+Open data
-Basic information
Entry | Database: PDB / ID: 7oob | |||||||||
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Title | Pol II-CSB-CSA-DDB1-UVSSA-ADPBeF3 (Structure2) | |||||||||
Components |
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Keywords | TRANSCRIPTION / DNA repair | |||||||||
Function / homology | Function and homology information double-strand break repair via synthesis-dependent strand annealing / negative regulation of double-strand break repair via nonhomologous end joining / regulation of transcription-coupled nucleotide-excision repair / nucleotide-excision repair complex / B-WICH complex / single strand break repair / regulation of transcription elongation by RNA polymerase II / DNA translocase activity / DNA protection / positive regulation by virus of viral protein levels in host cell ...double-strand break repair via synthesis-dependent strand annealing / negative regulation of double-strand break repair via nonhomologous end joining / regulation of transcription-coupled nucleotide-excision repair / nucleotide-excision repair complex / B-WICH complex / single strand break repair / regulation of transcription elongation by RNA polymerase II / DNA translocase activity / DNA protection / positive regulation by virus of viral protein levels in host cell / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Major Pathway / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / epigenetic programming in the zygotic pronuclei / double-strand break repair via classical nonhomologous end joining / spindle assembly involved in female meiosis / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / response to superoxide / photoreceptor cell maintenance / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / reciprocal meiotic recombination / response to UV-B / ATP-dependent chromatin remodeler activity / RNA polymerase binding / positive regulation of DNA-templated transcription, elongation / biological process involved in interaction with symbiont / positive regulation of transcription by RNA polymerase III / WD40-repeat domain binding / regulation of mitotic cell cycle phase transition / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / positive regulation of transcription by RNA polymerase I / : / protein tyrosine kinase activator activity / : / negative regulation of reproductive process / negative regulation of developmental process / site of DNA damage / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA Polymerase I Transcription Initiation / organelle membrane / transcription elongation by RNA polymerase I / cullin family protein binding / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / positive regulation of double-strand break repair via homologous recombination / viral release from host cell / response to X-ray / RNA polymerase III activity / transcription by RNA polymerase I / transcription by RNA polymerase III / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase I activity / pyrimidine dimer repair / ectopic germ cell programmed cell death / positive regulation of translational initiation / RNA polymerase I complex / ATP-dependent activity, acting on DNA / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / RNA polymerase II activity / protein autoubiquitination / positive regulation of viral genome replication / RNA polymerase II, core complex / response to UV / positive regulation of gluconeogenesis / JNK cascade / DNA-directed RNA polymerase complex / translation initiation factor binding / positive regulation of DNA repair / neurogenesis / proteasomal protein catabolic process / positive regulation of RNA splicing / transcription elongation factor complex / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Sus scrofa (pig) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Kokic, G. / Cramer, P. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Nature / Year: 2021 Title: Structural basis of human transcription-DNA repair coupling. Authors: Goran Kokic / Felix R Wagner / Aleksandar Chernev / Henning Urlaub / Patrick Cramer / Abstract: Transcription-coupled DNA repair removes bulky DNA lesions from the genome and protects cells against ultraviolet (UV) irradiation. Transcription-coupled DNA repair begins when RNA polymerase II ...Transcription-coupled DNA repair removes bulky DNA lesions from the genome and protects cells against ultraviolet (UV) irradiation. Transcription-coupled DNA repair begins when RNA polymerase II (Pol II) stalls at a DNA lesion and recruits the Cockayne syndrome protein CSB, the E3 ubiquitin ligase, CRL4 and UV-stimulated scaffold protein A (UVSSA). Here we provide five high-resolution structures of Pol II transcription complexes containing human transcription-coupled DNA repair factors and the elongation factors PAF1 complex (PAF) and SPT6. Together with biochemical and published data, the structures provide a model for transcription-repair coupling. Stalling of Pol II at a DNA lesion triggers replacement of the elongation factor DSIF by CSB, which binds to PAF and moves upstream DNA to SPT6. The resulting elongation complex, EC, uses the CSA-stimulated translocase activity of CSB to pull on upstream DNA and push Pol II forward. If the lesion cannot be bypassed, CRL4 spans over the Pol II clamp and ubiquitylates the RPB1 residue K1268, enabling recruitment of TFIIH to UVSSA and DNA repair. Conformational changes in CRL4 lead to ubiquitylation of CSB and to release of transcription-coupled DNA repair factors before transcription may continue over repaired DNA. | |||||||||
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 | 7oob.cif.gz | 1.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7oob.ent.gz | 1.6 MB | Display | PDB format |
PDBx/mmJSON format | 7oob.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oo/7oob ftp://data.pdbj.org/pub/pdb/validation_reports/oo/7oob | HTTPS FTP |
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-Related structure data
Related structure data | 13009MC 7oo3C 7oopC 7opcC 7opdC 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-directed RNA polymerase II subunit ... , 6 types, 6 molecules ACEFGI
#1: Protein | Mass: 217450.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P11414 |
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#3: Protein | Mass: 31439.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LCH3 |
#5: Protein | Mass: 24644.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LSI7 |
#6: Protein | Mass: 14477.001 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SKN8 |
#7: Protein | Mass: 19314.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LJZ9 |
#9: Protein | Mass: 14541.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P60899 |
-Protein , 5 types, 5 molecules BDKLd
#2: Protein | Mass: 134041.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LGP4, DNA-directed RNA polymerase |
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#4: Protein | Mass: 16331.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287ADR4 |
#11: Protein | Mass: 13310.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1UK25 |
#12: Protein | Mass: 7018.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LN51 |
#14: Protein | Mass: 127369.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q16531 |
-DNA-directed RNA polymerases I, II, and III subunit ... , 2 types, 2 molecules HJ
#8: Protein | Mass: 17162.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1ULF2 |
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#10: Protein | Mass: 7655.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VYD0 |
-DNA excision repair protein ERCC- ... , 2 types, 2 molecules ba
#13: Protein | Mass: 168945.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC6, CSB / Production host: Trichoplusia ni (cabbage looper) References: UniProt: Q03468, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement |
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#18: Protein | Mass: 44107.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC8, CKN1, CSA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q13216 |
-DNA chain , 2 types, 2 molecules NT
#15: DNA chain | Mass: 14494.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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#16: DNA chain | Mass: 14269.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
-RNA chain , 1 types, 1 molecules P
#17: RNA chain | Mass: 3264.036 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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-Non-polymers , 4 types, 12 molecules
#19: Chemical | ChemComp-ZN / #20: Chemical | #21: Chemical | ChemComp-ADP / | #22: Chemical | ChemComp-BEF / | |
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-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
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid type: Quantifoil R2/1 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
-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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 41.2 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10940 |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1855061 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 100000 Details: Different final number of particles was used for different focused refined maps. Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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