+
Open data
-
Basic information
Entry | Database: PDB / ID: 6o9m | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the human apo TFIIH | ||||||
![]() |
| ||||||
![]() | TRANSCRIPTION / Transcription initiation / Molecular dynamics / Gene regulation / Community network analysis / Global protein dynamics / RNA polymerase | ||||||
Function / homology | ![]() MMXD complex / core TFIIH complex portion of holo TFIIH complex / Cytosolic iron-sulfur cluster assembly / central nervous system myelin formation / positive regulation of mitotic recombination / hair cell differentiation / hair follicle maturation / ventricular system development / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly ...MMXD complex / core TFIIH complex portion of holo TFIIH complex / Cytosolic iron-sulfur cluster assembly / central nervous system myelin formation / positive regulation of mitotic recombination / hair cell differentiation / hair follicle maturation / ventricular system development / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / CAK-ERCC2 complex / transcription factor TFIIK complex / UV protection / embryonic cleavage / adult heart development / DNA 5'-3' helicase / G protein-coupled receptor internalization / regulation of cyclin-dependent protein serine/threonine kinase activity / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / nuclear thyroid hormone receptor binding / RNA Polymerase I Transcription Termination / transcription preinitiation complex / regulation of mitotic cell cycle phase transition / DNA 3'-5' helicase / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / 3'-5' DNA helicase activity / spinal cord development / erythrocyte maturation / hematopoietic stem cell proliferation / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / bone mineralization / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / mRNA Capping / ATPase activator activity / regulation of G1/S transition of mitotic cell cycle / DNA topological change / intrinsic apoptotic signaling pathway by p53 class mediator / RNA Polymerase I Transcription Initiation / hematopoietic stem cell differentiation / embryonic organ development / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / transcription by RNA polymerase I / transcription elongation by RNA polymerase I / Formation of HIV elongation complex in the absence of HIV Tat / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / transcription-coupled nucleotide-excision repair / response to UV / Cyclin A:Cdk2-associated events at S phase entry / cyclin-dependent protein kinase holoenzyme complex / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / isomerase activity / hormone-mediated signaling pathway / RNA Polymerase II Pre-transcription Events / extracellular matrix organization / DNA helicase activity / insulin-like growth factor receptor signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / post-embryonic development / determination of adult lifespan / nucleotide-excision repair / positive regulation of smooth muscle cell proliferation / chromosome segregation / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase I Promoter Escape / transcription elongation by RNA polymerase II / promoter-specific chromatin binding / G1/S transition of mitotic cell cycle / cellular response to gamma radiation / NoRC negatively regulates rRNA expression / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / spindle / multicellular organism growth / Formation of Incision Complex in GG-NER / response to calcium ion / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Cyclin D associated events in G1 / intracellular protein localization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / 4 iron, 4 sulfur cluster binding / single-stranded 3'-5' DNA helicase activity / double-stranded DNA helicase activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å | ||||||
![]() | Yan, C.L. / Dodd, T. / He, Y. / Tainer, J.A. / Tsutakawa, S.E. / Ivanov, I. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: The cryo-electron microscopy structure of human transcription factor IIH. Authors: Basil J Greber / Thi Hoang Duong Nguyen / Jie Fang / Pavel V Afonine / Paul D Adams / Eva Nogales / ![]() Abstract: Human transcription factor IIH (TFIIH) is part of the general transcriptional machinery required by RNA polymerase II for the initiation of eukaryotic gene transcription. Composed of ten subunits ...Human transcription factor IIH (TFIIH) is part of the general transcriptional machinery required by RNA polymerase II for the initiation of eukaryotic gene transcription. Composed of ten subunits that add up to a molecular mass of about 500 kDa, TFIIH is also essential for nucleotide excision repair. The seven-subunit TFIIH core complex formed by XPB, XPD, p62, p52, p44, p34, and p8 is competent for DNA repair, while the CDK-activating kinase subcomplex, which includes the kinase activity of CDK7 as well as the cyclin H and MAT1 subunits, is additionally required for transcription initiation. Mutations in the TFIIH subunits XPB, XPD, and p8 lead to severe premature ageing and cancer propensity in the genetic diseases xeroderma pigmentosum, Cockayne syndrome, and trichothiodystrophy, highlighting the importance of TFIIH for cellular physiology. Here we present the cryo-electron microscopy structure of human TFIIH at 4.4 Å resolution. The structure reveals the molecular architecture of the TFIIH core complex, the detailed structures of its constituent XPB and XPD ATPases, and how the core and kinase subcomplexes of TFIIH are connected. Additionally, our structure provides insight into the conformational dynamics of TFIIH and the regulation of its activity. | ||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 574.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 442.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 103.9 KB | Display | |
Data in CIF | ![]() | 153.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3802M ![]() 6o9lC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
-TFIIH basal transcription factor complex helicase ... , 2 types, 2 molecules 07
#1: Protein | Mass: 87021.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|---|
#8: Protein | Mass: 89404.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-General transcription factor IIH subunit ... , 5 types, 5 molecules 12456
#2: Protein | Mass: 62116.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|---|
#3: Protein | Mass: 52245.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#5: Protein | Mass: 34416.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#6: Protein | Mass: 8060.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#7: Protein | Mass: 44481.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein , 1 types, 1 molecules 3
#4: Protein | Mass: 35873.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|
-Non-polymers , 2 types, 7 molecules 


#9: Chemical | ChemComp-SF4 / |
---|---|
#10: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: apo TFIIH / Type: COMPLEX / Entity ID: #1-#8 / Source: NATURAL |
---|---|
Source (natural) | Organism: ![]() |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: C-flat |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-
Electron microscopy imaging
Microscopy | Model: FEI TITAN |
---|---|
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-
Processing
EM software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: NONE | |||||||||||||||||||||||||
3D reconstruction | Resolution: 4.4 Å / Num. of particles: 122900 / Symmetry type: POINT | |||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL Details: Initial model assembled from high-resolution structures and homology models, subsequently rebuilt in COOT, refined into the Cryo-EM map using Phenix and fully validated. |