+Open data
-Basic information
Entry | Database: PDB / ID: 8b3f | |||||||||
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Title | Pol II-CSB-CSA-DDB1-ELOF1 | |||||||||
Components |
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Keywords | TRANSCRIPTION / DNA repair / ubiquitin / cryo-EM | |||||||||
Function / homology | Function and homology information double-strand break repair via synthesis-dependent strand annealing / regulation of transcription-coupled nucleotide-excision repair / negative regulation of double-strand break repair via nonhomologous end joining / nucleotide-excision repair complex / single strand break repair / B-WICH complex / DNA translocase activity / regulation of transcription elongation by RNA polymerase II / DNA protection / positive regulation by virus of viral protein levels in host cell ...double-strand break repair via synthesis-dependent strand annealing / regulation of transcription-coupled nucleotide-excision repair / negative regulation of double-strand break repair via nonhomologous end joining / nucleotide-excision repair complex / single strand break repair / B-WICH complex / DNA translocase activity / regulation of transcription elongation by RNA polymerase II / DNA protection / 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 / epigenetic programming in the zygotic pronuclei / double-strand break repair via classical nonhomologous end joining / 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 / photoreceptor cell maintenance / response to superoxide / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / reciprocal meiotic recombination / 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 / Cul4A-RING E3 ubiquitin ligase complex / WD40-repeat domain binding / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / positive regulation of transcription by RNA polymerase I / protein tyrosine kinase activator activity / : / negative regulation of reproductive process / negative regulation of developmental process / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / site of DNA damage / RNA polymerase III activity / RNA Polymerase I Transcription Initiation / organelle membrane / cullin family protein binding / viral release from host cell / response to X-ray / positive regulation of double-strand break repair via homologous recombination / pyrimidine dimer repair / transcription elongation by RNA polymerase I / RNA polymerase II activity / positive regulation of transcription initiation by RNA polymerase II / ectopic germ cell programmed cell death / proteasomal protein catabolic process / ATP-dependent activity, acting on DNA / RNA polymerase I complex / protein autoubiquitination / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / positive regulation of viral genome replication / tRNA transcription by RNA polymerase III / RNA polymerase II, core complex / translation elongation factor activity / RNA polymerase I activity / response to UV / JNK cascade / positive regulation of gluconeogenesis / translation initiation factor binding / positive regulation of DNA repair / neurogenesis / helicase activity / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / transcription elongation factor complex / DNA damage checkpoint signaling / regulation of DNA-templated transcription elongation / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Sus scrofa domesticus (domestic pig) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Kokic, G. / Cramer, P. | |||||||||
Funding support | Germany, European Union, 2items
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Citation | Journal: To Be Published Title: Pol II-CSB-CSA-DDB1-ELOF1 structure. Authors: Kokic, G. / Cramer, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8b3f.cif.gz | 1.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8b3f.ent.gz | 1.6 MB | Display | PDB format |
PDBx/mmJSON format | 8b3f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8b3f_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8b3f_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8b3f_validation.xml.gz | 148.3 KB | Display | |
Data in CIF | 8b3f_validation.cif.gz | 233.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/8b3f ftp://data.pdbj.org/pub/pdb/validation_reports/b3/8b3f | HTTPS FTP |
-Related structure data
Related structure data | 15826MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-DNA-directed RNA polymerase ... , 7 types, 7 molecules ABCEFGI
#1: Protein | Mass: 217450.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) References: UniProt: A0A7M4DUC2, DNA-directed RNA polymerase |
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#2: Protein | Mass: 133201.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) References: UniProt: A0A0B8RVL1, DNA-directed RNA polymerase |
#3: Protein | Mass: 31439.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: A0A481DF93 |
#5: Protein | Mass: 24644.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic 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 domesticus (domestic 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 domesticus (domestic pig) |
#9: Protein | Mass: 14541.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: P60899 |
-RNA polymerase II subunit ... , 2 types, 2 molecules DL
#4: Protein | Mass: 16331.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: A0A287ADR4 |
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#12: Protein | Mass: 7018.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: I3LN51 |
-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 domesticus (domestic 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 domesticus (domestic pig) / References: UniProt: A0A7K6NXI9 |
-Protein , 3 types, 3 molecules KMd
#11: Protein | Mass: 13310.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: A0A4X1UK25 |
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#13: Protein | Mass: 9475.881 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ELOF1, hCG_29982 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A024R7E8 |
#19: Protein | Mass: 127097.469 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 |
-DNA chain , 2 types, 2 molecules NT
#14: DNA chain | Mass: 16027.309 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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#16: DNA chain | Mass: 15824.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
-RNA chain , 1 types, 1 molecules P
#15: RNA chain | Mass: 3264.036 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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-DNA excision repair protein ERCC- ... , 2 types, 2 molecules ab
#17: 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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#18: Protein | Mass: 168945.797 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 |
-Non-polymers , 2 types, 10 molecules
#20: Chemical | ChemComp-ZN / #21: 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
Component | Name: Pol II-CSB-CSA-DDB1-ELOF1 complex. / Type: COMPLEX / Entity ID: #1-#19 / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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 defocus max: 3000 nm / Nominal defocus min: 140 nm |
Image recording | Electron dose: 42 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 220655 / Symmetry type: POINT | ||||||||||||||||||||||||
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