polymerase II pre-initiation complex with open promoter DNA Deposited 2021-03-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain O 1–339（339 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.60 Å
7ZWC Structure of SNAPc:TBP-TFIIA-TFIIB sub-complex bound to U5 snRNA promoter Deposited 2022-05-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain O 1–339（339 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7ZWD Structure of SNAPc containing Pol II pre-initiation complex bound to U5 snRNA promoter (CC) Deposited 2022-05-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric
Chain O 1–339（339 aa）
Not recorded ZN ZINC ION × 11 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ZX7 Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter (CC) Deposited 2022-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric
Chain O 1–339（339 aa）
Not recorded ZN ZINC ION × 11 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7ZX8 Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter (OC) Deposited 2022-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric
Chain O 1–339（339 aa）
Not recorded ZN ZINC ION × 11 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ZXE Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter (OC) Deposited 2022-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain O 1–339（339 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8BVW RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W) Deposited 2022-12-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric
Chain O 1–339（339 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 4.00 Å
8BYQ RNA polymerase II pre-initiation complex with the proximal +1 nucleosome (PIC-Nuc10W) Deposited 2022-12-14 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 O 1–339（339 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 16 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8BZ1 RNA polymerase II core pre-initiation complex with the proximal +1 nucleosome (cPIC-Nuc10W) Deposited 2022-12-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain O 1–339（339 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8GXQ PIC-Mediator in complex with +1 nucleosome (T40N) in MH-binding state Deposited 2022-09-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric
Chain DP 1–339（339 aa）
Not recorded ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.04 Å
8GXS PIC-Mediator in complex with +1 nucleosome (T40N) in H-binding state Deposited 2022-09-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric
Chain DP 1–339（339 aa）
Not recorded ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.16 Å
8ITY human RNA polymerase III pre-initiation complex closed DNA 1 Deposited 2023-03-23 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain U 1–339（339 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
8IUE RNA polymerase III pre-initiation complex melting complex 1 Deposited 2023-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain U 1–339（339 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.10 Å
8IUH RNA polymerase III pre-initiation complex open complex 1 Deposited 2023-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain U 1–339（339 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.40 Å
8S51 RNA polymerase II core initially transcribing complex with an ordered RNA of 8 nt Deposited 2024-02-22 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 O 1–339（339 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8S52 RNA polymerase II core initially transcribing complex with an ordered RNA of 10 nt Deposited 2024-02-22 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 O 1–339（339 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8S5N RNA polymerase II core initially transcribing complex with an ordered RNA of 12 nt Deposited 2024-02-24 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 O 1–339（339 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8WAK Structure of transcribing complex 2 (TC2), the initially transcribing complex with Pol II positioned 2nt downstream of TSS. Deposited 2023-09-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain P 1–339（339 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.47 Å
8WAL Structure of transcribing complex 3 (TC3), the initially transcribing complex with Pol II positioned 3nt downstream of TSS. Deposited 2023-09-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain P 1–339（339 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.52 Å
8WAN Structure of transcribing complex 4 (TC4), the initially transcribing complex with Pol II positioned 4nt downstream of TSS. Deposited 2023-09-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain P 1–339（339 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.07 Å
8WAO Structure of transcribing complex 5 (TC5), the initially transcribing complex with Pol II positioned 5nt downstream of TSS. Deposited 2023-09-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain P 1–339（339 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å
8WAP Structure of transcribing complex 6 (TC6), the initially transcribing complex with Pol II positioned 6nt downstream of TSS. Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain P 1–339（339 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.85 Å
8WAQ Structure of transcribing complex 7 (TC7), the initially transcribing complex with Pol II positioned 7nt downstream of TSS. Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain P 1–339（339 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.29 Å
8WAR Structure of transcribing complex 8 (TC8), the initially transcribing complex with Pol II positioned 8nt downstream of TSS. Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain P 1–339（339 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
8WAS Structure of transcribing complex 9 (TC9), the initially transcribing complex with Pol II positioned 9nt downstream of TSS. Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain P 1–339（339 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.13 Å
9FSO Human RNA Polymerase III Class III Open Pre-initiation Complex 1 (OC1) Deposited 2024-06-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain R 159–339（181 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.28 Å
9FSP RNA Polymerase III Class III Open Pre-initation Complex 2 (OC2) Deposited 2024-06-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain R 159–339（181 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
9FSQ RNA Polymerase III Class III Melting Pre-Initiation Complex (MC) Deposited 2024-06-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain R 159–339（181 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.51 Å
9FSR RNA Polymerase III Class III Open Mini Pre-initiation Complex 1 (OC1-mini) Deposited 2024-06-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain R 159–339（181 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.76 Å
9FSS RNA Polymerase III Class III Open Mini Pre-Initiation complex 2 (OC2-mini) Deposited 2024-06-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain R 159–339（181 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.14 Å
9K3B Human RNA Polymerase III de novo transcribing complex 10 overall (TC10-overall) Deposited 2024-10-18 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 U 1–339（339 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.80 Å
9K3U Human RNA Polymerase III de novo transcribing complex 5 (TC5) Deposited 2024-10-20 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 U 1–339（339 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.00 Å
9K3V Human RNA Polymerase III de novo transcribing complex 4 (TC4) Deposited 2024-10-20 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 U 1–339（339 aa）
Not recorded ZN ZINC ION × 7 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.50 Å
9LXN Human RNA Polymerase III de novo transcribing complex 5 (TC5)(without 3'dATP) Deposited 2025-02-18 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 U 1–339（339 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.30 Å

76 other PDB entries and 81 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TBP_HUMAN
Isoform —
PDB entities 16
Chains and sequence ranges Author chain P； PDBConstruct 1–339； UniProt 1–339

General transcription factor IIE subunit 1

Homo sapiens

UniProt P29083

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 × 21 DNA 2 PDB declaration: 23-meric（23） Consistent with all polymer counts Chain Q； UniProt 1–439 Not recorded DNA-directed RNA polymerase II subunit RPB1 × 1 （P24928） DNA-directed RNA polymerase II subunit RPB2 × 1 （P30876） DNA-directed RNA polymerase II subunit RPB3 × 1 （P19387） DNA-directed RNA polymerase II subunit RPB4 × 1 （O15514） DNA-directed RNA polymerase II subunit RPB5 × 1 （P19388） DNA-directed RNA polymerase II subunit RPB6 × 1 （P61218） DNA-directed RNA polymerase II subunit RPB7 × 1 （P62487） DNA-directed RNA polymerase II subunit RPB8 × 1 （P52434） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36954） DNA-directed RNA polymerase II subunit RPB10 × 1 （P62875） DNA-directed RNA polymerase II subunit RPB11-a × 1 （P52435） DNA-directed RNA polymerase II subunit RPB12 × 1 （P53803） Transcription initiation factor IIB × 1 （Q00403） Transcription initiation factor IIA subunit 1 × 1 （P52655） Transcription initiation factor IIA subunit 2 × 1 （P52657） TATA-box-binding protein × 1 （P20226） Transcription initiation factor IIE subunit beta × 1 （P29084） General transcription factor IIF subunit 1 × 1 （P35269） General transcription factor IIF subunit 2 × 1 （P13984） Transcription elongation factor A protein 1 × 1 （P23193） SCP-X × 1 SCP-Y × 1 MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV). Resolution 3.90 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 5IYC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1VD4 Solution structure of the zinc finger domain of TFIIE alpha Deposited 2004-03-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 113–174（62 aa） Fragment：Zinc Finger Domain
Not recorded ZN ZINC ION × 1 SOLUTION NMR
NMR measurement conditions pH 6；305 K；Ionic strength (raw mmCIF value) 50mM NaCl；Pressure ambient
NMR sample composition 3-4mM TFIIE alpha Zinc finger domain, U-15N, U-15N, 13C; 20mM potassium phosphate beffer, 0.03mM ZnCl2, 5mM d-DTT | 90% H2O/10% D2O
NMR sample composition 3-4mM TFIIE alpha Zinc finger domain, U-15N, U-15N, 13C; 20mM potassium phosphate beffer, 0.03mM ZnCl2, 5mM d-DTT | 99.9% D2O
Resolution not provided
2JTX NMR structure of the TFIIE-alpha carboxyl terminus Deposited 2007-08-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 336–439（104 aa） Fragment：carboxyl terminus, residues 336-439
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.5；300 K；Ionic strength (raw mmCIF value) 0.2；Pressure ambient
NMR sample composition 1 mM TFIIE-alpha;, 20 mM sodium phosphate, 200 mM sodium chloride, 1 mM EDTA, 100% D2O | 100% D2O
NMR sample composition 1 mM [U-100% 15N] TFIIE-alpha;, 20 mM sodium phosphate, 200 mM sodium chloride, 1 mM EDTA, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] TFIIE-alpha;, 20 mM sodium phosphate, 200 mM sodium chloride, 1 mM EDTA, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] TFIIE-alpha;, 20 mM sodium phosphate, 200 mM sodium chloride, 1 mM EDTA, 100% D2O | 100% D2O
Resolution not provided
2RNQ Solution structure of the C-terminal acidic domain of TFIIE alpha Deposited 2008-01-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 378–439（62 aa） Fragment：C-terminal acidic doman, UNP residues 378-439
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；295 K；Ionic strength (raw mmCIF value) 0；Pressure ambient
NMR sample composition 1-2mM TFIIE-ALPHA, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1-2mM TFIIE-ALPHA, 100% D2O | 100% D2O
NMR sample composition 1-2mM [U-100% 15N] TFIIE-ALPHA, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1-2mM [U-100% 13C; U-100% 15N] TFIIE-ALPHA, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1-2mM [U-100% 13C; U-100% 15N] TFIIE-ALPHA, 100% D2O | 100% D2O
Resolution not provided
2RNR Solution structure of the complex between TFIIE alpha C-terminal acidic domain and TFIIH p62 PH domain Deposited 2008-01-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 378–439（62 aa） Fragment：C-terminal acidic domain, UNP residues 378-439
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；305 K；Ionic strength (raw mmCIF value) 0；Pressure ambient
NMR sample composition 0.5MM [U-100% 15N] TFIIE-ALPHA, 0.5MM TFIIH P62; 20MM POTASSIUM PHOSPHATE, 5MM [U-99% 2H] DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.5MM [U-100% 13C; U-100% 15N] TFIIE-ALPHA, 0.5MM TFIIH P62; 20MM POTASSIUM PHOSPHATE, 5MM [U-99% 2H] DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.5MM [U-100% 13C; U-100% 15N] TFIIE-ALPHA, 0.5MM TFIIH P62; 20MM POTASSIUM PHOSPHATE, 5MM [U-99% 2H] DTT, 100% D2O | 100% D2O
NMR sample composition 0.5MM [U-100% 15N] TFIIH P62, 0.5mM TFIIE-ALPHA; 20MM POTASSIUM PHOSPHATE, 5MM [U-99% 2H] DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.5MM [U-100% 13C; U-100% 15N] TFIIH P62, 0.5MM TFIIE-ALPHA; 20MM POTASSIUM PHOSPHATE, 5MM [U-99% 2H] DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.5MM [U-100% 13C; U-100% 15N] TFIIH P62, 0.5MM TFIIE-ALPHA; 20MM POTASSIUM PHOSPHATE, 5MM [U-99% 2H] DTT, 100% D2O | 100% D2O
Resolution not provided
5GPY Crystal structure of the human TFIIE complex Deposited 2016-08-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–217（217 aa） Fragment：UNP residues 1-217
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.9；293 K；12% PEG3350
Resolution 2.10 Å R-free 0.237
5IY6 Human holo-PIC in the closed state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain Q 1–439（439 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.20 Å
5IY7 Human holo-PIC in the open state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain Q 1–439（439 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 8.60 Å
5IY8 Human holo-PIC in the initial transcribing state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain Q 1–439（439 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.90 Å
5IY9 Human holo-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric
Chain Q 1–439（439 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 6.30 Å
5IYA Human core-PIC in the closed state Deposited 2016-03-24 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain Q 1–439（439 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 5.40 Å
5IYB Human core-PIC in the open state Deposited 2016-03-24 Parsed fields agree Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain Q 1–439（439 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
5IYD Human core-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain Q 1–439（439 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
6O9L Human holo-PIC in the closed state Deposited 2019-03-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 31 PDB declaration: 33-meric
Chain Q 1–439（439 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
7EG9 TFIID-based intermediate PIC on SCP promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 39 PDB declaration: 41-meric
Chain U 1–439（439 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7EGA TFIID-based intermediate PIC on PUMA promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 39 PDB declaration: 41-meric
Chain U 1–439（439 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
7EGB TFIID-based holo PIC on SCP promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain U 1–439（439 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7EGC p53-bound TFIID-based holo PIC on HDM2 promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain U 1–439（439 aa）
Not recorded ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7ENA TFIID-based PIC-Mediator holo-complex in pre-assembled state (pre-hPIC-MED) Deposited 2021-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 74 PDB declaration: 76-meric
Chain EA 1–439（439 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.07 Å
7ENC TFIID-based PIC-Mediator holo-complex in fully-assembled state (hPIC-MED) Deposited 2021-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 74 PDB declaration: 76-meric
Chain EA 1–439（439 aa）
Not recorded ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.13 Å
7LBM Structure of the human Mediator-bound transcription pre-initiation complex Deposited 2021-01-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 54 PDB declaration: 56-meric
Chain Q 1–439（439 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7NVR Human Mediator with RNA Polymerase II Pre-initiation complex Deposited 2021-03-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 56 PDB declaration: 58-meric
Chain W 1–439（439 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 18 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7NVS RNA polymerase II core pre-initiation complex with closed promoter DNA in proximal position Deposited 2021-03-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain W 1–439（439 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7NVT RNA polymerase II core pre-initiation complex with closed promoter DNA in distal position Deposited 2021-03-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain W 1–439（439 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7NVU RNA polymerase II core pre-initiation complex with open promoter DNA Deposited 2021-03-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain W 1–439（439 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
7NVV XPB-containing part of TFIIH in a post-translocated state (with ADP-BeF3) Deposited 2021-03-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain W 1–439（439 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7NVW TFIIH in a pre-translocated state (without ADP-BeF3) Deposited 2021-03-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain W 1–439（439 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7NVX TFIIH in a post-translocated state (with ADP-BeF3) Deposited 2021-03-16 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain W 1–439（439 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7NVY RNA polymerase II pre-initiation complex with closed promoter DNA in proximal position Deposited 2021-03-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain W 1–439（439 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 7.30 Å
7NVZ RNA polymerase II pre-initiation complex with closed promoter DNA in distal position Deposited 2021-03-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain W 1–439（439 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 7.20 Å
7NW0 RNA polymerase II pre-initiation complex with open promoter DNA Deposited 2021-03-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain W 1–439（439 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.60 Å
8BVW RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W) Deposited 2022-12-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric
Chain W 1–273（273 aa）
Chain W 274–439（166 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 4.00 Å
8BYQ RNA polymerase II pre-initiation complex with the proximal +1 nucleosome (PIC-Nuc10W) Deposited 2022-12-14 Different construct 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 W 1–196（196 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 16 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8GXQ PIC-Mediator in complex with +1 nucleosome (T40N) in MH-binding state Deposited 2022-09-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric
Chain EA 1–439（439 aa）
Not recorded ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.04 Å
8GXS PIC-Mediator in complex with +1 nucleosome (T40N) in H-binding state Deposited 2022-09-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric
Chain EA 1–439（439 aa）
Not recorded ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.16 Å
8S51 RNA polymerase II core initially transcribing complex with an ordered RNA of 8 nt Deposited 2024-02-22 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 W 1–439（439 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8S52 RNA polymerase II core initially transcribing complex with an ordered RNA of 10 nt Deposited 2024-02-22 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 W 1–439（439 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8S54 RNA polymerase II early elongation complex bound to TFIIE and TFIIF - state b (composite structure) Deposited 2024-02-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: 18-meric
Chain W 1–439（439 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8S55 RNA polymerase II early elongation complex bound to TFIIE and TFIIF - state a (composite structure) Deposited 2024-02-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: 19-meric
Chain W 1–439（439 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8S5N RNA polymerase II core initially transcribing complex with an ordered RNA of 12 nt Deposited 2024-02-24 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 W 1–439（439 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8WAK Structure of transcribing complex 2 (TC2), the initially transcribing complex with Pol II positioned 2nt downstream of TSS. Deposited 2023-09-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain U 1–439（439 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.47 Å
8WAL Structure of transcribing complex 3 (TC3), the initially transcribing complex with Pol II positioned 3nt downstream of TSS. Deposited 2023-09-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain U 1–439（439 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.52 Å
8WAN Structure of transcribing complex 4 (TC4), the initially transcribing complex with Pol II positioned 4nt downstream of TSS. Deposited 2023-09-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain U 1–439（439 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.07 Å
8WAO Structure of transcribing complex 5 (TC5), the initially transcribing complex with Pol II positioned 5nt downstream of TSS. Deposited 2023-09-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain U 1–439（439 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å
8WAP Structure of transcribing complex 6 (TC6), the initially transcribing complex with Pol II positioned 6nt downstream of TSS. Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain U 1–439（439 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.85 Å
8WAQ Structure of transcribing complex 7 (TC7), the initially transcribing complex with Pol II positioned 7nt downstream of TSS. Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain U 1–439（439 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.29 Å
8WAR Structure of transcribing complex 8 (TC8), the initially transcribing complex with Pol II positioned 8nt downstream of TSS. Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain U 1–439（439 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
8WAS Structure of transcribing complex 9 (TC9), the initially transcribing complex with Pol II positioned 9nt downstream of TSS. Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain U 1–439（439 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.13 Å

47 other PDB entries and 47 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name T2EA_HUMAN
Isoform —
PDB entities 17
Chains and sequence ranges Author chain Q； PDBConstruct 1–439； UniProt 1–439

Transcription initiation factor IIE subunit beta

Homo sapiens

UniProt P29084

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 × 21 DNA 2 PDB declaration: 23-meric（23） Consistent with all polymer counts Chain R； UniProt 1–291 Not recorded DNA-directed RNA polymerase II subunit RPB1 × 1 （P24928） DNA-directed RNA polymerase II subunit RPB2 × 1 （P30876） DNA-directed RNA polymerase II subunit RPB3 × 1 （P19387） DNA-directed RNA polymerase II subunit RPB4 × 1 （O15514） DNA-directed RNA polymerase II subunit RPB5 × 1 （P19388） DNA-directed RNA polymerase II subunit RPB6 × 1 （P61218） DNA-directed RNA polymerase II subunit RPB7 × 1 （P62487） DNA-directed RNA polymerase II subunit RPB8 × 1 （P52434） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36954） DNA-directed RNA polymerase II subunit RPB10 × 1 （P62875） DNA-directed RNA polymerase II subunit RPB11-a × 1 （P52435） DNA-directed RNA polymerase II subunit RPB12 × 1 （P53803） Transcription initiation factor IIB × 1 （Q00403） Transcription initiation factor IIA subunit 1 × 1 （P52655） Transcription initiation factor IIA subunit 2 × 1 （P52657） TATA-box-binding protein × 1 （P20226） General transcription factor IIE subunit 1 × 1 （P29083） General transcription factor IIF subunit 1 × 1 （P35269） General transcription factor IIF subunit 2 × 1 （P13984） Transcription elongation factor A protein 1 × 1 （P23193） SCP-X × 1 SCP-Y × 1 MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV). Resolution 3.90 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 5IYC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1D8J SOLUTION STRUCTURE OF THE CENTRAL CORE DOMAIN OF TFIIE BETA Deposited 1999-10-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 66–146（81 aa） Fragment：CENTRAL CORE DOMAIN
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；300 K；Ionic strength (raw mmCIF value) 500mM NACL；Pressure AMBIENT
NMR sample composition 1-2MM PROTEIN U-15N,13C; 20MM PHOSPHATE BUFFER, 500MM NACL
NMR sample composition 1-2MM PROTEIN ; 20MM PHOSPHATE BUFFER, 500MM NACL
Resolution not provided
1D8K SOLUTION STRUCTURE OF THE CENTRAL CORE DOMAIN OF TFIIE BETA Deposited 1999-10-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 66–146（81 aa） Fragment：CENTRAL CORE DOMAIN
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；300 K；Ionic strength (raw mmCIF value) 500mM NACL；Pressure AMBIENT
NMR sample composition 1-2MM PROTEIN U-15N,13C; 20MM PHOSPHATE BUFFER, 500MM NACL
NMR sample composition 1-2MM PROTEIN U-15N; 20MM PHOSPHATE BUFFER, 500MM NACL
NMR sample composition 1-2MM PROTEIN ; 20MM PHOSPHATE BUFFER, 500MM NACL
Resolution not provided
5GPY Crystal structure of the human TFIIE complex Deposited 2016-08-05 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 141–244（104 aa） Fragment：UNP residues 141-244
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.9；293 K；12% PEG3350
Resolution 2.10 Å R-free 0.237
5IY6 Human holo-PIC in the closed state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain R 1–291（291 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.20 Å
5IY7 Human holo-PIC in the open state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain R 1–291（291 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 8.60 Å
5IY8 Human holo-PIC in the initial transcribing state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain R 1–291（291 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.90 Å
5IY9 Human holo-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric
Chain R 1–291（291 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 6.30 Å
5IYA Human core-PIC in the closed state Deposited 2016-03-24 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain R 1–291（291 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 5.40 Å
5IYB Human core-PIC in the open state Deposited 2016-03-24 Parsed fields agree Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain R 1–291（291 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
5IYD Human core-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain R 1–291（291 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
6O9L Human holo-PIC in the closed state Deposited 2019-03-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 31 PDB declaration: 33-meric
Chain R 1–291（291 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
7EG9 TFIID-based intermediate PIC on SCP promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 39 PDB declaration: 41-meric
Chain V 1–291（291 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7EGA TFIID-based intermediate PIC on PUMA promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 39 PDB declaration: 41-meric
Chain V 1–291（291 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
7EGB TFIID-based holo PIC on SCP promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain V 1–291（291 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7EGC p53-bound TFIID-based holo PIC on HDM2 promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain V 1–291（291 aa）
Not recorded ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7ENA TFIID-based PIC-Mediator holo-complex in pre-assembled state (pre-hPIC-MED) Deposited 2021-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 74 PDB declaration: 76-meric
Chain EB 1–291（291 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.07 Å
7ENC TFIID-based PIC-Mediator holo-complex in fully-assembled state (hPIC-MED) Deposited 2021-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 74 PDB declaration: 76-meric
Chain EB 1–291（291 aa）
Not recorded ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.13 Å
7LBM Structure of the human Mediator-bound transcription pre-initiation complex Deposited 2021-01-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 54 PDB declaration: 56-meric
Chain R 1–291（291 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7NVR Human Mediator with RNA Polymerase II Pre-initiation complex Deposited 2021-03-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 56 PDB declaration: 58-meric
Chain X 1–291（291 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 18 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7NVS RNA polymerase II core pre-initiation complex with closed promoter DNA in proximal position Deposited 2021-03-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain X 1–291（291 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7NVT RNA polymerase II core pre-initiation complex with closed promoter DNA in distal position Deposited 2021-03-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain X 1–291（291 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7NVU RNA polymerase II core pre-initiation complex with open promoter DNA Deposited 2021-03-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain X 1–291（291 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
7NVY RNA polymerase II pre-initiation complex with closed promoter DNA in proximal position Deposited 2021-03-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain X 1–291（291 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 7.30 Å
7NVZ RNA polymerase II pre-initiation complex with closed promoter DNA in distal position Deposited 2021-03-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain X 1–291（291 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 7.20 Å
7NW0 RNA polymerase II pre-initiation complex with open promoter DNA Deposited 2021-03-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain X 1–291（291 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.60 Å
8BVW RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W) Deposited 2022-12-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric
Chain X 1–291（291 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 4.00 Å
8BYQ RNA polymerase II pre-initiation complex with the proximal +1 nucleosome (PIC-Nuc10W) Deposited 2022-12-14 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 X 1–291（291 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 16 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8GXQ PIC-Mediator in complex with +1 nucleosome (T40N) in MH-binding state Deposited 2022-09-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric
Chain EB 1–291（291 aa）
Not recorded ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.04 Å
8GXS PIC-Mediator in complex with +1 nucleosome (T40N) in H-binding state Deposited 2022-09-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric
Chain EB 1–291（291 aa）
Not recorded ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.16 Å
8S51 RNA polymerase II core initially transcribing complex with an ordered RNA of 8 nt Deposited 2024-02-22 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 X 1–291（291 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8S52 RNA polymerase II core initially transcribing complex with an ordered RNA of 10 nt Deposited 2024-02-22 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 X 1–291（291 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8S55 RNA polymerase II early elongation complex bound to TFIIE and TFIIF - state a (composite structure) Deposited 2024-02-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: 19-meric
Chain X 1–291（291 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8S5N RNA polymerase II core initially transcribing complex with an ordered RNA of 12 nt Deposited 2024-02-24 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 X 1–291（291 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8WAK Structure of transcribing complex 2 (TC2), the initially transcribing complex with Pol II positioned 2nt downstream of TSS. Deposited 2023-09-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain V 1–291（291 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.47 Å
8WAL Structure of transcribing complex 3 (TC3), the initially transcribing complex with Pol II positioned 3nt downstream of TSS. Deposited 2023-09-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain V 1–291（291 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.52 Å
8WAN Structure of transcribing complex 4 (TC4), the initially transcribing complex with Pol II positioned 4nt downstream of TSS. Deposited 2023-09-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain V 1–291（291 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.07 Å
8WAO Structure of transcribing complex 5 (TC5), the initially transcribing complex with Pol II positioned 5nt downstream of TSS. Deposited 2023-09-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain V 1–291（291 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å
8WAP Structure of transcribing complex 6 (TC6), the initially transcribing complex with Pol II positioned 6nt downstream of TSS. Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain V 1–291（291 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.85 Å
8WAQ Structure of transcribing complex 7 (TC7), the initially transcribing complex with Pol II positioned 7nt downstream of TSS. Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain V 1–291（291 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.29 Å
8WAR Structure of transcribing complex 8 (TC8), the initially transcribing complex with Pol II positioned 8nt downstream of TSS. Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain V 1–291（291 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
8WAS Structure of transcribing complex 9 (TC9), the initially transcribing complex with Pol II positioned 9nt downstream of TSS. Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain V 1–291（291 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.13 Å

41 other PDB entries and 41 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name T2EB_HUMAN
Isoform —
PDB entities 18
Chains and sequence ranges Author chain R； PDBConstruct 1–291； UniProt 1–291

General transcription factor IIF subunit 1

Homo sapiens

UniProt P35269

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 × 21 DNA 2 PDB declaration: 23-meric（23） Consistent with all polymer counts Chain S； UniProt 1–517 Not recorded DNA-directed RNA polymerase II subunit RPB1 × 1 （P24928） DNA-directed RNA polymerase II subunit RPB2 × 1 （P30876） DNA-directed RNA polymerase II subunit RPB3 × 1 （P19387） DNA-directed RNA polymerase II subunit RPB4 × 1 （O15514） DNA-directed RNA polymerase II subunit RPB5 × 1 （P19388） DNA-directed RNA polymerase II subunit RPB6 × 1 （P61218） DNA-directed RNA polymerase II subunit RPB7 × 1 （P62487） DNA-directed RNA polymerase II subunit RPB8 × 1 （P52434） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36954） DNA-directed RNA polymerase II subunit RPB10 × 1 （P62875） DNA-directed RNA polymerase II subunit RPB11-a × 1 （P52435） DNA-directed RNA polymerase II subunit RPB12 × 1 （P53803） Transcription initiation factor IIB × 1 （Q00403） Transcription initiation factor IIA subunit 1 × 1 （P52655） Transcription initiation factor IIA subunit 2 × 1 （P52657） TATA-box-binding protein × 1 （P20226） General transcription factor IIE subunit 1 × 1 （P29083） Transcription initiation factor IIE subunit beta × 1 （P29084） General transcription factor IIF subunit 2 × 1 （P13984） Transcription elongation factor A protein 1 × 1 （P23193） SCP-X × 1 SCP-Y × 1 MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV). Resolution 3.90 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 5IYC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1F3U CRYSTAL STRUCTURE OF THE RAP30/74 INTERACTION DOMAINS OF HUMAN TFIIF Deposited 2000-06-06 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 2–172（171 aa） Fragment：RESIDUES 2-172
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；278 K；PEG 1500, lithium nitrate, bis-Tris, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Resolution 1.70 Å R-free 0.260
1F3U CRYSTAL STRUCTURE OF THE RAP30/74 INTERACTION DOMAINS OF HUMAN TFIIF Deposited 2000-06-06 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 2–172（171 aa） Fragment：RESIDUES 2-172
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；278 K；PEG 1500, lithium nitrate, bis-Tris, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Resolution 1.70 Å R-free 0.260
1F3U CRYSTAL STRUCTURE OF THE RAP30/74 INTERACTION DOMAINS OF HUMAN TFIIF Deposited 2000-06-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 2–172（171 aa） Fragment：RESIDUES 2-172
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；278 K；PEG 1500, lithium nitrate, bis-Tris, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Resolution 1.70 Å R-free 0.260
1F3U CRYSTAL STRUCTURE OF THE RAP30/74 INTERACTION DOMAINS OF HUMAN TFIIF Deposited 2000-06-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 2–172（171 aa） Fragment：RESIDUES 2-172
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；278 K；PEG 1500, lithium nitrate, bis-Tris, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Resolution 1.70 Å R-free 0.260
1I27 CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF THE RAP74 SUBUNIT OF HUMAN TRANSCRIPTION FACTOR IIF (TFIIF) Deposited 2001-02-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 449–517（69 aa） Fragment：RAP74 SUBUNIT, C-TERMINAL DOMAIN
Mutation：YES ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；282 K；Zinc Sulfate, Lithium chloride, PEG 2000 MME, polyvinylpyrrolidone 15K, glucosamine hydrochloride, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 282K
Resolution 1.02 Å R-free 0.146
1J2X Crystal structure of RAP74 C-terminal domain complexed with FCP1 C-terminal peptide Deposited 2003-01-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 449–517（69 aa） Fragment：C-terminal domain
Not recorded SO4 SULFATE ION × 2 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；PEGMME 550, zinc sulfate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Resolution 2.00 Å R-free 0.254
1NHA Solution Structure of the Carboxyl-Terminal Domain of RAP74 and NMR Characterization of the FCP-Binding Sites of RAP74 and CTD of RAP74, the subunit of Human TFIIF Deposited 2002-12-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 436–517（82 aa） Fragment：C-Terminal Domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 20mM sodium phosphate buffer；Pressure ambient
NMR sample composition 1mM cterRAP74 unlabeled, 20mM sodium phosphate, and 1mM EDTA | 100% D2O
NMR sample composition 1mM cterRAP74 U-15N, 20mM sodium phosphate, and 1mM EDTA | 90% H2O/10% D2O
NMR sample composition 1mM cterRAP74 U-15N and U-13C, 20mM sodium phosphate, and 1mM EDTA | 90% H2O/10% D2O
NMR sample composition 1mM cterRAP74 U-15N and U-13C, 20mM sodium phosphate, and 1mM EDTA | 100% D2O
Resolution not provided
1ONV NMR Structure of a Complex Containing the TFIIF Subunit RAP74 and the RNAP II CTD Phosphatase FCP1 Deposited 2003-03-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 436–517（82 aa） Fragment：C-Terminal Domain of RAP74, sequence database residues 436-517
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 20mM sodium phosphate buffer；Pressure ambient
NMR sample composition 1mM cterRAP74/cterFCP1, 20mM sodium phosphate, and 1mM EDTA | 100% D2O
NMR sample composition 1mM U-15N cterRAP74/cterFCP1, 20mM sodium phosphate, and 1mM EDTA | 90% H2O/10% D2O
NMR sample composition 1mM U-15N,13C cterRAP74/cterFCP1, 20mM sodium phosphate, and 1mM EDTA | 90% H2O/10% D2O
NMR sample composition 1mM cterRAP74/U-15N cterFCP1, 20mM sodium phosphate, and 1mM EDTA | 90% H2O/10% D2O
NMR sample composition 1mM cterRAP74/U-15N,13C cterFCP1, 20mM sodium phosphate, and 1mM EDTA | 90% H2O/10% D2O
NMR sample composition 1mM U-15N,C13 cterRAP74/cterFCP1, 20mM sodium phosphate, and 1mM EDTA; | 100% D2O
NMR sample composition 1mM cterRAP74/U-15N,13C cterFCP1, 20mM sodium phosphate, and 1mM EDTA | 100% D2O
Resolution not provided
2K7L NMR structure of a complex formed by the C-terminal domain of human RAP74 and a phosphorylated peptide from the central domain of the FCP1 Deposited 2008-08-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 451–517（67 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 10-40；Pressure ambient
NMR sample composition 1 mM [U-98% 15N] cterRAP74, 1 mM centFCP1-T584PO4, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-98% 13C; U-98% 15N] cterRAP74, 1 mM centFCP1-T584PO4, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-98% 13C; U-98% 15N] cterRAP74, 1 mM centFCP1-T584PO4, 100% D2O | 100% D2O
Resolution not provided
5IY6 Human holo-PIC in the closed state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain S 1–517（517 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.20 Å
5IY7 Human holo-PIC in the open state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain S 1–517（517 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 8.60 Å
5IY8 Human holo-PIC in the initial transcribing state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain S 1–517（517 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.90 Å
5IY9 Human holo-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric
Chain S 1–517（517 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 6.30 Å
5IYA Human core-PIC in the closed state Deposited 2016-03-24 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain S 1–517（517 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 5.40 Å
5IYB Human core-PIC in the open state Deposited 2016-03-24 Parsed fields agree Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain S 1–517（517 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
5IYD Human core-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain S 1–517（517 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
6O9L Human holo-PIC in the closed state Deposited 2019-03-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 31 PDB declaration: 33-meric
Chain S 1–517（517 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
7EDX p53-bound TFIID-based core PIC on HDM2 promoter Deposited 2021-03-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 37 PDB declaration: 39-meric
Chain S 1–517（517 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7EG7 TFIID-based core PIC on SCP promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 37 PDB declaration: 39-meric
Chain S 1–517（517 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.20 Å
7EG8 TFIID-based core PIC on PUMA promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 37 PDB declaration: 39-meric
Chain S 1–517（517 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.40 Å
7EG9 TFIID-based intermediate PIC on SCP promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 39 PDB declaration: 41-meric
Chain S 1–517（517 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7EGA TFIID-based intermediate PIC on PUMA promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 39 PDB declaration: 41-meric
Chain S 1–517（517 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
7EGB TFIID-based holo PIC on SCP promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain S 1–517（517 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7EGC p53-bound TFIID-based holo PIC on HDM2 promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain S 1–517（517 aa）
Not recorded ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7ENA TFIID-based PIC-Mediator holo-complex in pre-assembled state (pre-hPIC-MED) Deposited 2021-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 74 PDB declaration: 76-meric
Chain FA 1–517（517 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.07 Å
7ENC TFIID-based PIC-Mediator holo-complex in fully-assembled state (hPIC-MED) Deposited 2021-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 74 PDB declaration: 76-meric
Chain FA 1–517（517 aa）
Not recorded ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.13 Å
7LBM Structure of the human Mediator-bound transcription pre-initiation complex Deposited 2021-01-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 54 PDB declaration: 56-meric
Chain S 1–517（517 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7NVR Human Mediator with RNA Polymerase II Pre-initiation complex Deposited 2021-03-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 56 PDB declaration: 58-meric
Chain Q 1–517（517 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 18 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7NVS RNA polymerase II core pre-initiation complex with closed promoter DNA in proximal position Deposited 2021-03-16 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 1–517（517 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7NVT RNA polymerase II core pre-initiation complex with closed promoter DNA in distal position Deposited 2021-03-16 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 1–517（517 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7NVU RNA polymerase II core pre-initiation complex with open promoter DNA Deposited 2021-03-16 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 1–517（517 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
7NVY RNA polymerase II pre-initiation complex with closed promoter DNA in proximal position Deposited 2021-03-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain Q 1–517（517 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 7.30 Å
7NVZ RNA polymerase II pre-initiation complex with closed promoter DNA in distal position Deposited 2021-03-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain Q 1–517（517 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 7.20 Å
7NW0 RNA polymerase II pre-initiation complex with open promoter DNA Deposited 2021-03-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain Q 1–517（517 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.60 Å
7ZWD Structure of SNAPc containing Pol II pre-initiation complex bound to U5 snRNA promoter (CC) Deposited 2022-05-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric
Chain Q 1–517（517 aa）
Not recorded ZN ZINC ION × 11 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ZX7 Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter (CC) Deposited 2022-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric
Chain Q 1–517（517 aa）
Not recorded ZN ZINC ION × 11 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7ZX8 Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter (OC) Deposited 2022-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric
Chain Q 1–517（517 aa）
Not recorded ZN ZINC ION × 11 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8BVW RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W) Deposited 2022-12-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric
Chain Q 1–517（517 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 4.00 Å
8BYQ RNA polymerase II pre-initiation complex with the proximal +1 nucleosome (PIC-Nuc10W) Deposited 2022-12-14 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 Q 1–517（517 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 16 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8BZ1 RNA polymerase II core pre-initiation complex with the proximal +1 nucleosome (cPIC-Nuc10W) Deposited 2022-12-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain Q 1–517（517 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8GXQ PIC-Mediator in complex with +1 nucleosome (T40N) in MH-binding state Deposited 2022-09-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric
Chain FA 1–517（517 aa）
Not recorded ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.04 Å
8GXS PIC-Mediator in complex with +1 nucleosome (T40N) in H-binding state Deposited 2022-09-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric
Chain FA 1–517（517 aa）
Not recorded ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.16 Å
8S51 RNA polymerase II core initially transcribing complex with an ordered RNA of 8 nt Deposited 2024-02-22 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 Q 1–517（517 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8S52 RNA polymerase II core initially transcribing complex with an ordered RNA of 10 nt Deposited 2024-02-22 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 Q 1–517（517 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8S54 RNA polymerase II early elongation complex bound to TFIIE and TFIIF - state b (composite structure) Deposited 2024-02-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: 18-meric
Chain Q 1–517（517 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8S55 RNA polymerase II early elongation complex bound to TFIIE and TFIIF - state a (composite structure) Deposited 2024-02-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: 19-meric
Chain Q 1–517（517 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8S5N RNA polymerase II core initially transcribing complex with an ordered RNA of 12 nt Deposited 2024-02-24 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 Q 1–517（517 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8WAK Structure of transcribing complex 2 (TC2), the initially transcribing complex with Pol II positioned 2nt downstream of TSS. Deposited 2023-09-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain S 1–517（517 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.47 Å
8WAL Structure of transcribing complex 3 (TC3), the initially transcribing complex with Pol II positioned 3nt downstream of TSS. Deposited 2023-09-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain S 1–517（517 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.52 Å
8WAN Structure of transcribing complex 4 (TC4), the initially transcribing complex with Pol II positioned 4nt downstream of TSS. Deposited 2023-09-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain S 1–517（517 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.07 Å
8WAO Structure of transcribing complex 5 (TC5), the initially transcribing complex with Pol II positioned 5nt downstream of TSS. Deposited 2023-09-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain S 1–517（517 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å
8WAP Structure of transcribing complex 6 (TC6), the initially transcribing complex with Pol II positioned 6nt downstream of TSS. Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain S 1–517（517 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.85 Å
8WAQ Structure of transcribing complex 7 (TC7), the initially transcribing complex with Pol II positioned 7nt downstream of TSS. Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain S 1–517（517 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.29 Å
8WAR Structure of transcribing complex 8 (TC8), the initially transcribing complex with Pol II positioned 8nt downstream of TSS. Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain S 1–517（517 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
8WAS Structure of transcribing complex 9 (TC9), the initially transcribing complex with Pol II positioned 9nt downstream of TSS. Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain S 1–517（517 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.13 Å
8WAT De novo transcribing complex 10 (TC10), the early elongation complex with Pol II positioned 10nt downstream of TSS Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: octadecameric
Chain S 1–517（517 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.82 Å
8WAU De novo transcribing complex 11 (TC11), the early elongation complex with Pol II positioned 11nt downstream of TSS Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: octadecameric
Chain S 1–517（517 aa）
Not recorded W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.78 Å
8WAV De novo transcribing complex 12 (TC12), the early elongation complex with Pol II positioned 12nt downstream of TSS Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: octadecameric
Chain S 1–517（517 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
8WAW De novo transcribing complex 13 (TC13), the early elongation complex with Pol II positioned 13nt downstream of TSS Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: octadecameric
Chain S 1–517（517 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.02 Å
8WAX De novo transcribing complex 14 (TC14), the early elongation complex with Pol II positioned 14nt downstream of TSS Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: octadecameric
Chain S 1–517（517 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.75 Å
8WAY De novo transcribing complex 15 (TC15), the early elongation complex with Pol II positioned 15nt downstream of TSS Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: octadecameric
Chain S 1–517（517 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.85 Å
8WAZ De novo transcribing complex 16 (TC16), the early elongation complex with Pol II positioned 16nt downstream of TSS Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: octadecameric
Chain S 1–517（517 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.76 Å
8WB0 De novo transcribing complex 17 (TC17), the early elongation complex with Pol II positioned 17nt downstream of TSS Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: octadecameric
Chain S 1–517（517 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.94 Å

60 other PDB entries and 63 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name T2FA_HUMAN
Isoform —
PDB entities 19
Chains and sequence ranges Author chain S； PDBConstruct 1–517； UniProt 1–517

General transcription factor IIF subunit 2

Homo sapiens

UniProt P13984

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 × 21 DNA 2 PDB declaration: 23-meric（23） Consistent with all polymer counts Chain T； UniProt 1–249 Not recorded DNA-directed RNA polymerase II subunit RPB1 × 1 （P24928） DNA-directed RNA polymerase II subunit RPB2 × 1 （P30876） DNA-directed RNA polymerase II subunit RPB3 × 1 （P19387） DNA-directed RNA polymerase II subunit RPB4 × 1 （O15514） DNA-directed RNA polymerase II subunit RPB5 × 1 （P19388） DNA-directed RNA polymerase II subunit RPB6 × 1 （P61218） DNA-directed RNA polymerase II subunit RPB7 × 1 （P62487） DNA-directed RNA polymerase II subunit RPB8 × 1 （P52434） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36954） DNA-directed RNA polymerase II subunit RPB10 × 1 （P62875） DNA-directed RNA polymerase II subunit RPB11-a × 1 （P52435） DNA-directed RNA polymerase II subunit RPB12 × 1 （P53803） Transcription initiation factor IIB × 1 （Q00403） Transcription initiation factor IIA subunit 1 × 1 （P52655） Transcription initiation factor IIA subunit 2 × 1 （P52657） TATA-box-binding protein × 1 （P20226） General transcription factor IIE subunit 1 × 1 （P29083） Transcription initiation factor IIE subunit beta × 1 （P29084） General transcription factor IIF subunit 1 × 1 （P35269） Transcription elongation factor A protein 1 × 1 （P23193） SCP-X × 1 SCP-Y × 1 MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV). Resolution 3.90 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 5IYC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BBY DNA-BINDING DOMAIN FROM HUMAN RAP30, NMR, MINIMIZED AVERAGE Deposited 1998-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 175–243（69 aa） Fragment：DNA-BINDING DOMAIN
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.2；297 K；Ionic strength (raw mmCIF value) 10mM PHOSPHATE, 50mM NACL；Pressure 1
NMR sample composition AQUEOUS
Resolution not provided
1F3U CRYSTAL STRUCTURE OF THE RAP30/74 INTERACTION DOMAINS OF HUMAN TFIIF Deposited 2000-06-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–119（118 aa） Fragment：RESIDUES 2-119
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；278 K；PEG 1500, lithium nitrate, bis-Tris, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Resolution 1.70 Å R-free 0.260
1F3U CRYSTAL STRUCTURE OF THE RAP30/74 INTERACTION DOMAINS OF HUMAN TFIIF Deposited 2000-06-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2–119（118 aa） Fragment：RESIDUES 2-119
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；278 K；PEG 1500, lithium nitrate, bis-Tris, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Resolution 1.70 Å R-free 0.260
1F3U CRYSTAL STRUCTURE OF THE RAP30/74 INTERACTION DOMAINS OF HUMAN TFIIF Deposited 2000-06-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 2–119（118 aa） Fragment：RESIDUES 2-119
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；278 K；PEG 1500, lithium nitrate, bis-Tris, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Resolution 1.70 Å R-free 0.260
1F3U CRYSTAL STRUCTURE OF THE RAP30/74 INTERACTION DOMAINS OF HUMAN TFIIF Deposited 2000-06-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 2–119（118 aa） Fragment：RESIDUES 2-119
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；278 K；PEG 1500, lithium nitrate, bis-Tris, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Resolution 1.70 Å R-free 0.260
2BBY DNA-BINDING DOMAIN FROM HUMAN RAP30, NMR, 30 STRUCTURES Deposited 1998-04-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 175–243（69 aa） Fragment：DNA-BINDING DOMAIN
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.2；297 K；Ionic strength (raw mmCIF value) 10mM PHOSPHATE, 50mM NACL；Pressure 1
NMR sample composition AQUEOUS
Resolution not provided
5IY6 Human holo-PIC in the closed state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain T 1–249（249 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.20 Å
5IY7 Human holo-PIC in the open state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain T 1–249（249 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 8.60 Å
5IY8 Human holo-PIC in the initial transcribing state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain T 1–249（249 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.90 Å
5IY9 Human holo-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric
Chain T 1–249（249 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 6.30 Å
5IYA Human core-PIC in the closed state Deposited 2016-03-24 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain T 1–249（249 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 5.40 Å
5IYB Human core-PIC in the open state Deposited 2016-03-24 Parsed fields agree Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain T 1–249（249 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
5IYD Human core-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different oligomeric state Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain T 1–249（249 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
6O9L Human holo-PIC in the closed state Deposited 2019-03-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 31 PDB declaration: 33-meric
Chain T 1–249（249 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
7EDX p53-bound TFIID-based core PIC on HDM2 promoter Deposited 2021-03-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 37 PDB declaration: 39-meric
Chain T 1–249（249 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7EG7 TFIID-based core PIC on SCP promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 37 PDB declaration: 39-meric
Chain T 1–249（249 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.20 Å
7EG8 TFIID-based core PIC on PUMA promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 37 PDB declaration: 39-meric
Chain T 1–249（249 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.40 Å
7EG9 TFIID-based intermediate PIC on SCP promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 39 PDB declaration: 41-meric
Chain T 1–249（249 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7EGA TFIID-based intermediate PIC on PUMA promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 39 PDB declaration: 41-meric
Chain T 1–249（249 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
7EGB TFIID-based holo PIC on SCP promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain T 1–249（249 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7EGC p53-bound TFIID-based holo PIC on HDM2 promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain T 1–249（249 aa）
Not recorded ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7ENA TFIID-based PIC-Mediator holo-complex in pre-assembled state (pre-hPIC-MED) Deposited 2021-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 74 PDB declaration: 76-meric
Chain FB 1–249（249 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.07 Å
7ENC TFIID-based PIC-Mediator holo-complex in fully-assembled state (hPIC-MED) Deposited 2021-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 74 PDB declaration: 76-meric
Chain FB 1–249（249 aa）
Not recorded ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.13 Å
7LBM Structure of the human Mediator-bound transcription pre-initiation complex Deposited 2021-01-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 54 PDB declaration: 56-meric
Chain T 1–249（249 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7NVR Human Mediator with RNA Polymerase II Pre-initiation complex Deposited 2021-03-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 56 PDB declaration: 58-meric
Chain R 1–249（249 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 18 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7NVS RNA polymerase II core pre-initiation complex with closed promoter DNA in proximal position Deposited 2021-03-16 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 R 1–249（249 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7NVT RNA polymerase II core pre-initiation complex with closed promoter DNA in distal position Deposited 2021-03-16 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 R 1–249（249 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7NVU RNA polymerase II core pre-initiation complex with open promoter DNA Deposited 2021-03-16 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 R 1–249（249 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
7NVY RNA polymerase II pre-initiation complex with closed promoter DNA in proximal position Deposited 2021-03-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain R 1–249（249 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 7.30 Å
7NVZ RNA polymerase II pre-initiation complex with closed promoter DNA in distal position Deposited 2021-03-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain R 1–249（249 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 7.20 Å
7NW0 RNA polymerase II pre-initiation complex with open promoter DNA Deposited 2021-03-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain R 1–249（249 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.60 Å
7ZWD Structure of SNAPc containing Pol II pre-initiation complex bound to U5 snRNA promoter (CC) Deposited 2022-05-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric
Chain R 1–249（249 aa）
Not recorded ZN ZINC ION × 11 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ZX7 Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter (CC) Deposited 2022-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric
Chain R 1–249（249 aa）
Not recorded ZN ZINC ION × 11 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7ZX8 Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter (OC) Deposited 2022-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric
Chain R 1–249（249 aa）
Not recorded ZN ZINC ION × 11 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8BVW RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W) Deposited 2022-12-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric
Chain R 1–249（249 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 4.00 Å
8BYQ RNA polymerase II pre-initiation complex with the proximal +1 nucleosome (PIC-Nuc10W) Deposited 2022-12-14 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 R 1–249（249 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 16 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8BZ1 RNA polymerase II core pre-initiation complex with the proximal +1 nucleosome (cPIC-Nuc10W) Deposited 2022-12-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain R 1–249（249 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8GXQ PIC-Mediator in complex with +1 nucleosome (T40N) in MH-binding state Deposited 2022-09-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric
Chain FB 1–249（249 aa）
Not recorded ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.04 Å
8GXS PIC-Mediator in complex with +1 nucleosome (T40N) in H-binding state Deposited 2022-09-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric
Chain FB 1–249（249 aa）
Not recorded ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.16 Å
8S51 RNA polymerase II core initially transcribing complex with an ordered RNA of 8 nt Deposited 2024-02-22 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 R 1–249（249 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8S52 RNA polymerase II core initially transcribing complex with an ordered RNA of 10 nt Deposited 2024-02-22 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 R 1–249（249 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8S54 RNA polymerase II early elongation complex bound to TFIIE and TFIIF - state b (composite structure) Deposited 2024-02-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: 18-meric
Chain R 1–249（249 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8S55 RNA polymerase II early elongation complex bound to TFIIE and TFIIF - state a (composite structure) Deposited 2024-02-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: 19-meric
Chain R 1–249（249 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8S5N RNA polymerase II core initially transcribing complex with an ordered RNA of 12 nt Deposited 2024-02-24 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 R 1–249（249 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8WAK Structure of transcribing complex 2 (TC2), the initially transcribing complex with Pol II positioned 2nt downstream of TSS. Deposited 2023-09-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain T 1–249（249 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.47 Å
8WAL Structure of transcribing complex 3 (TC3), the initially transcribing complex with Pol II positioned 3nt downstream of TSS. Deposited 2023-09-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain T 1–249（249 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.52 Å
8WAN Structure of transcribing complex 4 (TC4), the initially transcribing complex with Pol II positioned 4nt downstream of TSS. Deposited 2023-09-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain T 1–249（249 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.07 Å
8WAO Structure of transcribing complex 5 (TC5), the initially transcribing complex with Pol II positioned 5nt downstream of TSS. Deposited 2023-09-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain T 1–249（249 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å
8WAP Structure of transcribing complex 6 (TC6), the initially transcribing complex with Pol II positioned 6nt downstream of TSS. Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain T 1–249（249 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.85 Å
8WAQ Structure of transcribing complex 7 (TC7), the initially transcribing complex with Pol II positioned 7nt downstream of TSS. Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain T 1–249（249 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.29 Å
8WAR Structure of transcribing complex 8 (TC8), the initially transcribing complex with Pol II positioned 8nt downstream of TSS. Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain T 1–249（249 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
8WAS Structure of transcribing complex 9 (TC9), the initially transcribing complex with Pol II positioned 9nt downstream of TSS. Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain T 1–249（249 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.13 Å
8WAT De novo transcribing complex 10 (TC10), the early elongation complex with Pol II positioned 10nt downstream of TSS Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: octadecameric
Chain T 1–249（249 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.82 Å
8WAU De novo transcribing complex 11 (TC11), the early elongation complex with Pol II positioned 11nt downstream of TSS Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: octadecameric
Chain T 1–249（249 aa）
Not recorded W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.78 Å
8WAV De novo transcribing complex 12 (TC12), the early elongation complex with Pol II positioned 12nt downstream of TSS Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: octadecameric
Chain T 1–249（249 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
8WAW De novo transcribing complex 13 (TC13), the early elongation complex with Pol II positioned 13nt downstream of TSS Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: octadecameric
Chain T 1–249（249 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.02 Å
8WAX De novo transcribing complex 14 (TC14), the early elongation complex with Pol II positioned 14nt downstream of TSS Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: octadecameric
Chain T 1–249（249 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.75 Å
8WAY De novo transcribing complex 15 (TC15), the early elongation complex with Pol II positioned 15nt downstream of TSS Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: octadecameric
Chain T 1–249（249 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.85 Å
8WAZ De novo transcribing complex 16 (TC16), the early elongation complex with Pol II positioned 16nt downstream of TSS Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: octadecameric
Chain T 1–249（249 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.76 Å
8WB0 De novo transcribing complex 17 (TC17), the early elongation complex with Pol II positioned 17nt downstream of TSS Deposited 2023-09-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: octadecameric
Chain T 1–249（249 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.94 Å

57 other PDB entries and 60 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name T2FB_HUMAN
Isoform —
PDB entities 20
Chains and sequence ranges Author chain T； PDBConstruct 1–249； UniProt 1–249

Transcription elongation factor A protein 1

Homo sapiens

UniProt P23193

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 × 21 DNA 2 PDB declaration: 23-meric（23） Consistent with all polymer counts Chain U； UniProt 1–301 Not recorded DNA-directed RNA polymerase II subunit RPB1 × 1 （P24928） DNA-directed RNA polymerase II subunit RPB2 × 1 （P30876） DNA-directed RNA polymerase II subunit RPB3 × 1 （P19387） DNA-directed RNA polymerase II subunit RPB4 × 1 （O15514） DNA-directed RNA polymerase II subunit RPB5 × 1 （P19388） DNA-directed RNA polymerase II subunit RPB6 × 1 （P61218） DNA-directed RNA polymerase II subunit RPB7 × 1 （P62487） DNA-directed RNA polymerase II subunit RPB8 × 1 （P52434） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36954） DNA-directed RNA polymerase II subunit RPB10 × 1 （P62875） DNA-directed RNA polymerase II subunit RPB11-a × 1 （P52435） DNA-directed RNA polymerase II subunit RPB12 × 1 （P53803） Transcription initiation factor IIB × 1 （Q00403） Transcription initiation factor IIA subunit 1 × 1 （P52655） Transcription initiation factor IIA subunit 2 × 1 （P52657） TATA-box-binding protein × 1 （P20226） General transcription factor IIE subunit 1 × 1 （P29083） Transcription initiation factor IIE subunit beta × 1 （P29084） General transcription factor IIF subunit 1 × 1 （P35269） General transcription factor IIF subunit 2 × 1 （P13984） SCP-X × 1 SCP-Y × 1 MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV). Resolution 3.90 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 5IYC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1TFI A NOVEL ZN FINGER MOTIF IN THE BASAL TRANSCRIPTIONAL MACHINERY: THREE-DIMENSIONAL NMR STUDIES OF THE NUCLEIC-ACID BINDING DOMAIN OF TRANSCRIPTIONAL ELONGATION FACTOR TFIIS Deposited 1993-04-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 252–301（50 aa）
Not recorded ZN ZINC ION × 1 SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
3NDQ Structure of Human TFIIS Domain II Deposited 2010-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 131–232（102 aa） Fragment：TFIIS Domain II, residues 131-232
Not recorded NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；1.0 M Ammonium sulphate, 0.1 M 2-(N-morpholino)ethanesulfonic acid , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 1.93 Å R-free 0.208
5IY6 Human holo-PIC in the closed state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain U 1–301（301 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.20 Å
5IY7 Human holo-PIC in the open state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain U 1–301（301 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 8.60 Å
5IY8 Human holo-PIC in the initial transcribing state Deposited 2016-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain U 1–301（301 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.90 Å
5IYA Human core-PIC in the closed state Deposited 2016-03-24 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain U 1–301（301 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 5.40 Å
5IYB Human core-PIC in the open state Deposited 2016-03-24 Parsed fields agree Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain U 1–301（301 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
6O9L Human holo-PIC in the closed state Deposited 2019-03-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 31 PDB declaration: 33-meric
Chain U 1–301（301 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
6ZUY Human TFIIS N-terminal domain (TND) Deposited 2020-07-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–79（79 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 225；Pressure 1
NMR sample composition 0.5 mM [U-13C; U-15N] TFIIS, 25 mM deuterated TRIS, 200 mM sodium phospate, 1 mM TCEP, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
6ZV4 Human TFIIS N-terminal domain in complex with IWS1 Deposited 2020-07-23 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 1–77（77 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 225；Pressure 1
NMR sample composition 0.35 mM [U-13C; U-15N] TFIIS-IWS1, 25 mM [U-2H] TRIS, 200 mM sodium chloride, 1 mM TCEP, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
7CNF Solution strcture of HsTFIIS LW domain Deposited 2020-07-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–96（96 aa） Fragment：LW domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 175；Pressure 1
NMR sample composition 2.5 g/L [U-95% 13C] glucose, 0.5 g/L [U-15N] Ammonium Chloride, 25 mM NA sodium phosphate, 2 mM NA EDTA, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
7UNC Pol II-DSIF-SPT6-PAF1c-TFIIS complex with rewrapped nucleosome Deposited 2022-04-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 29 PDB declaration: 32-meric
Chain O 1–301（301 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 3.00 Å
7UND Pol II-DSIF-SPT6-PAF1c-TFIIS-nucleosome complex (stalled at +38) Deposited 2022-04-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain O 1–301（301 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8A40 Structure of mammalian Pol II-TFIIS elongation complex Deposited 2022-06-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric
Chain U 1–301（301 aa）
Not recorded ZN ZINC ION × 11 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8UIS Structure of transcription complex Pol II-DSIF-NELF-TFIIS Deposited 2023-10-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: nonadecameric
Chain S 1–301（301 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 3.23 Å
9EGX RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-hexasome, bp +27 Deposited 2024-11-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 29 PDB declaration: 32-meric
Chain S 1–301（301 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9EGY RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-nucleosome, bp +27 Deposited 2024-11-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain S 1–301（301 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9EGZ RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, bp +27 Deposited 2024-11-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain S 1–301（301 aa）
Not recorded ZN ZINC ION × 12 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9EH0 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 30 bp upstream Deposited 2024-11-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain S 1–301（301 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9EH1 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 20 bp upstream Deposited 2024-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain S 132–301（170 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9EH2 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-FACT nucleosome upstream Deposited 2024-11-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain S 1–301（301 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9J0N Paused elongation complex of mammalian RNA polymerase II with nucleosome (PEC2-nuc) Deposited 2024-08-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 27 PDB declaration: 30-meric
Chain M 1–301（301 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9MLC Pol II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome activated elongation complex Composite map T Deposited 2024-12-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 24 PDB declaration: 27-meric
Chain S 1–301（301 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
9S0U State 3 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to distal upstream H3 Deposited 2025-07-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain S 1–301（301 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.72 Å
9S3G State 1 MAP3 RNA Pol II activated elongation complex with SETD2 and upstream hexasome Deposited 2025-07-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain S 1–301（301 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å

25 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TCEA1_HUMAN
Isoform —
PDB entities 21
Chains and sequence ranges Author chain U； PDBConstruct 1–301； UniProt 1–301

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 5iyc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5iyc
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5iyc
Deposition date deposition_date2016-03-24
Structure title titleHuman core-PIC in the initial transcribing state
Keywords keywordsinitiation, RNA polymerase II, human, TRANSCRIPTION, TRANSFERASE-DNA complex; TRANSCRIPTION, TRANSFERASE/DNA
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier60.35 Å
Radius of gyration Rg (electron density) rg_electron59.95 Å
Forward intensity I(0) i07341630000.00
Molecular weight molecular_weight686140.0 kDa
Excluded volume excluded_volume843560 ų
Envelope volume envelope_volume1276200 ų
Hydration-shell volume shell_volume167700 ų
Envelope diameter envelope_diameter202.5 Å
Shell Rg shell_rg67.89 Å
Envelope Rg envelope_rg59.68 Å
Shape Rg shape_rg59.98 Å
Total Rg total_rg59.98 Å
Total atoms total_atoms47927
Residues n_residues5737
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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax196.1 Å
Rg (real space) rg_real60.09 Å
Rg uncertainty (real space) rg_real_error1.67 Å
I(0) (real space) i0_real7.3420e+09
I(0) uncertainty (real space) i0_real_error1.4000e+08
Rg (reciprocal space) rg_reciprocal60.56 Å
I(0) (reciprocal space) i0_reciprocal7347000000.0000
Solution quality estimate total_estimate0.8684
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary75.4 Å
Skewness Skewness skewness0.229
Kurtosis Kurtosis kurtosis-0.371
Angular range angular_range— – 0.1300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1123000000.0000
Real-space data points n_real_points27
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.865; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.946; Smooth: 0.750
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (25)

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7. Fold Classification (SCOP + CATH) 23 domains

CATH v4.4 (23 domains)

Domain ID domain_id5iycA01
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_id5iycA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily140 —
Domain ID domain_id5iycB01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1110 — Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3
Homologous superfamily homologous superfamily10 — RNA polymerase Rpb2, domain 2
Domain ID domain_id5iycB02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1800 — DCoH-like
Homologous superfamily homologous superfamily10 — RNA polymerase alpha subunit dimerisation domain
Domain ID domain_id5iycC01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily10 — RNA polymerase, RBP11-like subunit
Domain ID domain_id5iycC02
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology120 — RNA Polymerase Alpha Subunit; Chain A, domain 2
Homologous superfamily homologous superfamily12 — DNA-directed RNA polymerase, insert domain
Domain ID domain_id5iycD00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily40 — RNA Polymerase II, Rpb4 subunit
Domain ID domain_id5iycE01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1340 — Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1
Homologous superfamily homologous superfamily10 — RNA polymerase, Rpb5, N-terminal domain
Domain ID domain_id5iycE02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology940 — Eukaryotic RPB6 RNA polymerase subunit
Homologous superfamily homologous superfamily20 — RPB5-like RNA polymerase subunit
Domain ID domain_id5iycF00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology940 — Eukaryotic RPB6 RNA polymerase subunit
Homologous superfamily homologous superfamily10 — RNA polymerase subunit, RPB6/omega
Domain ID domain_id5iycG01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily120 — RNA polymerase Rpb7-like, N-terminal domain
Domain ID domain_id5iycG02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily140 — Nucleic acid-binding proteins
Domain ID domain_id5iycH01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily140 — Nucleic acid-binding proteins
Domain ID domain_id5iycI02
Class class2 — Mainly Beta
Architecture architecture20 — Single Sheet
Topology topology25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily10 —
Domain ID domain_id5iycJ00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily60 — Homeodomain-like
Domain ID domain_id5iycK00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily10 — RNA polymerase, RBP11-like subunit
Domain ID domain_id5iycL00
Class class2 — Mainly Beta
Architecture architecture20 — Single Sheet
Topology topology28 — Rubrerythrin, domain 2
Homologous superfamily homologous superfamily30 — RNA polymerase ii, chain L
Domain ID domain_id5iycM01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily10 — Cyclin-like
Domain ID domain_id5iycM02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily10 — Cyclin-like
Domain ID domain_id5iycO01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily190 — Transcription factor IIA gamma subunit, alpha-helical domain
Domain ID domain_id5iycO02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology18 — TATA box binding Protein, subunit D; domain 2
Homologous superfamily homologous superfamily10 — Transcription factor IIA (TFIIA), beta-barrel domain
Domain ID domain_id5iycP01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology310 — TATA-Binding Protein
Homologous superfamily homologous superfamily10 — TATA-Binding Protein
Domain ID domain_id5iycP02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology310 — TATA-Binding Protein
Homologous superfamily homologous superfamily10 — TATA-Binding Protein
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8. Citations (1)

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9. Files and Curves (10)