TFIIH basal transcription factor complex helicase XPD subunit
Homo sapiens
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 × 30 DNA 2 PDB declaration: 32-meric（32） Consistent with all polymer counts | Chain 0； UniProt 1–760 | Not recorded | General transcription factor IIH subunit 1 × 1 （P32780） General transcription factor IIH subunit 4 × 1 （Q92759） CDK-activating kinase assembly factor MAT1 × 1 （P51948） General transcription factor IIH subunit 3 × 1 （Q13889） General transcription factor IIH subunit 5 × 1 （Q6ZYL4） General transcription factor IIH subunit 2 × 1 （Q13888） General transcription and DNA repair factor IIH helicase subunit XPB × 1 （P19447） RPB1 × 1 DNA-directed RNA polymerase subunit beta × 1 （I3LGP4） DNA-directed RNA polymerase II subunit RPB3 × 1 （I3LCH3） RPOL4c domain-containing protein × 1 （A0A287ADR4） DNA-directed RNA polymerase II subunit E × 1 （I3LSI7） DNA-directed RNA polymerase II subunit F × 1 （F1SKN8） DNA-directed RNA polymerase II subunit RPB7 × 1 （I3LJZ9） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （A0A4X1ULF2） DNA-directed RNA polymerase II subunit RPB9 × 1 （P60899） DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 （A0A4X1VYD0） RNA_pol_L_2 domain-containing protein × 1 （A0A4X1UK25） RNA polymerase II subunit K × 1 （I3LN51） Transcription initiation factor IIB × 1 （Q00403） Non-template DNA × 1 TATA-box-binding protein × 1 （P20226） General transcription factor IIF subunit 1 × 1 （P35269） General transcription factor IIF subunit 2 × 1 （P13984） Template DNA × 1 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） Unassigned peptide, likely TFIIE-beta × 1 Unassigned peptide, likely XPB × 1 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 |
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 7NVZ | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 28JM Cryo-EM structure of the human holo-TFIIH and XPC initial encounter complex Deposited 2026-02-03 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain B
1–760（760 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；Leica EM GP2
|
Resolution 3.29 Å |
| 28JS Cryo-EM structure of the human holo-TFIIH-XPC complex bound to bulky lesion-mimic DNA (composite map) Deposited 2026-02-03 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric |
Chain B
1–760（760 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 5 CA CALCIUM ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；Leica EM GP2
|
Resolution 3.32 Å |
| 28JV Cryo-EM structure of the human holo-TFIIH-XPC complex bound to bulky lesion-mimic DNA (consensus map) Deposited 2026-02-04 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric |
Chain B
1–760（760 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 5 CA CALCIUM ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；Leica EM GP2
|
Resolution 3.91 Å |
| 28KE Cryo-EM structure of the human holo-TFIIH-XPC-XPA complex bound to bulky lesion-mimic DNA Deposited 2026-02-04 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric |
Chain B
1–760（760 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；Leica EM GP2
|
Resolution 3.60 Å |
| 5IVW Human core TFIIH bound to DNA within the PIC Deposited 2016-03-21 | 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
1–760（760 aa）
|
Not recorded | No recorded non-water small molecule |
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 10.00 Å |
| 5IY6 Human holo-PIC in the closed state Deposited 2016-03-24 | Different oligomeric state Different ligand/ion Different experimental conditions | Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric |
Chain W
1–760（760 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 ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric |
Chain W
1–760（760 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 ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric |
Chain W
1–760（760 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 experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric |
Chain W
1–760（760 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 |
| 5OF4 The cryo-EM structure of human TFIIH Deposited 2017-07-10 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric |
Chain B
1–760（760 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE；3-4 minute incubation, 2 second blot
|
Resolution 4.40 Å |
| 6O9L Human holo-PIC in the closed state Deposited 2019-03-14 | Different oligomeric state Different ligand/ion Different experimental conditions | Assembly 1 Protein–DNA Heteromer；Protein × 31 PDB declaration: 33-meric |
Chain 0
1–760（760 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 |
| 6O9M Structure of the human apo TFIIH Deposited 2019-03-14 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain 0
1–760（760 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 6 |
ELECTRON MICROSCOPY
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.40 Å |
| 6RO4 Structure of the core TFIIH-XPA-DNA complex Deposited 2019-05-10 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric |
Chain B
1–760（760 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；4 ul of sample was applied to glow-discharged grids which were blotted for 5s and plunge-frozen in liquid ethane.
|
Resolution 3.50 Å |
| 6TUN Helicase domain complex Deposited 2020-01-07 | 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
245–439（195 aa）
|
Not recorded | CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；100 mM Tris pH 8.5
25% PEG8000
|
Resolution 2.07 Å R-free 0.227 |
| 6TUN Helicase domain complex Deposited 2020-01-07 | 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 B
245–439（195 aa）
|
Not recorded | CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；100 mM Tris pH 8.5
25% PEG8000
|
Resolution 2.07 Å R-free 0.227 |
| 7AD8 Core TFIIH-XPA-DNA complex with modelled p62 subunit Deposited 2020-09-14 | Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain B
1–760（760 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7EGB TFIID-based holo PIC on SCP promoter Deposited 2021-03-24 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric |
Chain 7
1–760（760 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 Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric |
Chain 7
1–760（760 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 7
1–760（760 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 7
1–760（760 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 X
1–760（760 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 structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 56 PDB declaration: 58-meric |
Chain 0
1–760（760 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 |
| 7NVW TFIIH in a pre-translocated state (without ADP-BeF3) Deposited 2021-03-16 | Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain 0
1–760（760 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 structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain 0
1–760（760 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 structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 30 PDB declaration: 32-meric |
Chain 0
1–760（760 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 |
| 7NW0 RNA polymerase II pre-initiation complex with open promoter DNA Deposited 2021-03-16 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 30 PDB declaration: 32-meric |
Chain 0
1–760（760 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 mutation/modification Different oligomeric state Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric |
Chain 1
1–760（760 aa）
|
Mutation：0 | 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 structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric |
Chain 1
1–760（760 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 |
| 8EBS Initial DNA-lesion (Cy5) binding by XPC and TFIIH Deposited 2022-08-31 | 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
1–760（760 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 5 CA CALCIUM ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 8EBT XPA repositioning Core7 of TFIIH relative to XPC-DNA lesion (Cy5) Deposited 2022-08-31 | 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 B
1–730（730 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 6 CA CALCIUM ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 8EBU XPC release from Core7-XPA-DNA (Cy5) Deposited 2022-08-31 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain B
1–760（760 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8EBV Initial DNA-lesion (AP) binding by XPC and TFIIH complex 1 Deposited 2022-08-31 | 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
1–760（760 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 5 CA CALCIUM ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.10 Å |
| 8EBW Initial DNA-lesion (AP) binding by XPC and TFIIH complex2 Deposited 2022-08-31 | 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
1–760（760 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 5 CA CALCIUM ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.60 Å |
| 8EBX XPA repositioning Core7 of TFIIH relative to XPC-DNA lesion (AP) Deposited 2022-08-31 | 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
1–760（760 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 6 CA CALCIUM ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 8EBY XPC release from Core7-XPA-DNA (AP) Deposited 2022-08-31 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain B
1–760（760 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 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 HA
1–760（760 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 HA
1–760（760 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 |
| 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 7
1–760（760 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 7
1–760（760 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 7
1–760（760 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 7
1–760（760 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 7
1–760（760 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 7
1–760（760 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 | Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric |
Chain 7
1–760（760 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 7
1–760（760 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 |
| 9PCP NER dual incision complex - NoG Deposited 2025-06-28 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric |
Chain B
1–760（760 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 6 CA CALCIUM ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å |
| 9PD3 NER dual incision complex - DuIS Deposited 2025-06-30 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric |
Chain B
1–760（760 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 9PD4 NER dual incision complex - DuIM Deposited 2025-06-30 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric |
Chain B
1–760（760 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 9PD5 NER dual incision complex - NoF Deposited 2025-06-30 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric |
Chain B
1–760（760 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.70 Å |
| 9XYU NER complex - C7CAD.ATP Deposited 2025-08-26 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric |
Chain B
1–760（760 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
49 other PDB entries and 50 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | ERCC2_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain 0； PDBConstruct 1–760； UniProt 1–760 |
