+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13004 | |||||||||
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Title | Pol II-CSB-CSA-DDB1-UVSSA (Structure1) | |||||||||
Map data | Main map. | |||||||||
Sample |
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Keywords | transcription / DNA repair | |||||||||
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 / single strand break repair / regulation of transcription elongation by RNA polymerase II / DNA protection / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation ...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 protection / 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 / positive regulation by virus of viral protein levels in host cell / 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 / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / double-strand break repair via classical nonhomologous end joining / response to superoxide / photoreceptor cell maintenance / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / 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 / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / Cul4B-RING E3 ubiquitin ligase complex / organelle membrane / negative regulation of reproductive process / negative regulation of developmental process / protein tyrosine kinase activator activity / positive regulation of transcription by RNA polymerase I / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA polymerase III activity / RNA polymerase II complex binding / site of DNA damage / RNA Polymerase I Transcription Initiation / cullin family protein binding / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / viral release from host cell / response to X-ray / RNA polymerase II activity / positive regulation of double-strand break repair via homologous recombination / ectopic germ cell programmed cell death / pyrimidine dimer repair / transcription-coupled nucleotide-excision repair / transcription elongation by RNA polymerase I / positive regulation of transcription initiation by RNA polymerase II / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / ATP-dependent activity, acting on DNA / positive regulation of translational initiation / protein autoubiquitination / proteasomal protein catabolic process / positive regulation of viral genome replication / RNA polymerase II, core complex / response to UV / JNK cascade / positive regulation of gluconeogenesis / translation initiation factor binding / positive regulation of DNA repair / neurogenesis / positive regulation of RNA splicing / transcription elongation factor complex / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / regulation of DNA-templated transcription elongation / DNA damage checkpoint signaling / helicase activity / nucleotide-excision repair / promoter-specific chromatin binding Similarity search - Function | |||||||||
Biological species | Sus scrofa (pig) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 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_13004.map.gz | 114.3 MB | EMDB map data format | |
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Header (meta data) | emd-13004-v30.xml emd-13004.xml | 65.8 KB 65.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13004_fsc.xml | 14.1 KB | Display | FSC data file |
Images | emd_13004.png | 159.2 KB | ||
Masks | emd_13004_msk_1.map emd_13004_msk_2.map emd_13004_msk_3.map emd_13004_msk_4.map emd_13004_msk_5.map | 244.1 MB 244.1 MB 244.1 MB 244.1 MB 244.1 MB | Mask map | |
Filedesc metadata | emd-13004.cif.gz | 13.1 KB | ||
Others | emd_13004_additional_1.map.gz emd_13004_additional_10.map.gz emd_13004_additional_2.map.gz emd_13004_additional_3.map.gz emd_13004_additional_4.map.gz emd_13004_additional_5.map.gz emd_13004_additional_6.map.gz emd_13004_additional_7.map.gz emd_13004_additional_8.map.gz emd_13004_additional_9.map.gz emd_13004_half_map_1.map.gz emd_13004_half_map_2.map.gz | 216.5 MB 217 MB 194.2 MB 194.6 MB 194.2 MB 194.6 MB 194.7 MB 194.6 MB 194.8 MB 194.8 MB 225.9 MB 226 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13004 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13004 | HTTPS FTP |
-Validation report
Summary document | emd_13004_validation.pdf.gz | 903.3 KB | Display | EMDB validaton report |
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Full document | emd_13004_full_validation.pdf.gz | 902.9 KB | Display | |
Data in XML | emd_13004_validation.xml.gz | 21 KB | Display | |
Data in CIF | emd_13004_validation.cif.gz | 27.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13004 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13004 | HTTPS FTP |
-Related structure data
Related structure data | 7oo3MC 7oobC 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_13004.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Main map. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
+Mask #5
+Additional map: Half map corresponding to the map focused refined on CSA-UVSSA.
+Additional map: Half map corresponding to the map focused refined on CSA-UVSSA.
+Additional map: Half map corresponding to the map focused refined on CSB.
+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 CSA-DDB1.
+Additional map: Half map corresponding to the map focused refined on DDB1.
+Additional map: Half map corresponding to the map focused refined on DDB1.
+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.
+Half map: Half map corresponding to the main map.
+Half map: Half map corresponding to the main map.
-Sample components
+Entire : RNA polymerase II elongation complex with CSB, CSA-DDB1 and UVSSA.
+Supramolecule #1: RNA polymerase II elongation complex with CSB, CSA-DDB1 and UVSSA.
+Supramolecule #2: DNA directed RNA polymerase
+Supramolecule #3: NTS, TS & RNA
+Supramolecule #4: DNA Repair proteins, CSB element and scaffold protein
+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 #16: DNA excision repair protein ERCC-8
+Macromolecule #17: DNA excision repair protein ERCC-6
+Macromolecule #18: CSB element
+Macromolecule #19: UV-stimulated scaffold protein A
+Macromolecule #20: DNA damage-binding protein 1
+Macromolecule #13: NTS
+Macromolecule #14: TS
+Macromolecule #15: RNA
+Macromolecule #21: ZINC ION
+Macromolecule #22: MAGNESIUM 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: 10300 / Average electron dose: 40.4 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 |