+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3802 | |||||||||
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Title | The cryo-EM structure of human TFIIH | |||||||||
Map data | Postprocessed (b-factor sharpened, low pass filtered) masked map used for atomic coordinate refinement. | |||||||||
Sample |
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Keywords | transcription initiation / DNA repair / multiprotein complex / kinase / helicase / TRANSCRIPTION | |||||||||
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 / ventricular system development / hair follicle maturation / hair cell differentiation / nucleotide-excision repair factor 3 complex ...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 / ventricular system development / hair follicle maturation / hair cell differentiation / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / CAK-ERCC2 complex / UV protection / transcription factor TFIIK complex / embryonic cleavage / DNA 5'-3' helicase / G protein-coupled receptor internalization / adult heart development / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / cyclin-dependent protein serine/threonine kinase activator activity / DNA 3'-5' helicase / transcription preinitiation complex / RNA Polymerase I Transcription Termination / nuclear thyroid hormone receptor binding / 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 / regulation of cyclin-dependent protein serine/threonine kinase activity / 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 / regulation of G1/S transition of mitotic cell cycle / RNA Polymerase I Transcription Initiation / transcription by RNA polymerase I / 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 / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / Formation of RNA Pol II elongation complex / cyclin-dependent protein kinase holoenzyme complex / response to UV / Cyclin A:Cdk2-associated events at S phase entry / RNA Polymerase II Pre-transcription Events / DNA helicase activity / hormone-mediated signaling pathway / 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 / positive regulation of smooth muscle cell proliferation / 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 / response to calcium ion / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / G1/S transition of mitotic cell cycle / Cyclin D associated events in G1 / protein localization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / 4 iron, 4 sulfur cluster binding / protein-macromolecule adaptor activity Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.4 Å | |||||||||
Authors | Greber BJ / Nguyen THD / Fang J / Afonine PV / Adams PD / Nogales E | |||||||||
Funding support | United States, 2 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3802.map.gz | 4.6 MB | EMDB map data format | |
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Header (meta data) | emd-3802-v30.xml emd-3802.xml | 36.6 KB 36.6 KB | Display Display | EMDB header |
Images | emd_3802.png | 140.7 KB | ||
Masks | emd_3802_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-3802.cif.gz | 8.5 KB | ||
Others | emd_3802_half_map_1.map.gz emd_3802_half_map_2.map.gz | 49.7 MB 49.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3802 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3802 | HTTPS FTP |
-Validation report
Summary document | emd_3802_validation.pdf.gz | 748.5 KB | Display | EMDB validaton report |
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Full document | emd_3802_full_validation.pdf.gz | 748 KB | Display | |
Data in XML | emd_3802_validation.xml.gz | 12 KB | Display | |
Data in CIF | emd_3802_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3802 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3802 | HTTPS FTP |
-Related structure data
Related structure data | 5of4MC 6o9mM 8816C 8817C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_3802.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Postprocessed (b-factor sharpened, low pass filtered) masked map used for atomic coordinate refinement. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_3802_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: None
File | emd_3802_half_map_1.map | ||||||||||||
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Annotation | None | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: None
File | emd_3802_half_map_2.map | ||||||||||||
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Annotation | None | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : TFIIH
+Supramolecule #1: TFIIH
+Supramolecule #2: TFIIH core complex
+Supramolecule #3: TFIIH CDK-activating kinase (CAK) subcomplex
+Macromolecule #1: TFIIH basal transcription factor complex helicase XPB subunit,XPB...
+Macromolecule #2: TFIIH basal transcription factor complex helicase XPD subunit
+Macromolecule #3: General transcription factor IIH subunit 4,p52,General transcript...
+Macromolecule #4: General transcription factor IIH subunit 2
+Macromolecule #5: General transcription factor IIH subunit 3
+Macromolecule #6: General transcription factor IIH subunit 5
+Macromolecule #7: MAT1
+Macromolecule #8: Unassigned secondary structure elements.
+Macromolecule #9: Unassigned secondary structure elements (p52 region)
+Macromolecule #10: Unassigned secondary structure elements (XPB NTE region)
+Macromolecule #11: IRON/SULFUR CLUSTER
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.0049 mg/mL | ||||||||||||||||||||||||
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Buffer | pH: 7.8 Component:
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Grid | Model: C-flat-4/2 / Material: COPPER / Mesh: 400 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278.15 K / Instrument: FEI VITROBOT MARK IV / Details: 3-4 minute incubation, 2 second blot. | ||||||||||||||||||||||||
Details | Natively purified complex at approx. 10 nM concentration |
-Electron microscopy
Microscope | FEI TITAN |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3840 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-30 / Number grids imaged: 4 / Number real images: 8300 / Average exposure time: 8.7 sec. / Average electron dose: 40.0 e/Å2 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. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 37879 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 2.0 µm |
Sample stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |
+Image processing
-Atomic model buiding 1
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. |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-5of4: PDB-6o9m: |