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Open data
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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 informationregulation of transcription-coupled nucleotide-excision repair / negative regulation of double-strand break repair via nonhomologous end joining / nucleotide-excision repair complex / : / response to auditory stimulus / regulation of transcription elongation by RNA polymerase II / B-WICH complex / DNA protection / single strand break repair / Formation of RNA Pol II elongation complex ...regulation of transcription-coupled nucleotide-excision repair / negative regulation of double-strand break repair via nonhomologous end joining / nucleotide-excision repair complex / : / response to auditory stimulus / regulation of transcription elongation by RNA polymerase II / B-WICH complex / DNA protection / single strand break repair / 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 - 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 / response to superoxide / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / mRNA Splicing - Major Pathway / double-strand break repair via classical nonhomologous end joining / photoreceptor cell maintenance / chromatin-protein adaptor activity / positive regulation by virus of viral protein levels in host cell / ATP-dependent chromatin remodeler activity / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / RNA polymerase binding / response to UV-B / positive regulation of DNA-templated transcription, elongation / UV-damage excision repair / positive regulation of transcription by RNA polymerase III / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / ATP-dependent DNA damage sensor activity / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / organelle membrane / positive regulation of transcription by RNA polymerase I / negative regulation of reproductive process / negative regulation of developmental process / protein tyrosine kinase activator activity / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA Polymerase I Transcription Initiation / cullin family protein binding / viral release from host cell / site of DNA damage / positive regulation of translational initiation / pyrimidine dimer repair / response to X-ray / positive regulation of transcription initiation by RNA polymerase II / ATP-dependent activity, acting on DNA / ectopic germ cell programmed cell death / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / ubiquitin-like ligase-substrate adaptor activity / positive regulation of viral genome replication / response to UV / RNA polymerase II, core complex / positive regulation of double-strand break repair via homologous recombination / tRNA transcription by RNA polymerase III / protein autoubiquitination / proteasomal protein catabolic process / transcription by RNA polymerase I / JNK cascade / translation initiation factor binding / neurogenesis / transcription-coupled nucleotide-excision repair / positive regulation of gluconeogenesis / positive regulation of DNA repair / DNA damage checkpoint signaling / positive regulation of RNA splicing / regulation of DNA-templated transcription elongation / transcription elongation factor complex / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / response to gamma radiation / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / promoter-specific chromatin binding / P-body / Recognition of DNA damage by PCNA-containing replication complex / helicase activity / base-excision repair / regulation of circadian rhythm Similarity search - Function | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Biological species | Homo sapiens (human)![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 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: 2021Title: 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. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Structure visualization
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| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 7oob.cif.gz | 1.9 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb7oob.ent.gz | 1.5 MB | Display | PDB format |
| PDBx/mmJSON format | 7oob.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 7oob_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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| Full document | 7oob_full_validation.pdf.gz | 1.4 MB | Display | |
| Data in XML | 7oob_validation.xml.gz | 146.1 KB | Display | |
| Data in CIF | 7oob_validation.cif.gz | 234.6 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oo/7oob ftp://data.pdbj.org/pub/pdb/validation_reports/oo/7oob | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 13009MC ![]() 7oo3C ![]() 7oopC ![]() 7opcC ![]() 7opdC M: map data used to model this data C: citing same article ( |
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| Similar structure data |
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Links
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Assembly
| Deposited unit | ![]()
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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) ![]() |
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| #3: Protein | Mass: 31439.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #5: Protein | Mass: 24644.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #6: Protein | Mass: 14477.001 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #7: Protein | Mass: 19314.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #9: Protein | Mass: 14541.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-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) ![]() |
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| #4: Protein | Mass: 16331.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #11: Protein | Mass: 13310.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #12: Protein | Mass: 7018.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #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) ![]() |
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| #10: Protein | Mass: 7655.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-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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| Has protein modification | N |
-Experimental details
-Experiment
| Experiment | Method: ELECTRON MICROSCOPY |
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| EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
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| Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||
| Source (natural) |
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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 % |
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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 FIELD |
| 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 |
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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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About Yorodumi




Homo sapiens (human)

Germany, 2items
Citation
UCSF Chimera
















PDBj










































Trichoplusia ni (cabbage looper)
