+Open data
-Basic information
Entry | Database: PDB / ID: 7opc | |||||||||
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Title | Pol II-CSB-CRL4CSA-UVSSA-SPT6-PAF (Structure 4) | |||||||||
Components |
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Keywords | TRANSCRIPTION / DNA repair / ubiquitin | |||||||||
Function / homology | Function and homology information Prolactin receptor signaling / Regulation of BACH1 activity / negative regulation of double-strand break repair via nonhomologous end joining / Recognition of DNA damage by PCNA-containing replication complex / regulation of transcription-coupled nucleotide-excision repair / blastocyst growth / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / inner cell mass cell differentiation / Dual Incision in GG-NER ...Prolactin receptor signaling / Regulation of BACH1 activity / negative regulation of double-strand break repair via nonhomologous end joining / Recognition of DNA damage by PCNA-containing replication complex / regulation of transcription-coupled nucleotide-excision repair / blastocyst growth / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / inner cell mass cell differentiation / Dual Incision in GG-NER / Dual incision in TC-NER / Ski complex / Formation of Incision Complex in GG-NER / positive regulation of mRNA 3'-end processing / Gap-filling DNA repair synthesis and ligation in TC-NER / mRNA decay by 3' to 5' exoribonuclease / RNA polymerase II C-terminal domain phosphoserine binding / nucleotide-excision repair complex / 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 / 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 / negative regulation of granulocyte differentiation / regulation of isotype switching / regulation of muscle cell differentiation / Degradation of beta-catenin by the destruction complex / endodermal cell fate commitment / regulation of mRNA export from nucleus / eukaryotic initiation factor 4E binding / negative regulation of myeloid cell differentiation / blastocyst hatching / : / Interleukin-1 signaling / positive regulation of cell cycle G1/S phase transition / KEAP1-NFE2L2 pathway / anaphase-promoting complex / GLI3 is processed to GLI3R by the proteasome / B-WICH complex / trophectodermal cell differentiation / single strand break repair / protein tyrosine kinase activator activity / cullin-RING-type E3 NEDD8 transferase / Neddylation / regulation of mRNA processing / nucleosome organization / cullin-RING ubiquitin ligase complex / regulation of transcription elongation by RNA polymerase II / Antigen processing: Ubiquitination & Proteasome degradation / DNA protection / regulation of DNA damage checkpoint / positive regulation by virus of viral protein levels in host cell / 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 / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / 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 / regulation of nucleotide-excision repair / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / double-strand break repair via classical nonhomologous end joining / photoreceptor cell maintenance / response to superoxide / VCB complex / positive regulation of protein autoubiquitination / blastocyst formation / Cul4-RING E3 ubiquitin ligase complex / mRNA 3'-end processing / UV-damage excision repair Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) Sus scrofa (pig) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | |||||||||
Authors | Kokic, G. / Cramer, P. | |||||||||
Funding support | Germany, 2items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7opc.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7opc.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 7opc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7opc_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7opc_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7opc_validation.xml.gz | 213.2 KB | Display | |
Data in CIF | 7opc_validation.cif.gz | 355.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/7opc ftp://data.pdbj.org/pub/pdb/validation_reports/op/7opc | HTTPS FTP |
-Related structure data
Related structure data | 13015MC 7oo3C 7oobC 7oopC 7opdC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-DNA-directed RNA polymerase II subunit ... , 6 types, 6 molecules ACEFGI
#1: Protein | Mass: 217450.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P11414 |
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#3: Protein | Mass: 31439.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LCH3 |
#5: Protein | Mass: 24644.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LSI7 |
#6: Protein | Mass: 14477.001 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SKN8 |
#7: Protein | Mass: 19314.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LJZ9 |
#9: Protein | Mass: 14541.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P60899 |
-Protein , 10 types, 10 molecules BDKMYZcdef
#2: Protein | Mass: 134041.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LGP4, DNA-directed RNA polymerase |
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#4: Protein | Mass: 16331.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287ADR4 |
#11: Protein | Mass: 13310.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1UK25 |
#13: Protein | Mass: 199602.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SUPT6H, KIAA0162, SPT6H / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q7KZ85 |
#21: Protein | Mass: 33617.465 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: WDR61 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9GZS3 |
#22: Protein | Mass: 60673.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDC73, C1orf28, HRPT2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6P1J9 |
#25: Protein | Mass: 80993.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UVSSA, KIAA1530 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q2YD98 |
#26: Protein | Mass: 127369.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q16531 |
#27: Protein | Mass: 88086.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CUL4A / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q13619 |
#28: Protein | Mass: 12289.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rbx1 / Production host: Trichoplusia ni (cabbage looper) References: UniProt: P62878, RING-type E3 ubiquitin transferase, cullin-RING-type E3 NEDD8 transferase |
-DNA-directed RNA polymerases I, II, and III subunit ... , 2 types, 2 molecules HJ
#8: Protein | Mass: 17162.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1ULF2 |
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#10: Protein | Mass: 7655.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VYD0 |
-RNA polymerase ... , 2 types, 2 molecules LV
#12: Protein | Mass: 7018.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LN51 |
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#20: Protein | Mass: 60052.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PAF1, PD2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8N7H5 |
-DNA chain , 2 types, 2 molecules NT
#14: DNA chain | Mass: 14494.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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#18: DNA chain | Mass: 14269.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
-RNA polymerase-associated protein ... , 2 types, 2 molecules SU
#17: Protein | Mass: 134510.203 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTR9, KIAA0155, SH2BP1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6PD62 |
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#19: Protein | Mass: 75514.172 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LEO1, RDL / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8WVC0 |
-DNA excision repair protein ERCC- ... , 2 types, 2 molecules ab
#23: Protein | Mass: 44107.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC8, CKN1, CSA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q13216 |
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#24: Protein | Mass: 168973.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC6, CSB / Production host: Trichoplusia ni (cabbage looper) References: UniProt: Q03468, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement |
-RNA chain / Protein/peptide , 2 types, 2 molecules PR
#15: RNA chain | Mass: 14490.756 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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#16: Protein/peptide | Mass: 3422.209 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper) |
-Non-polymers , 2 types, 9 molecules
#29: Chemical | ChemComp-ZN / #30: Chemical | ChemComp-MG / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||||||||
Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||||||
Specimen support | Grid type: Quantifoil R2/1 | ||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X |
Image recording | Electron dose: 40.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 100000 Details: Different number of particles was used for different focused refined maps. Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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