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Yorodumi- EMDB-22587: Structure of TFIIH in TFIIH/Rad4-Rad23-Rad33 DNA opening complex -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22587 | |||||||||
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Title | Structure of TFIIH in TFIIH/Rad4-Rad23-Rad33 DNA opening complex | |||||||||
Map data | Structure of TFIIH in TFIIH/Rad4-Rad23-Rad33 DNA opening complex | |||||||||
Sample |
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Function / homology | Function and homology information regulation of mitotic recombination / RNA polymerase II promoter clearance / phosphatidylinositol-5-phosphate binding / positive regulation of mitotic recombination / nucleotide-excision repair factor 3 complex / DNA translocase activity / nucleotide-excision repair, preincision complex assembly / transcription open complex formation at RNA polymerase II promoter / DNA 5'-3' helicase / transcriptional start site selection at RNA polymerase II promoter ...regulation of mitotic recombination / RNA polymerase II promoter clearance / phosphatidylinositol-5-phosphate binding / positive regulation of mitotic recombination / nucleotide-excision repair factor 3 complex / DNA translocase activity / nucleotide-excision repair, preincision complex assembly / transcription open complex formation at RNA polymerase II promoter / DNA 5'-3' helicase / transcriptional start site selection at RNA polymerase II promoter / phosphatidylinositol-3-phosphate binding / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / DNA 3'-5' helicase / transcription preinitiation complex / DNA duplex unwinding / poly(A)+ mRNA export from nucleus / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / 3'-5' DNA helicase activity / TP53 Regulates Transcription of DNA Repair Genes / 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 / RNA Polymerase II Pre-transcription Events / Formation of TC-NER Pre-Incision Complex / RNA Polymerase I Promoter Escape / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription by RNA polymerase I / ATPase activator activity / Dual incision in TC-NER / ATP-dependent activity, acting on DNA / DNA helicase activity / isomerase activity / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / ubiquitin protein ligase activity / double-stranded DNA binding / 4 iron, 4 sulfur cluster binding / 5'-3' DNA helicase activity / transcription by RNA polymerase II / damaged DNA binding / DNA repair / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / nucleus / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Baker's yeast (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | van Eeuwen T / Min JH / Murakami K | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2021 Title: Cryo-EM structure of TFIIH/Rad4-Rad23-Rad33 in damaged DNA opening in nucleotide excision repair. Authors: Trevor van Eeuwen / Yoonjung Shim / Hee Jong Kim / Tingting Zhao / Shrabani Basu / Benjamin A Garcia / Craig D Kaplan / Jung-Hyun Min / Kenji Murakami / Abstract: The versatile nucleotide excision repair (NER) pathway initiates as the XPC-RAD23B-CETN2 complex first recognizes DNA lesions from the genomic DNA and recruits the general transcription factor ...The versatile nucleotide excision repair (NER) pathway initiates as the XPC-RAD23B-CETN2 complex first recognizes DNA lesions from the genomic DNA and recruits the general transcription factor complex, TFIIH, for subsequent lesion verification. Here, we present a cryo-EM structure of an NER initiation complex containing Rad4-Rad23-Rad33 (yeast homologue of XPC-RAD23B-CETN2) and 7-subunit coreTFIIH assembled on a carcinogen-DNA adduct lesion at 3.9-9.2 Å resolution. A ~30-bp DNA duplex could be mapped as it straddles between Rad4 and the Ssl2 (XPB) subunit of TFIIH on the 3' and 5' side of the lesion, respectively. The simultaneous binding with Rad4 and TFIIH was permitted by an unwinding of DNA at the lesion. Translocation coupled with torque generation by Ssl2 and Rad4 would extend the DNA unwinding at the lesion and deliver the damaged strand to Rad3 (XPD) in an open form suitable for subsequent lesion scanning and verification. | |||||||||
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_22587.map.gz | 164.2 MB | EMDB map data format | |
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Header (meta data) | emd-22587-v30.xml emd-22587.xml | 29.5 KB 29.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22587_fsc.xml | 13.9 KB | Display | FSC data file |
Images | emd_22587.png | 165.8 KB | ||
Others | emd_22587_additional_1.map.gz emd_22587_half_map_1.map.gz emd_22587_half_map_2.map.gz | 14.7 MB 179.6 MB 179.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22587 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22587 | HTTPS FTP |
-Validation report
Summary document | emd_22587_validation.pdf.gz | 778.5 KB | Display | EMDB validaton report |
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Full document | emd_22587_full_validation.pdf.gz | 778.1 KB | Display | |
Data in XML | emd_22587_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | emd_22587_validation.cif.gz | 27.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22587 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22587 | HTTPS FTP |
-Related structure data
Related structure data | 7k01MC 7k04C 7m2uC C: citing same article (ref.) M: atomic model generated by this map |
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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_22587.map.gz / Format: CCP4 / Size: 226.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Structure of TFIIH in TFIIH/Rad4-Rad23-Rad33 DNA opening complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Additional map
File | emd_22587_additional_1.map | ||||||||||||
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Annotation | Additional map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half-volume 1
File | emd_22587_half_map_1.map | ||||||||||||
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Annotation | half-volume 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half-volume 2
File | emd_22587_half_map_2.map | ||||||||||||
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Annotation | half-volume 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Ternary complex of TFIIH/Rad4-Rad23-Rad33 with AAF damaged DNA
+Supramolecule #1: Ternary complex of TFIIH/Rad4-Rad23-Rad33 with AAF damaged DNA
+Macromolecule #1: General transcription and DNA repair factor IIH subunit TFB1
+Macromolecule #2: General transcription and DNA repair factor IIH subunit TFB4
+Macromolecule #3: DNA repair helicase RAD25
+Macromolecule #4: RNA polymerase II transcription factor B subunit 5
+Macromolecule #5: General transcription and DNA repair factor IIH subunit TFB2
+Macromolecule #6: DNA repair helicase RAD3
+Macromolecule #7: General transcription and DNA repair factor IIH subunit SSL1
+Macromolecule #8: ZINC ION
+Macromolecule #9: IRON/SULFUR CLUSTER
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 Component:
Details: Sample dialyzed for 30 minutes into above buffer prior to grid making | ||||||||
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: Pelco easyGLOW glow discharge apparatus | ||||||||
Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM CPC Details: Grids were manually blotted for 2-3 seconds prior to plunge freezing. | ||||||||
Details | Sample was prepared by Grafix. Sample was monodispersed and well behaved by visual inspection |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum |
Details | Images collected with image shift |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 6223 / Average exposure time: 2.6 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |