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1pfj

Solution structure of the N-terminal PH/PTB domain of the TFIIH P62 subunit

Method: SOLUTION NMR Dmax: 51.9 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

TFIIH basal transcription factor complex p62 subunit

Homo sapiens

UniProt P32780

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–108 Fragment：N-terminal PH/PTB domain No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7.4；293 K；Ionic strength (raw mmCIF value) 20mM；Pressure ambient NMR measurement conditions：pH 7.4；293 K；Ionic strength (raw mmCIF value) 20mM；Pressure ambient NMR measurement conditions：pH 7.4；298 K；Ionic strength (raw mmCIF value) 20mM；Pressure ambient NMR measurement conditions：pH 7.4；293 K；Ionic strength (raw mmCIF value) 20mM；Pressure ambient NMR sample composition：1.5mM P62 U-15N,13C; 20mM deuterated TRIS; 90% H2O, 10% D2O | 90% H2O/10% D2O NMR sample composition：1.2mM P62 U-15N; 20mM deuterated TRIS; 90% H2O, 10% D2O | 90% H2O/10% D2O NMR sample composition：0.9mM P62 U-15N; 20mM deuterated TRIS + 26ug C12E6/hexanol; 90% H2O, 10% D2O | 90% H2O, 10% D2O; 26 ug C12E6/hexanol NMR sample composition：1.5mM P62; 20mM deuterated TRIS; 90% H2O, 10% D2O | 90% H2O/10% D2O Resolution not provided

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 1PFJ 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain C 1–548（548 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain C 1–548（548 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain C 1–548（548 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain C 1–548（548 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
2DII Solution structure of the BSD domain of human TFIIH basal transcription factor complex p62 subunit Deposited 2006-03-30 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 103–150（48 aa） Fragment：BSD domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 120；Pressure ambient
NMR sample composition 1.07mM BSD domain U-15N,13C; 20mM d-Tris HCl (pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O | 90% H2O/10% 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 experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–108（108 aa） Fragment：PH domain, UNP residues 1-108
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
2RUK Solution structure of the complex between p53 transactivation domain 2 and TFIIH p62 PH domain Deposited 2014-09-24 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–108（108 aa） Fragment：TFIIH p62 PH domain, UNP residues 1-108
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；305 K；Ionic strength (raw mmCIF value) 0.02；Pressure ambient
NMR sample composition 0.4 mM [U-99% 13C; U-99% 15N] TFIIH p62 PH domain-1, 0.48 mM p53 TAD2-2, 20 mM potassium phosphate-3, 5 mM [U-2H] DTT-4, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.4 mM [U-99% 13C; U-99% 15N] TFIIH p62 PH domain-5, 0.48 mM p53 TAD2-6, 20 mM potassium phosphate-7, 5 mM [U-2H] DTT-8, 100% D2O | 100% D2O
Resolution not provided
2RVB Solution structure of the complex between XPC acidic domain and TFIIH p62 PH domain Deposited 2015-07-01 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–108（108 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；305 K；Ionic strength (raw mmCIF value) 0.02；Pressure ambient
NMR sample composition 0.4 mM [U-99% 13C; U-99% 15N] XPC acidic domain-1, 0.48 mM TFIIH p62 PH domain-2, 20 mM potassium phosphate-3, 5 mM [U-2H] DTT-4, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.4 mM [U-99% 13C; U-99% 15N] XPC acidic domain-5, 0.48 mM TFIIH p62 PH domain-6, 20 mM potassium phosphate-7, 5 mM [U-2H] DTT-8, 100% D2O | 100% D2O
NMR sample composition 0.4 mM [U-99% 13C; U-99% 15N] TFIIH p62 PH domain-9, 0.48 mM XPC acidic domain-10, 20 mM potassium phosphate-11, 5 mM [U-2H] DTT-12, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.4 mM [U-99% 13C; U-99% 15N] TFIIH p62 PH domain-13, 0.48 mM XPC acidic domain-14, 20 mM potassium phosphate-15, 5 mM [U-2H] DTT-16, 100% D2O | 100% D2O
Resolution not provided
5GOW Solution structure of the complex between DP1 acidic region and TFIIH p62 PH domain Deposited 2016-07-29 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–108（108 aa） Fragment：UNP residues 1-108
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；305 K；Ionic strength (raw mmCIF value) 0.02；Pressure 760
NMR sample composition 0.35 mM [U-99% 13C; U-99% 15N] DP1, 0.42 mM TFIIH p62, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.35 mM [U-99% 13C; U-99% 15N] DP1, 0.42 mM TFIIH p62, 100% D2O | 100% D2O
NMR sample composition 0.35 mM [U-99% 13C; U-99% 15N] TFIIH p62, 0.42 mM DP1, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.35 mM [U-99% 13C; U-99% 15N] TFIIH p62, 0.42 mM DP1, 100% D2O | 100% D2O
Resolution not provided
5XV8 Solution structure of the complex between UVSSA acidic region and TFIIH p62 PH domain Deposited 2017-06-27 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–108（107 aa） Fragment：UNP residues 2-108
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；305 K；Ionic strength (raw mmCIF value) 20；Pressure 760
NMR sample composition 0.40 mM [U-99% 13C; U-99% 15N] UVSSA, 0.48 mM TFIIH p62, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.40 mM [U-99% 13C; U-99% 15N] UVSSA, 0.48 mM TFIIH p62, 100% D2O | 100% D2O
NMR sample composition 0.40 mM [U-99% 13C; U-99% 15N] TFIIH p62, 0.48 mM UVSSA, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.40 mM [U-99% 13C; U-99% 15N] TFIIH p62, 0.48 mM UVSSA, 100% D2O | 100% D2O
Resolution not provided
6O9L Human holo-PIC in the closed state Deposited 2019-03-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 31 PDB declaration: 33-meric
Chain 1 1–548（548 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain 1 1–548（548 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7AD8 Core TFIIH-XPA-DNA complex with modelled p62 subunit Deposited 2020-09-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain I 1–548（548 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
7BUL Solution structure of the tandem PH and BSD1 domains of TFIIH p62 Deposited 2020-04-07 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–158（158 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；293 K；Ionic strength (raw mmCIF value) 20；Pressure 1
NMR sample composition 1.2 mM [U-99% 13C; U-99% 15N] TFIIH p62, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.9 mM [U-99% 13C; U-99% 15N] TFIIH p62, 100% D2O | 100% D2O
Resolution not provided
7EGB TFIID-based holo PIC on SCP promoter Deposited 2021-03-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain 1 1–548（548 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain 1 1–548（548 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 74 PDB declaration: 76-meric
Chain 1 1–548（548 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 74 PDB declaration: 76-meric
Chain 1 1–548（548 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 54 PDB declaration: 56-meric
Chain Y 1–548（548 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 56 PDB declaration: 58-meric
Chain 1 1–548（548 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain 1 1–548（548 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain 1 1–548（548 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain 1 1–548（548 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain 1 1–548（548 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain 1 1–548（548 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric
Chain 2 1–548（548 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric
Chain 2 1–548（548 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–548（548 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 111–548（438 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–548（548 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–548（548 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–548（548 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–548（548 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–548（548 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric
Chain HB 1–548（548 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric
Chain HB 1–548（548 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain 1 1–548（548 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain 1 1–548（548 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain 1 1–548（548 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain 1 1–548（548 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain 1 1–548（548 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain 1 1–548（548 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain 1 1–548（548 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain 1 1–548（548 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric
Chain C 1–548（548 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric
Chain C 1–548（548 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain C 1–548（548 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain C 1–548（548 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain C 1–548（548 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 49 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TF2H1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–108； UniProt 1–108

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 1pfj

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1pfj
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1pfj
Deposition date deposition_date2003-05-27
Structure title titleSolution structure of the N-terminal PH/PTB domain of the TFIIH P62 subunit
Keywords keywordsPH/PTB domain, Structural Proteomics in Europe, SPINE, Structural Genomics, TRANSCRIPTION; TRANSCRIPTION
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier14.43 Å
Radius of gyration Rg (electron density) rg_electron13.77 Å
Forward intensity I(0) i0727102000.00
Molecular weight molecular_weight233520.0 kDa
Excluded volume excluded_volume295220 ų
Envelope volume envelope_volume32233 ų
Hydration-shell volume shell_volume16022 ų
Envelope diameter envelope_diameter56.0 Å
Shell Rg shell_rg23.21 Å
Envelope Rg envelope_rg17.68 Å
Shape Rg shape_rg13.70 Å
Total Rg total_rg14.22 Å
Total atoms total_atoms33497
Residues n_residues2052
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 dmax51.9 Å
Rg (real space) rg_real14.39 Å
Rg uncertainty (real space) rg_real_error0.42 Å
I(0) (real space) i0_real7.2710e+08
I(0) uncertainty (real space) i0_real_error9.4560e+06
Rg (reciprocal space) rg_reciprocal14.39 Å
I(0) (reciprocal space) i0_reciprocal727100000.0000
Solution quality estimate total_estimate0.7295
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary17.7 Å
Skewness Skewness skewness0.259
Kurtosis Kurtosis kurtosis-0.175
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha222000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.675; Stabil: 1.000; Sysdev: 0.499; Positv: 1.000; Valcen: 0.958; Smooth: 0.998
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1pfja_
Class classb — All beta proteins
Fold Fold foldb.55 — PH domain-like barrel
Superfamily Superfamily superfamilyb.55.1 — PH domain-like
Family Family familyb.55.1.9 — TFIIH domain

CATH v4.4 (1 domains)

Domain ID domain_id1pfjA00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
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8. Citations (1)

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9. Files and Curves (10)