7dti

Solution structure of the complex between RNA polymerase subunit RPB6 and TFIIH p62 PH domain

Method: SOLUTION NMR D_max: 97.1 Å Quality: GOOD

▼

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

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

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–127	Not recorded	General transcription factor IIH subunit 1 × 1 （A0A2K6V299）	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

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 7DTI	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 ligand/ion Different experimental method Different experimental conditions 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 ligand/ion Different experimental method Different experimental conditions 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 ligand/ion Different experimental method Different experimental conditions 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 experimental method Different experimental conditions 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 3.90 Å
5IYC Human core-PIC in the initial transcribing state Deposited 2016-03-24	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 3.90 Å
5IYD Human core-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24	Different oligomeric state Different ligand/ion Different experimental method 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	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 method 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	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 method 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 method 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 method 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 method 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 method 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 method 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 experimental method 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 method 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 method 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 method 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 experimental conditions	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
7DU2 RNA polymerase III EC complex in post-translocation state Deposited 2021-01-07	Different oligomeric state Different ligand/ion Different experimental method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 experimental method 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 method 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 × 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–130； UniProt 1–127

General transcription factor IIH subunit 1

Homo sapiens

UniProt A0A2K6V299

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 8–115	Not recorded	DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （P61218）	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

Other States of the Same Protein in the Database

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	A0A2K6V299_SAIBB
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–111； UniProt 8–115

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	7dti
Deposition date deposition_date	2021-01-05
Structure title title	Solution structure of the complex between RNA polymerase subunit RPB6 and TFIIH p62 PH domain
Keywords keywords	RNA polymerase, general transcription factor, NUCLEAR PROTEIN; NUCLEAR PROTEIN
Experimental Method method	SOLUTION NMR

▼

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

Radius of gyration Rg (Guinier) rg_guinier	29.24 Å
Radius of gyration Rg (electron density) rg_electron	29.14 Å
Forward intensity I(0) i0	4139070000.00
Molecular weight molecular_weight	534970.0 kDa
Excluded volume excluded_volume	666490 Å³
Envelope volume envelope_volume	270460 Å³
Hydration-shell volume shell_volume	59310 Å³
Envelope diameter envelope_diameter	110.6 Å
Shell Rg shell_rg	44.36 Å
Envelope Rg envelope_rg	37.13 Å
Shape Rg shape_rg	29.06 Å
Total Rg total_rg	29.73 Å
Total atoms total_atoms	74840
Residues n_residues	4700
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

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

Maximum dimension Dmax dmax	97.1 Å
Rg (real space) rg_real	29.34 Å
Rg uncertainty (real space) rg_real_error	1.11 Å
I(0) (real space) i0_real	4.1390e+09
I(0) uncertainty (real space) i0_real_error	6.8780e+07
Rg (reciprocal space) rg_reciprocal	29.30 Å
I(0) (reciprocal space) i0_reciprocal	4139000000.0000
Solution quality estimate total_estimate	0.8122
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	21.6 Å
Skewness Skewness skewness	0.249
Kurtosis Kurtosis kurtosis	-0.696
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3251000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.791; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.761; Smooth: 0.422

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	DNA-directed RNA polymerases I, II, and III subunit RPABC2
Molecular weight formula_weight	14773.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	74840

GSHMSDNEDNFDGDDFDDVEEDEGLDDLENAEEEGQENVEILPSGERPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVDELIITD

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	General transcription factor IIH subunit 1
Molecular weight formula_weight	12588.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GSHMATSSEEVLLIVKKVRQKKQDGALYLMAERIAWAPEGKDRFTISHMYADIKCQKISPEGKAKIQLQLVLHAGDTTNFHFSNESTAVKERDAVKDLLQQLLPKFKRKAN

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

▶

8. Citations (1)

▶

fit	/app/data/saxs_computation/dt/7dti/7dti.fit
pddf	/app/data/pr_computation/dt/7dti/7dti.pr.out
profile	/app/data/saxs_computation/dt/7dti/7dti.dat

Solution structure of the complex between RNA polymerase subunit RPB6 and TFIIH p62 PH domain

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

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

State in the Current Structure

Other States of the Same Protein in the Database

General transcription factor IIH subunit 1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)