+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4970 | |||||||||||||||
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Title | Structure of the core TFIIH-XPA-DNA complex | |||||||||||||||
Map data | Composite map produced from focused refined maps (deposited as additional EM maps). | |||||||||||||||
Sample |
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Keywords | Complex / Helicase / Translocase / DNA repair | |||||||||||||||
Function / homology | Function and homology information nucleotide-excision repair factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair, DNA damage recognition / 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 / response to auditory stimulus / positive regulation of mitotic recombination ...nucleotide-excision repair factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair, DNA damage recognition / 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 / response to auditory stimulus / 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 / UV-damage excision repair / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / DNA 3'-5' helicase / nuclear thyroid hormone receptor binding / transcription preinitiation complex / RNA Polymerase I Transcription Termination / regulation of mitotic cell cycle phase transition / hematopoietic stem cell proliferation / 3'-5' DNA helicase activity / regulation of cyclin-dependent protein serine/threonine kinase 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 / intercellular bridge / spinal cord development / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / RNA polymerase II general transcription initiation factor activity / 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 / RNA Polymerase I Transcription Initiation / transcription by RNA polymerase I / DNA topological change / ATPase activator activity / intrinsic apoptotic signaling pathway by p53 class mediator / protein localization to nucleus / hematopoietic stem cell differentiation / transcription elongation by RNA polymerase I / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / hormone-mediated signaling pathway / Formation of HIV elongation complex in the absence of HIV Tat / embryonic organ development / transcription-coupled nucleotide-excision repair / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / response to UV / RNA Polymerase II Pre-transcription Events / DNA helicase activity / extracellular matrix organization / insulin-like growth factor receptor signaling pathway / isomerase activity / post-embryonic development / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / chromosome segregation / RNA Polymerase I Promoter Escape / determination of adult lifespan / promoter-specific chromatin binding / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / transcription elongation by RNA polymerase II / NoRC negatively regulates rRNA expression / base-excision repair / multicellular organism growth / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Dual Incision in GG-NER / cellular response to gamma radiation / Formation of Incision Complex in GG-NER / spindle / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / sequence-specific double-stranded DNA binding / protein localization / double-stranded DNA binding / protein-macromolecule adaptor activity / 4 iron, 4 sulfur cluster binding / 5'-3' DNA helicase activity / in utero embryonic development / response to oxidative stress / transcription by RNA polymerase II Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||||||||
Authors | Kokic G / Chernev A / Tegunov D / Dienemann C / Urlaub H / Cramer P | |||||||||||||||
Funding support | Germany, 4 items
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Citation | Journal: Nat Commun / Year: 2019 Title: Structural basis of TFIIH activation for nucleotide excision repair. Authors: Goran Kokic / Aleksandar Chernev / Dimitry Tegunov / Christian Dienemann / Henning Urlaub / Patrick Cramer / Abstract: Nucleotide excision repair (NER) is the major DNA repair pathway that removes UV-induced and bulky DNA lesions. There is currently no structure of NER intermediates, which form around the large ...Nucleotide excision repair (NER) is the major DNA repair pathway that removes UV-induced and bulky DNA lesions. There is currently no structure of NER intermediates, which form around the large multisubunit transcription factor IIH (TFIIH). Here we report the cryo-EM structure of an NER intermediate containing TFIIH and the NER factor XPA. Compared to its transcription conformation, the TFIIH structure is rearranged such that its ATPase subunits XPB and XPD bind double- and single-stranded DNA, consistent with their translocase and helicase activities, respectively. XPA releases the inhibitory kinase module of TFIIH, displaces a 'plug' element from the DNA-binding pore in XPD, and together with the NER factor XPG stimulates XPD activity. Our results explain how TFIIH is switched from a transcription to a repair factor, and provide the basis for a mechanistic analysis of the NER pathway. | |||||||||||||||
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_4970.map.gz | 33.9 MB | EMDB map data format | |
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Header (meta data) | emd-4970-v30.xml emd-4970.xml | 43.2 KB 43.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4970_fsc_1.xml emd_4970_fsc_2.xml | 11.4 KB 11.4 KB | Display Display | FSC data file |
Images | emd_4970.png | 98.3 KB | ||
Masks | emd_4970_msk_1.map | 125 MB | Mask map | |
Filedesc metadata | emd-4970.cif.gz | 8.8 KB | ||
Others | emd_4970_additional_1.map.gz emd_4970_additional_2.map.gz emd_4970_additional_3.map.gz emd_4970_additional_4.map.gz emd_4970_additional_5.map.gz emd_4970_additional_6.map.gz emd_4970_additional_7.map.gz emd_4970_additional_8.map.gz emd_4970_additional_9.map.gz | 112.8 MB 112.8 MB 38.7 MB 98.8 MB 98.8 MB 7.2 MB 6.4 MB 6.4 MB 5.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4970 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4970 | HTTPS FTP |
-Validation report
Summary document | emd_4970_validation.pdf.gz | 401.3 KB | Display | EMDB validaton report |
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Full document | emd_4970_full_validation.pdf.gz | 400.8 KB | Display | |
Data in XML | emd_4970_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | emd_4970_validation.cif.gz | 7.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4970 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4970 | HTTPS FTP |
-Related structure data
Related structure data | 6ro4MC 7ad8M 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_4970.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Composite map produced from focused refined maps (deposited as additional EM maps). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
+Mask #1
+Additional map: Half map 1 corresponding to the composite map.
+Additional map: Half map 2 corresponding to the composite map.
+Additional map: Globally refined map.
+Additional map: Half map 1 corresponding to the globally refined map.
+Additional map: Half map 2 corresponding to the globally refined map.
+Additional map: Focused classified and refined map using a mask...
+Additional map: Focused classified and refined map using a mask...
+Additional map: Focused classified and refined map using a mask...
+Additional map: Focused classified and refined map using a mask...
-Sample components
+Entire : Core TFIIH-XPA-DNA complex
+Supramolecule #1: Core TFIIH-XPA-DNA complex
+Supramolecule #2: TFIIH-XPA
+Supramolecule #3: DNA
+Macromolecule #1: DNA1
+Macromolecule #2: DNA2
+Macromolecule #3: General transcription and DNA repair factor IIH helicase subunit XPB
+Macromolecule #4: General transcription factor IIH subunit 5
+Macromolecule #5: TFIIH basal transcription factor complex helicase XPD subunit
+Macromolecule #6: General transcription factor IIH subunit 3
+Macromolecule #7: General transcription factor IIH subunit 2
+Macromolecule #8: General transcription factor IIH subunit 4
+Macromolecule #9: DNA repair protein complementing XP-A cells
+Macromolecule #10: IRON/SULFUR CLUSTER
+Macromolecule #11: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R2/2 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: 4 ul of sample was applied to glow-discharged grids which were blotted for 5s and plunge-frozen in liquid ethane.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 41.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 130000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |