+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22576 | |||||||||
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Title | TFIIH/Rad4-23-33 Complex in NER focused on Rad4-33 | |||||||||
Map data | Cryo-EM map of TFIIH in complex with Rad4-Rad33 on AAF DNA with focused classification on Rad4-33-Ssl2 contacts. Composite map after multibody refinement. | |||||||||
Sample |
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Function / homology | Function and homology information nucleotide-excision repair factor 2 complex / single-strand break-containing DNA binding / XPC complex / nucleotide-excision repair, DNA damage recognition / regulation of mitotic recombination / RNA polymerase II promoter clearance / phosphatidylinositol-5-phosphate binding / positive regulation of mitotic recombination / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly ...nucleotide-excision repair factor 2 complex / single-strand break-containing DNA binding / XPC complex / nucleotide-excision repair, DNA damage recognition / regulation of mitotic recombination / RNA polymerase II promoter clearance / phosphatidylinositol-5-phosphate binding / positive regulation of mitotic recombination / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / DNA translocase activity / transcription open complex formation at RNA polymerase II promoter / phosphatidylinositol-3-phosphate binding / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / 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 / ATPase activator activity / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA topological change / Dual incision in TC-NER / transcription by RNA polymerase I / ATP-dependent activity, acting on DNA / mismatch repair / DNA helicase activity / transcription initiation at RNA polymerase II promoter / nucleotide-excision repair / ubiquitin protein ligase activity / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / 5'-3' DNA helicase activity / double-stranded DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA helicase / transcription by RNA polymerase II / damaged DNA binding / DNA repair / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.0 Å | |||||||||
Authors | van Eeuwen T / 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_22576.map.gz | 77.3 MB | EMDB map data format | |
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Header (meta data) | emd-22576-v30.xml emd-22576.xml | 19.4 KB 19.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22576_fsc.xml | 10.8 KB | Display | FSC data file |
Images | emd_22576.png | 53.3 KB | ||
Others | emd_22576_additional_1.map.gz emd_22576_additional_2.map.gz emd_22576_half_map_1.map.gz emd_22576_half_map_2.map.gz | 76.8 MB 55.6 MB 80.6 MB 80.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22576 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22576 | HTTPS FTP |
-Related structure data
Related structure data | 7m2uMC 7k01C 7k04C 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_22576.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM map of TFIIH in complex with Rad4-Rad33 on AAF DNA with focused classification on Rad4-33-Ssl2 contacts. Composite map after multibody refinement. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Cryo-EM map of TFIIH in complex with Rad4-Rad33...
File | emd_22576_additional_1.map | ||||||||||||
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Annotation | Cryo-EM map of TFIIH in complex with Rad4-Rad33 on AAF DNA with focused classification on Rad4-33-Ssl2 contacts. TFIIH body from multibody refinement used for composite map making. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Cryo-EM map of TFIIH in complex with Rad4-Rad33...
File | emd_22576_additional_2.map | ||||||||||||
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Annotation | Cryo-EM map of TFIIH in complex with Rad4-Rad33 on AAF DNA with focused classification on Rad4-33-Ssl2 contacts. Map locally filtered to FSC=0.5 by blocre | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered Half Map 1
File | emd_22576_half_map_1.map | ||||||||||||
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Annotation | Unfiltered Half Map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered Half Map 2
File | emd_22576_half_map_2.map | ||||||||||||
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Annotation | Unfiltered Half Map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Ternary complex of Saccharomyces cerevisiae TFIIH, DNA damage pro...
Entire | Name: Ternary complex of Saccharomyces cerevisiae TFIIH, DNA damage proteins Rad4-Rad23-Rad33 and N-acetoxy-acetominofluorinated DNA. |
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Components |
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-Supramolecule #1: Ternary complex of Saccharomyces cerevisiae TFIIH, DNA damage pro...
Supramolecule | Name: Ternary complex of Saccharomyces cerevisiae TFIIH, DNA damage proteins Rad4-Rad23-Rad33 and N-acetoxy-acetominofluorinated DNA. type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Experimental: 570 KDa |
-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:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 | ||||||||||||
Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM CPC Details: Manually blotted for 2-3 seconds prior to plunging. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy |
Specialist optics | Energy filter - Name: GIF Quantum LS |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 45.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |