[English] 日本語
Yorodumi- EMDB-8816: TFIIH reconstruction from particles sorted for density near the X... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8816 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | TFIIH reconstruction from particles sorted for density near the XPD ARCH domain using signal-subtracted classification. | |||||||||
Map data | Human TFIIH reconstruction obtained from particle images sorted for density near the XPD ARCH domain using signal-subtracted classification | |||||||||
Sample |
| |||||||||
Function / homology | Function and homology information MMXD complex / core TFIIH complex portion of holo TFIIH complex / positive 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 / hair follicle maturation / nucleotide-excision repair factor 3 complex ...MMXD complex / core TFIIH complex portion of holo TFIIH complex / positive 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 / hair follicle maturation / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / UV protection / CAK-ERCC2 complex / embryonic cleavage / 5'-3' DNA helicase activity / G protein-coupled receptor internalization / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / 3'-5' DNA helicase activity / 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 / ATPase activator activity / 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 / 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 / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / RNA Polymerase II Pre-transcription Events / DNA helicase activity / 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 / 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 / Gap-filling DNA repair synthesis and ligation in TC-NER / protein-macromolecule adaptor activity / 4 iron, 4 sulfur cluster binding / double-stranded DNA binding / DNA helicase / response to oxidative stress / in utero embryonic development / transcription by RNA polymerase II / damaged DNA binding / response to hypoxia / nuclear speck / positive regulation of apoptotic process / DNA repair / apoptotic process / nucleolus / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / zinc ion binding / nucleoplasm / ATP binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.4 Å | |||||||||
Authors | Greber BJ / Nguyen THD / Fang J / Afonine PV / Adams PD / Nogales E | |||||||||
Funding support | United States, 1 items
| |||||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8816.map.gz | 59.5 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-8816-v30.xml emd-8816.xml | 16.4 KB 16.4 KB | Display Display | EMDB header |
Images | emd_8816.png | 51.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8816 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8816 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_8816.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Human TFIIH reconstruction obtained from particle images sorted for density near the XPD ARCH domain using signal-subtracted classification | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : transcription factor IIH (TFIIH)
Entire | Name: transcription factor IIH (TFIIH) |
---|---|
Components |
|
-Supramolecule #1: transcription factor IIH (TFIIH)
Supramolecule | Name: transcription factor IIH (TFIIH) / type: complex / ID: 1 / Parent: 0 |
---|---|
Source (natural) | Organism: Homo sapiens (human) / Strain: HeLa / Organelle: Nucleus / Location in cell: Nucleus |
Molecular weight | Theoretical: 490 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.0049 mg/mL | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.8 Component:
| ||||||||||||||||||||||||
Grid | Model: Protochips 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 - 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 |
---|---|
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 FIELDBright-field microscopy / 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 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 - Sampling interval: 5.0 µm / 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. |
-Image processing
Particle selection | Number selected: 1500000 Details: Initial rounds of particle selection using DogPicker within APPION to generate templates for subsequent RELION autopicking. |
---|---|
CTF correction | Software - Name: CTFFIND (ver. 4) / Software - details: run from within RELION Details: Correction within RELION based on values determined in CTFFIND4. |
Startup model | Type of model: EMDB MAP EMDB ID: Details: Box and pixel size were adjusted before initial refinement. |
Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4) Details: Maximum-likelihood 3D classification within RELION. |
Final 3D classification | Number classes: 6 / Software - Name: RELION (ver. 1.4) Details: Signal-subtracted classification in RELION 1.4, using 6 classes. |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4) / Details: Maximum-likelihood 3D refinement within RELION. |
Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) Details: RELION 3D auto-refinement (gold standard). The final 3D classification used signal-subtracted particle images. The final reconstruction used the corresponding un-subtracted particle images. Number images used: 35900 |
Details | Micrographs were inspected for quality of Thon rings and ice contamination. Poor micrographs were rejected. |
-Atomic model buiding 1
Details | Fitting of a refined coordinate model obtained from a 4.4 Angstrom reconstruction of TFIIH from the same initial dataset (PDB ID 5OF4). |
---|---|
Refinement | Space: REAL / Protocol: RIGID BODY FIT |