+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0452 | |||||||||||||||
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Title | Cryo-EM structure of the human TFIIH core complex | |||||||||||||||
Map data | Sharpened and low-pass filtered cryo-EM map. | |||||||||||||||
Sample |
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Function / homology | Function and homology information MMXD complex / core TFIIH complex portion of holo TFIIH complex / positive regulation of DNA helicase activity / negative regulation of DNA helicase activity / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / central nervous system myelin formation / positive regulation of mitotic recombination / hair cell differentiation / ventricular system development ...MMXD complex / core TFIIH complex portion of holo TFIIH complex / positive regulation of DNA helicase activity / negative regulation of DNA helicase activity / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / central nervous system myelin formation / positive regulation of mitotic recombination / hair cell differentiation / ventricular system development / hair follicle maturation / cyclin-dependent protein kinase activating kinase holoenzyme complex / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / UV protection / CAK-ERCC2 complex / transcription factor TFIIK complex / embryonic cleavage / 5'-3' DNA helicase activity / adult heart development / G protein-coupled receptor internalization / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / cyclin-dependent protein serine/threonine kinase activator activity / 3'-5' DNA helicase activity / nuclear thyroid hormone receptor binding / transcription preinitiation complex / RNA Polymerase I Transcription Termination / regulation of mitotic cell cycle phase transition / 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 / spinal cord development / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / bone mineralization / 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 cyclin-dependent protein serine/threonine kinase activity / ATPase activator activity / regulation of G1/S transition of mitotic cell cycle / RNA Polymerase I Transcription Initiation / transcription elongation by RNA polymerase I / DNA topological change / intrinsic apoptotic signaling pathway by p53 class mediator / transcription-coupled nucleotide-excision repair / hematopoietic stem cell differentiation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / embryonic organ development / transcription by RNA polymerase I / Formation of HIV elongation complex in the absence of HIV Tat / Cyclin E associated events during G1/S transition / RNA Polymerase II Transcription Elongation / Cyclin A/B1/B2 associated events during G2/M transition / Formation of RNA Pol II elongation complex / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 / extracellular matrix organization / post-embryonic development / insulin-like growth factor receptor signaling pathway / chromosome segregation / determination of adult lifespan / promoter-specific chromatin binding / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / nucleotide-excision repair / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / positive regulation of smooth muscle cell proliferation / G1/S transition of mitotic cell cycle / multicellular organism growth / cellular response to gamma radiation / NoRC negatively regulates rRNA expression / protein localization / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / spindle / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / response to calcium ion / Gap-filling DNA repair synthesis and ligation in TC-NER / Cyclin D associated events in G1 / protein-macromolecule adaptor activity / RUNX1 regulates transcription of genes involved in differentiation of HSCs / 4 iron, 4 sulfur cluster binding Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) / Human (human) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||||||||
Authors | Greber BJ / Toso D / Fang J / Nogales E | |||||||||||||||
Funding support | United States, Switzerland, 4 items
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Citation | Journal: Elife / Year: 2019 Title: The complete structure of the human TFIIH core complex. Authors: Basil J Greber / Daniel B Toso / Jie Fang / Eva Nogales / Abstract: Transcription factor IIH (TFIIH) is a heterodecameric protein complex critical for transcription initiation by RNA polymerase II and nucleotide excision DNA repair. The TFIIH core complex is ...Transcription factor IIH (TFIIH) is a heterodecameric protein complex critical for transcription initiation by RNA polymerase II and nucleotide excision DNA repair. The TFIIH core complex is sufficient for its repair functions and harbors the XPB and XPD DNA-dependent ATPase/helicase subunits, which are affected by human disease mutations. Transcription initiation additionally requires the CdK activating kinase subcomplex. Previous structural work has provided only partial insight into the architecture of TFIIH and its interactions within transcription pre-initiation complexes. Here, we present the complete structure of the human TFIIH core complex, determined by phase-plate cryo-electron microscopy at 3.7 Å resolution. The structure uncovers the molecular basis of TFIIH assembly, revealing how the recruitment of XPB by p52 depends on a pseudo-symmetric dimer of homologous domains in these two proteins. The structure also suggests a function for p62 in the regulation of XPD, and allows the mapping of previously unresolved human disease mutations. | |||||||||||||||
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_0452.map.gz | 59.6 MB | EMDB map data format | |
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Header (meta data) | emd-0452-v30.xml emd-0452.xml | 31.2 KB 31.2 KB | Display Display | EMDB header |
Images | emd_0452.png | 166 KB | ||
Others | emd_0452_half_map_1.map.gz emd_0452_half_map_2.map.gz | 49.7 MB 49.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0452 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0452 | HTTPS FTP |
-Related structure data
Related structure data | 6nmiMC 0587C 0588C 0589C 0602C 0603C 0604C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10430 (Title: Phase-plate cryo-EM of human TFIIH / Data size: 9.2 TB Data #1: Unaligned movies of human TFIIH, using the Volta phase plate, dataset 1 [micrographs - multiframe] Data #2: Unaligned movies of human TFIIH, using the Volta phase plate, dataset 2 [micrographs - multiframe] Data #3: Unaligned movies of human TFIIH, using the Volta phase plate, dataset 3 [micrographs - multiframe] Data #4: Unaligned movies of human TFIIH, using the Volta phase plate, dataset 4 [micrographs - multiframe] Data #5: Unaligned movies of human TFIIH, using the Volta phase plate, dataset 5 [micrographs - multiframe] Data #6: Unaligned movies of human TFIIH, using the Volta phase plate, dataset 6 [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0452.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened and low-pass filtered cryo-EM map. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: Unfiltered half-map.
File | emd_0452_half_map_1.map | ||||||||||||
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Annotation | Unfiltered half-map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half-map.
File | emd_0452_half_map_2.map | ||||||||||||
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Annotation | Unfiltered half-map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Transcription factor IIH (TFIIH)
+Supramolecule #1: Transcription factor IIH (TFIIH)
+Macromolecule #1: General transcription and DNA repair factor IIH helicase subunit XPB
+Macromolecule #2: General transcription and DNA repair factor IIH helicase subunit XPD
+Macromolecule #3: General transcription factor IIH subunit 1, p62
+Macromolecule #4: General transcription factor IIH subunit 4, p52
+Macromolecule #5: General transcription factor IIH subunit 2, p44
+Macromolecule #6: General transcription factor IIH subunit 3, p34
+Macromolecule #7: General transcription factor IIH subunit 5, p8
+Macromolecule #8: CDK-activating kinase assembly factor MAT1
+Macromolecule #9: IRON/SULFUR CLUSTER
+Macromolecule #10: ZINC ION
-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: 7.9 Component:
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Grid | Model: C-flat / 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 / Details: Gatan Solarus | ||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: A thin film of continuous carbon was floated onto Protochips C-flat CF-4/2 holey carbon grids and glow discharged or plasma cleaned before application of 4 uL of sample solution.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 43478 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 0.7 µm / Nominal defocus min: 0.5 µm |
Specialist optics | Phase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Details | Residual beam tilt corrected in RELION 3. |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 7 / Number real images: 21437 / Average exposure time: 8.25 sec. / Average electron dose: 50.0 e/Å2 Details: Images were collected as dose-fractionated movie frames (33 or 50 frames per exposure). |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software:
Details: CTF correction during 3D reconstruction in RELION 3. | ||||||
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Startup model | Type of model: EMDB MAP EMDB ID: | ||||||
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3) | ||||||
Final 3D classification | Number classes: 8 / Avg.num./class: 100000 / Software - Name: RELION (ver. 3) | ||||||
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3) | ||||||
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 138659 |
-Atomic model buiding 1
Initial model | (PDB ID: , , , , , , ) |
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Details | Reference structures and homology models were docked and subsequently completely rebuilt according to the density. Parts of the structure were traced de novo. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-6nmi: |