+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13016 | |||||||||
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Title | Pol II-CSB-CRL4CSA-UVSSA-SPT6-PAF (Structure 5) | |||||||||
Map data | The main map. | |||||||||
Sample |
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Keywords | transcription / DNA repair / ubiquitin | |||||||||
Function / homology | Function and homology information Prolactin receptor signaling / blastocyst growth / Regulation of BACH1 activity / Recognition of DNA damage by PCNA-containing replication complex / negative regulation of double-strand break repair via nonhomologous end joining / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / regulation of transcription-coupled nucleotide-excision repair / inner cell mass cell differentiation / Dual Incision in GG-NER ...Prolactin receptor signaling / blastocyst growth / Regulation of BACH1 activity / Recognition of DNA damage by PCNA-containing replication complex / negative regulation of double-strand break repair via nonhomologous end joining / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / regulation of transcription-coupled nucleotide-excision repair / inner cell mass cell differentiation / Dual Incision in GG-NER / Dual incision in TC-NER / Ski complex / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / 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 / Regulation of RAS by GAPs / Regulation of RUNX2 expression and activity / Degradation of GLI1 by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of DVL / Orc1 removal from chromatin / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Cdc73/Paf1 complex / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Hedgehog 'on' state / regulation of isotype switching / negative regulation of granulocyte differentiation / regulation of muscle cell differentiation / Degradation of beta-catenin by the destruction complex / regulation of mRNA export from nucleus / negative regulation of myeloid cell differentiation / endodermal cell fate commitment / eukaryotic initiation factor 4E binding / : / Interleukin-1 signaling / positive regulation of cell cycle G1/S phase transition / blastocyst hatching / anaphase-promoting complex / KEAP1-NFE2L2 pathway / GLI3 is processed to GLI3R by the proteasome / B-WICH complex / trophectodermal cell differentiation / single strand break repair / Neddylation / cullin-RING-type E3 NEDD8 transferase / regulation of mRNA processing / Antigen processing: Ubiquitination & Proteasome degradation / regulation of transcription elongation by RNA polymerase II / nucleosome organization / cullin-RING ubiquitin ligase complex / 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 / regulation of DNA damage checkpoint / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Cul7-RING ubiquitin ligase complex / regulation of nucleotide-excision 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 - 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 / VCB complex / blastocyst formation / mRNA 3'-end processing / Cul4-RING E3 ubiquitin ligase complex / positive regulation of protein autoubiquitination / UV-damage excision repair / protein neddylation Similarity search - Function | |||||||||
Biological species | Sus scrofa (pig) / Homo sapiens (human) / Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 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
-Validation report
Summary document | emd_13016_validation.pdf.gz | 913.3 KB | Display | EMDB validaton report |
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Full document | emd_13016_full_validation.pdf.gz | 912.9 KB | Display | |
Data in XML | emd_13016_validation.xml.gz | 22.4 KB | Display | |
Data in CIF | emd_13016_validation.cif.gz | 29.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13016 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13016 | HTTPS FTP |
-Related structure data
Related structure data | 7opdMC 7oo3C 7oobC 7oopC 7opcC 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_13016.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | The 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
+Mask #6
+Additional map: Half map corresponding to the map focused refined...
+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 SPT6.
+Additional map: Half map corresponding to the map focused refined...
+Additional map: Half map corresponding to the map focused refined...
+Additional map: Half map corresponding to the map focused refined...
+Additional map: Half map corresponding to the map focused refined on PAF.
+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-CSB.
+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-CSB.
+Half map: Half map corresponding to the main map.
+Half map: Half map corresponding to the main map.
-Sample components
+Entire : Transcribing Pol II bound to TRC factors, SPT6 and PAF.
+Supramolecule #1: Transcribing Pol II bound to TRC factors, SPT6 and PAF.
+Supramolecule #2: DNA-directed RNA polymerase with RNA_pol_L_2 and RNA polymerase
+Supramolecule #3: Supplementary proteins
+Supramolecule #4: NTS, RNA, TS
+Supramolecule #5: E3 ubiquitin-protein ligase RBX1
+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 #27: Cullin-4A
+Macromolecule #28: E3 ubiquitin-protein ligase RBX1
+Macromolecule #14: NTS
+Macromolecule #18: TS
+Macromolecule #15: RNA
+Macromolecule #29: ZINC ION
+Macromolecule #30: 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) / 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 |