+Open data
-Basic information
Entry | Database: PDB / ID: 7m2u | ||||||
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Title | Nucleotide Excision Repair complex TFIIH Rad4-33 | ||||||
Components |
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Keywords | NUCLEAR PROTEIN/DNA / NER / nucleotide excision repair / TFIIH / Rad4 / XPC / NUCLEAR PROTEIN / NUCLEAR PROTEIN-DNA complex | ||||||
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 / DNA 3'-5' helicase / 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 / 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 / 3'-5' DNA helicase activity / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription by RNA polymerase I / DNA topological change / ATPase activator activity / Dual incision in TC-NER / ATP-dependent activity, acting on DNA / mismatch repair / DNA helicase activity / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / 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 / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.2 Å | ||||||
Authors | van Eeuwen, T. / Murakami, K. | ||||||
Funding support | United States, 1items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7m2u.cif.gz | 565.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7m2u.ent.gz | 433.1 KB | Display | PDB format |
PDBx/mmJSON format | 7m2u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7m2u_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7m2u_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7m2u_validation.xml.gz | 106.9 KB | Display | |
Data in CIF | 7m2u_validation.cif.gz | 160 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m2/7m2u ftp://data.pdbj.org/pub/pdb/validation_reports/m2/7m2u | HTTPS FTP |
-Related structure data
Related structure data | 22576MC 7k01C 7k04C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-DNA repair helicase ... , 2 types, 2 molecules 70
#1: Protein | Mass: 95461.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: SSL2, LOM3, RAD25, UVS112, YIL143C / Production host: Escherichia coli (E. coli) / References: UniProt: Q00578, DNA helicase |
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#5: Protein | Mass: 89899.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P06839, DNA helicase |
-DNA chain , 2 types, 2 molecules YW
#2: DNA chain | Mass: 3003.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 4297.832 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-General transcription and DNA repair factor IIH subunit ... , 5 types, 5 molecules 51462
#4: Protein | Mass: 7482.721 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q3E7C1 |
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#6: Protein | Mass: 72993.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P32776 |
#7: Protein | Mass: 37506.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q12004 |
#8: Protein | Mass: 52370.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q04673 |
#11: Protein | Mass: 58602.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q02939 |
-DNA repair protein ... , 2 types, 2 molecules AE
#9: Protein | Mass: 87315.445 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: RAD4, YER162C / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P14736 |
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#10: Protein | Mass: 20291.457 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: RAD33, YML011C, YM9571.07C / Production host: Escherichia coli (E. coli) / References: UniProt: Q04231 |
-Non-polymers , 3 types, 8 molecules
#12: Chemical | ChemComp-SF4 / | ||
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#13: Chemical | ChemComp-ZN / #14: Chemical | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Ternary Complex of TFIIH/Rad4-Rad33 on damaged DNA focused on Ssl2/DNA interaction Type: COMPLEX / Entity ID: #1-#11 / Source: MULTIPLE SOURCES | ||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||
Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) | ||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||
Specimen support | Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34000 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||
Refine LS restraints |
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