+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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Function / homology | Function and homology information 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 / regulation of transcription elongation by RNA polymerase II / single strand break repair / positive regulation by virus of viral protein levels in host cell / DNA protection / epigenetic programming in the zygotic pronuclei / B-WICH complex positively regulates rRNA expression ...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 / regulation of transcription elongation by RNA polymerase II / single strand break repair / positive regulation by virus of viral protein levels in host cell / DNA protection / epigenetic programming in the zygotic pronuclei / 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 / spindle assembly involved in female meiosis / 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 / double-strand break repair via classical nonhomologous end joining / 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 / : / Cul4-RING E3 ubiquitin ligase complex / photoreceptor cell maintenance / UV-damage excision repair / : / response to UV-B / ATP-dependent chromatin remodeler activity / RNA polymerase binding / positive regulation of DNA-templated transcription, elongation / 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 / Cul4A-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 / positive regulation of double-strand break repair via homologous recombination / positive regulation of transcription by RNA polymerase I / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / protein tyrosine kinase activator activity / negative regulation of reproductive process / negative regulation of developmental process / site of DNA damage / cullin family protein binding / RNA Polymerase I Transcription Initiation / transcription elongation by RNA polymerase I / positive regulation of translational initiation / RNA polymerase II activity / organelle membrane / response to X-ray / transcription-coupled nucleotide-excision repair / viral release from host cell / pyrimidine dimer repair / positive regulation of transcription initiation by RNA polymerase II / ectopic germ cell programmed cell death / RNA polymerase I complex / transcription by RNA polymerase I / positive regulation of viral genome replication / protein autoubiquitination / RNA polymerase III complex / ATP-dependent activity, acting on DNA / transcription by RNA polymerase III / RNA polymerase II, core complex / translation initiation factor binding / response to UV / positive regulation of gluconeogenesis / JNK cascade / positive regulation of DNA repair / neurogenesis / positive regulation of RNA splicing / transcription elongation factor complex / DNA-directed RNA polymerase complex / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / regulation of DNA-templated transcription elongation / DNA damage checkpoint signaling / helicase activity / promoter-specific chromatin binding / proteasomal protein catabolic process Similarity search - Function | |||||||||
Biological species | Sus scrofa (pig) / Homo sapiens (human) / Pig (pig) | |||||||||
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 | 54.4 KB 54.4 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 | |
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 |
-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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |