+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13010 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Pol II-CSB-CSA-DDB1-UVSSA-PAF-SPT6 (Structure 3) | |||||||||
Map data | The main map. | |||||||||
Sample |
| |||||||||
Keywords | transcription / DNA repair / TCR | |||||||||
Function / homology | Function and homology information blastocyst growth / negative regulation of double-strand break repair via nonhomologous end joining / regulation of transcription-coupled nucleotide-excision repair / inner cell mass cell differentiation / Ski complex / positive regulation of mRNA 3'-end processing / nucleotide-excision repair complex / mRNA decay by 3' to 5' exoribonuclease / RNA polymerase II C-terminal domain phosphoserine binding / Cdc73/Paf1 complex ...blastocyst growth / negative regulation of double-strand break repair via nonhomologous end joining / regulation of transcription-coupled nucleotide-excision repair / inner cell mass cell differentiation / Ski complex / positive regulation of mRNA 3'-end processing / nucleotide-excision repair complex / mRNA decay by 3' to 5' exoribonuclease / RNA polymerase II C-terminal domain phosphoserine binding / Cdc73/Paf1 complex / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / regulation of isotype switching / regulation of muscle cell differentiation / regulation of mRNA export from nucleus / negative regulation of myeloid cell differentiation / endodermal cell fate commitment / : / positive regulation of cell cycle G1/S phase transition / blastocyst hatching / B-WICH complex / trophectodermal cell differentiation / single strand break repair / regulation of mRNA processing / regulation of transcription elongation by RNA polymerase II / nucleosome organization / 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 / blastocyst formation / mRNA 3'-end processing / 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 / stem cell population maintenance / transcription elongation-coupled chromatin remodeling / ubiquitin ligase complex scaffold activity / Cul4B-RING E3 ubiquitin ligase complex / negative regulation of G1/S transition of mitotic cell cycle / interleukin-6-mediated signaling pathway / organelle membrane / negative regulation of gene expression, epigenetic / 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 / cell surface receptor signaling pathway via JAK-STAT / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / viral release from host cell / response to X-ray / RNA polymerase II activity / protein localization to nucleus / positive regulation of double-strand break repair via homologous recombination / positive regulation of Wnt signaling pathway / ectopic germ cell programmed cell death Similarity search - Function | |||||||||
Biological species | Sus scrofa (pig) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Kokic G / Cramer P | |||||||||
Funding support | Germany, 2 items
| |||||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
-Validation report
Summary document | emd_13010_validation.pdf.gz | 941.2 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_13010_full_validation.pdf.gz | 940.7 KB | Display | |
Data in XML | emd_13010_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | emd_13010_validation.cif.gz | 27.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13010 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13010 | HTTPS FTP |
-Related structure data
Related structure data | 7oopMC 7oo3C 7oobC 7opcC 7opdC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_13010.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | The main map. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-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 SPT6.
+Additional map: Half map corresponding to the map focused refined on PAF.
+Additional map: Half map corresponding to the map focused refined on SPT6.
+Additional map: Half map corresponding to the map focused refined on PAF.
+Additional map: Half map corresponding to the map focused refined on CSA-DDB1-CSB.
+Additional map: Half map corresponding to the map focused refined on CSA-DDB1-CSB.
+Additional map: Half map corresponding to the map focused refined on CSA-UVSSA.
+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: Mask for Pol II.
+Additional map: Half map corresponding to the map focused refined...
+Additional map: Half map corresponding to the map focused refined...
+Half map: Half map corresponding to the main map.
+Half map: Half map corresponding to the main map.
-Sample components
+Entire : Complex between transcribing Pol II, TCR factors and elongation f...
+Supramolecule #1: Complex between transcribing Pol II, TCR factors and elongation f...
+Supramolecule #2: DNA-directed RNA polymerase with RNA_pol_L_2 and RNA polymerase
+Supramolecule #3: Supplementory proteins
+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: Transcription elongation factor SPT6
+Macromolecule #16: LEO1 helix
+Macromolecule #17: RNA polymerase-associated protein CTR9 homolog
+Macromolecule #19: RNA polymerase-associated protein LEO1
+Macromolecule #20: RNA polymerase II-associated factor 1 homolog
+Macromolecule #21: WD repeat-containing protein 61
+Macromolecule #22: Parafibromin
+Macromolecule #23: DNA excision repair protein ERCC-8
+Macromolecule #24: DNA excision repair protein ERCC-6
+Macromolecule #25: UV-stimulated scaffold protein A
+Macromolecule #26: DNA damage-binding protein 1
+Macromolecule #14: NTS
+Macromolecule #18: TS
+Macromolecule #15: RNA
+Macromolecule #27: ZINC ION
+Macromolecule #28: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL |
---|---|
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 |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 8365 / 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 / Nominal magnification: 81000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |