+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13009 | |||||||||
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Title | Pol II-CSB-CSA-DDB1-UVSSA-ADPBeF3 (Structure2) | |||||||||
Map data | The main map. | |||||||||
Sample |
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Keywords | transcription / DNA repair | |||||||||
Function / homology | Function and homology information double-strand break repair via synthesis-dependent strand annealing / regulation of transcription-coupled nucleotide-excision repair / negative regulation of double-strand break repair via nonhomologous end joining / nucleotide-excision repair complex / B-WICH complex / single strand break repair / DNA translocase activity / regulation of transcription elongation by RNA polymerase II / DNA protection / positive regulation by virus of viral protein levels in host cell ...double-strand break repair via synthesis-dependent strand annealing / regulation of transcription-coupled nucleotide-excision repair / negative regulation of double-strand break repair via nonhomologous end joining / nucleotide-excision repair complex / B-WICH complex / single strand break repair / DNA translocase activity / regulation of transcription elongation by RNA polymerase II / 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 / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / epigenetic programming in the zygotic pronuclei / double-strand break repair via classical nonhomologous end joining / spindle assembly involved in female meiosis / response to superoxide / photoreceptor cell maintenance / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / reciprocal meiotic recombination / positive regulation of DNA-templated transcription, elongation / response to UV-B / RNA polymerase binding / ATP-dependent chromatin remodeler activity / 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 / RNA Polymerase I Transcription Initiation / organelle membrane / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / cullin family protein binding / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / viral release from host cell / positive regulation of double-strand break repair via homologous recombination / response to X-ray / pyrimidine dimer repair / transcription elongation by RNA polymerase I / positive regulation of transcription initiation by RNA polymerase II / ectopic germ cell programmed cell death / proteasomal protein catabolic process / positive regulation of translational initiation / ATP-dependent activity, acting on DNA / RNA polymerase I complex / protein autoubiquitination / RNA polymerase III complex / positive regulation of viral genome replication / transcription-coupled nucleotide-excision repair / RNA polymerase III activity / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA polymerase II activity / response to UV / JNK cascade / positive regulation of gluconeogenesis / translation initiation factor binding / positive regulation of DNA repair / helicase activity / neurogenesis / positive regulation of RNA splicing / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / transcription elongation factor complex / DNA damage checkpoint signaling Similarity search - Function | |||||||||
Biological species | Sus scrofa (pig) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Kokic G / Cramer P | |||||||||
Funding support | Germany, 2 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_13009.map.gz | 95.4 MB | EMDB map data format | |
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Header (meta data) | emd-13009-v30.xml emd-13009.xml | 55 KB 55 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13009_fsc.xml | 14.1 KB | Display | FSC data file |
Images | emd_13009.png | 150.5 KB | ||
Masks | emd_13009_msk_1.map emd_13009_msk_2.map emd_13009_msk_3.map emd_13009_msk_4.map | 244.1 MB 244.1 MB 244.1 MB 244.1 MB | Mask map | |
Filedesc metadata | emd-13009.cif.gz | 12.4 KB | ||
Others | emd_13009_additional_1.map.gz emd_13009_additional_2.map.gz emd_13009_additional_3.map.gz emd_13009_additional_4.map.gz emd_13009_additional_5.map.gz emd_13009_additional_6.map.gz emd_13009_half_map_1.map.gz emd_13009_half_map_2.map.gz | 195.8 MB 195.8 MB 194 MB 193.8 MB 194.6 MB 193.8 MB 221 MB 220.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13009 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13009 | HTTPS FTP |
-Validation report
Summary document | emd_13009_validation.pdf.gz | 760.8 KB | Display | EMDB validaton report |
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Full document | emd_13009_full_validation.pdf.gz | 760.4 KB | Display | |
Data in XML | emd_13009_validation.xml.gz | 21 KB | Display | |
Data in CIF | emd_13009_validation.cif.gz | 27.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13009 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13009 | HTTPS FTP |
-Related structure data
Related structure data | 7oobMC 7oo3C 7oopC 7opcC 7opdC M: atomic model generated by this map C: citing same article (ref.) |
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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_13009.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | The main map. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
+Mask #1
+Mask #2
+Mask #3
+Mask #4
+Additional map: Half map corresponding to the map focused refined on Pol II.
+Additional map: Half map corresponding to the map focused refined on Pol II.
+Additional map: Half map corresponding to the map focused refined on CSA-DDB1.
+Additional map: Half map corresponding to the map focused refined on CSA-DDB1.
+Additional map: Half map corresponding to the map focused refined on CSB.
+Additional map: Half map corresponding to the map focused refined on CSB.
+Half map: Half map corresponding to the main map.
+Half map: Half map corresponding to the main map.
-Sample components
+Entire : Complex between the transcribing RNA polymerase II and TCR factor...
+Supramolecule #1: Complex between the transcribing RNA polymerase II and TCR factor...
+Supramolecule #2: DNA-directed RNA polymerase with RNA_pol_L_2 and RNA polymerase
+Supramolecule #3: DNA excision repair protein ERCC-6 and ERCC-8, DNA damage-binding...
+Supramolecule #4: NTS, RNA, TS
+Macromolecule #1: DNA-directed RNA polymerase II subunit RPB1
+Macromolecule #2: DNA-directed RNA polymerase subunit beta
+Macromolecule #3: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #4: RPOL4c domain-containing protein
+Macromolecule #5: DNA-directed RNA polymerase II subunit E
+Macromolecule #6: DNA-directed RNA polymerase II subunit F
+Macromolecule #7: DNA-directed RNA polymerase II subunit RPB7
+Macromolecule #8: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #9: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #10: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #11: RNA_pol_L_2 domain-containing protein
+Macromolecule #12: RNA polymerase II subunit K
+Macromolecule #13: DNA excision repair protein ERCC-6
+Macromolecule #14: DNA damage-binding protein 1
+Macromolecule #18: DNA excision repair protein ERCC-8
+Macromolecule #15: NTS
+Macromolecule #16: TS
+Macromolecule #17: RNA
+Macromolecule #19: ZINC ION
+Macromolecule #20: MAGNESIUM ION
+Macromolecule #21: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #22: BERYLLIUM TRIFLUORIDE ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R2/1 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 10940 / Average electron dose: 41.2 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |