+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13015 | |||||||||
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Title | Pol II-CSB-CRL4CSA-UVSSA-SPT6-PAF (Structure 4) | |||||||||
Map data | The main map. | |||||||||
Sample |
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Function / homology | Function and homology information Prolactin receptor signaling / negative regulation of double-strand break repair via nonhomologous end joining / regulation of transcription-coupled nucleotide-excision repair / Regulation of BACH1 activity / Recognition of DNA damage by PCNA-containing replication complex / blastocyst growth / inner cell mass cell differentiation / Ski complex / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex ...Prolactin receptor signaling / negative regulation of double-strand break repair via nonhomologous end joining / regulation of transcription-coupled nucleotide-excision repair / Regulation of BACH1 activity / Recognition of DNA damage by PCNA-containing replication complex / blastocyst growth / inner cell mass cell differentiation / Ski complex / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / RNA polymerase II C-terminal domain phosphoserine binding / Dual Incision in GG-NER / Dual incision in TC-NER / positive regulation of mRNA 3'-end processing / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / nucleotide-excision repair complex / mRNA decay by 3' to 5' exoribonuclease / Regulation of RAS by GAPs / Regulation of RUNX2 expression and activity / Degradation of GLI1 by the proteasome / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of DVL / Orc1 removal from chromatin / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / Cdc73/Paf1 complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Hedgehog 'on' state / regulation of isotype switching / Degradation of beta-catenin by the destruction complex / regulation of mRNA export from nucleus / regulation of muscle cell differentiation / endodermal cell fate commitment / eukaryotic initiation factor 4E binding / negative regulation of myeloid cell differentiation / negative regulation of granulocyte differentiation / blastocyst hatching / Interleukin-1 signaling / positive regulation of cell cycle G1/S phase transition / regulation of transcription elongation by RNA polymerase II / KEAP1-NFE2L2 pathway / anaphase-promoting complex / nucleosome organization / GLI3 is processed to GLI3R by the proteasome / B-WICH complex / single strand break repair / trophectodermal cell differentiation / regulation of mRNA processing / cullin-RING-type E3 NEDD8 transferase / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / cullin-RING ubiquitin ligase complex / positive regulation by virus of viral protein levels in host cell / DNA protection / regulation of DNA damage checkpoint / regulation of nucleotide-excision repair / mRNA 3'-end processing / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / 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 / 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 / spindle assembly involved in female meiosis / 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 / blastocyst formation / Cul4-RING E3 ubiquitin ligase complex / VCB complex / photoreceptor cell maintenance / UV-damage excision repair / positive regulation of protein autoubiquitination / : / : Similarity search - Function | |||||||||
Biological species | Sus scrofa (pig) / Homo sapiens (human) / Mus musculus (house mouse) / Pig (pig) | |||||||||
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
-Related structure data
Related structure data | 7opcMC 7oo3C 7oobC 7oopC 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_13015.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. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 main map.
+Additional map: Half map corresponding to the map focused refined on CSB-CSA-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 PAF.
+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: Mask for PAF.
+Additional map: Half map corresponding to the main map.
+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...
+Additional map: Half map corresponding to the map focused refined on SPT6.
+Additional map: Half map corresponding to the map focused refined on CSB-CSA-DDB1.
+Additional map: Half map corresponding to the map focused refined on SPT6.
-Sample components
+Entire : Transcribing Pol II bound to CSB, CRL4CSA, UVSSA, PAF and SPT6.
+Supramolecule #1: Transcribing Pol II bound to CSB, CRL4CSA, UVSSA, PAF and SPT6.
+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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 81000 |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.4 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |