+Open data
-Basic information
Entry | Database: PDB / ID: 5of4 | |||||||||
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Title | The cryo-EM structure of human TFIIH | |||||||||
Components |
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Keywords | TRANSCRIPTION / transcription initiation / DNA repair / multiprotein complex / kinase / helicase | |||||||||
Function / homology | Function and homology information MMXD complex / core TFIIH complex portion of holo TFIIH complex / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / central nervous system myelin formation / positive regulation of mitotic recombination / hair follicle maturation / hair cell differentiation / 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 / nucleotide-excision repair, DNA duplex unwinding / central nervous system myelin formation / positive regulation of mitotic recombination / hair follicle maturation / hair cell differentiation / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / CAK-ERCC2 complex / UV protection / embryonic cleavage / DNA 5'-3' helicase / G protein-coupled receptor internalization / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / DNA 3'-5' helicase / transcription preinitiation complex / RNA Polymerase I Transcription Termination / regulation of mitotic cell cycle phase transition / hematopoietic stem cell proliferation / 3'-5' DNA helicase activity / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / transcription factor TFIID complex / bone mineralization / RNA polymerase II general transcription initiation factor activity / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / spinal cord development / 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 / erythrocyte maturation / RNA Polymerase I Transcription Initiation / ATPase activator activity / DNA topological change / intrinsic apoptotic signaling pathway by p53 class mediator / hematopoietic stem cell differentiation / Tat-mediated elongation of the HIV-1 transcript / transcription elongation by RNA polymerase I / transcription-coupled nucleotide-excision repair / embryonic organ development / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / response to UV / RNA Polymerase II Pre-transcription Events / DNA helicase activity / post-embryonic development / extracellular matrix organization / insulin-like growth factor receptor signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / determination of adult lifespan / isomerase activity / chromosome segregation / nucleotide-excision repair / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / promoter-specific chromatin binding / RNA Polymerase I Promoter Escape / transcription elongation by RNA polymerase II / NoRC negatively regulates rRNA expression / multicellular organism growth / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / cellular response to gamma radiation / Dual Incision in GG-NER / spindle / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / protein localization / 4 iron, 4 sulfur cluster binding / protein-macromolecule adaptor activity / 5'-3' DNA helicase activity / double-stranded DNA binding / in utero embryonic development / response to oxidative stress / transcription by RNA polymerase II / damaged DNA binding / response to hypoxia / nuclear speck / positive regulation of apoptotic process / DNA repair / regulation of DNA-templated transcription / nucleolus / regulation of transcription by RNA polymerase II / apoptotic process / ATP hydrolysis activity / DNA binding / zinc ion binding / nucleoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å | |||||||||
Authors | Greber, B.J. / Nguyen, T.H.D. / Fang, J. / Afonine, P.V. / Adams, P.D. / Nogales, E. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nature / Year: 2017 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5of4.cif.gz | 458.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5of4.ent.gz | 356.8 KB | Display | PDB format |
PDBx/mmJSON format | 5of4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5of4_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 5of4_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5of4_validation.xml.gz | 67.3 KB | Display | |
Data in CIF | 5of4_validation.cif.gz | 103.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/5of4 ftp://data.pdbj.org/pub/pdb/validation_reports/of/5of4 | HTTPS FTP |
-Related structure data
Related structure data | 3802MC 8816C 8817C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-TFIIH basal transcription factor complex helicase ... , 2 types, 2 molecules AB
#1: Protein | Mass: 62426.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa / References: UniProt: P19447, DNA helicase |
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#2: Protein | Mass: 87021.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa / References: UniProt: P18074, DNA helicase |
-General transcription factor IIH subunit ... , 4 types, 4 molecules DEFG
#3: Protein | Mass: 9875.401 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa / References: UniProt: Q92759 |
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#4: Protein | Mass: 44481.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa / References: UniProt: Q13888 |
#5: Protein | Mass: 34416.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa / References: UniProt: Q13889 |
#6: Protein | Mass: 8060.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa / References: UniProt: Q6ZYL4 |
-Protein , 2 types, 2 molecules HZ
#7: Protein | Mass: 10571.022 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sequence register unassigned. / Source: (natural) Homo sapiens (human) |
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#8: Protein | Mass: 22996.232 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sequence unassigned. / Source: (natural) Homo sapiens (human) |
-Unassigned secondary structure elements ... , 2 types, 2 molecules YX
#9: Protein | Mass: 19762.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sequence unassigned / Source: (natural) Homo sapiens (human) |
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#10: Protein | Mass: 6656.196 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
-Non-polymers , 1 types, 1 molecules
#11: Chemical | ChemComp-SF4 / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight |
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Source (natural) |
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Buffer solution | pH: 7.8 | ||||||||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.0049 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Natively purified complex at approx. 10 nM concentration | ||||||||||||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-4/2 | ||||||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278.15 K / Details: 3-4 minute incubation, 2 second blot |
-Electron microscopy imaging
Microscopy | Model: FEI TITAN |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Calibrated magnification: 37879 X / Nominal defocus max: 4500 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER |
Image recording | Average exposure time: 8.7 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 4 / Num. of real images: 8300 Details: 8300 micrographs collected in four session with identical acquisition settings. Sessions lasted 4, 2, 4, and 4 days and yielded 1200, 1700, 2800, and 2600 micrographs. |
Image scans | Sampling size: 5 µm / Width: 3840 / Height: 3710 / Movie frames/image: 30 / Used frames/image: 1-30 |
-Processing
Software | Name: REFMAC / Version: 5.8.0158 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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Image processing | Details: Micrographs were inspected for quality of Thon rings and ice contamination. Poor micrographs were rejected. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Details: Correction in RELION based on values determined in CTFFIND4. Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1500000 Details: Initial rounds of particle selection using DogPicker within APPION to generate templates for subsequent RELION autopicking. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 122900 / Algorithm: FOURIER SPACE / Details: RELION 3D auto-refinement (gold standard). / Num. of class averages: 3 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL Details: Initial model assembled from high-resolution structures and homology models. Subsequently rebuilt in O and COOT, refined into the cryo-EM map using PHENIX and REFMAC, and fully validated. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 4.4→166.32 Å / Cor.coef. Fo:Fc: 0.939 / SU B: 54.849 / SU ML: 0.668 / ESU R: 1.679 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 193.578 Å2
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Refinement step | Cycle: 1 / Total: 17200 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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