+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15825 | |||||||||
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Title | Structure of the Pol II-TCR-ELOF1 complex. | |||||||||
Map data | Main, composite map. The maps used to make the main map are deposited as additional EM maps. | |||||||||
Sample |
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Keywords | DNA repair / ubiquitin / transcription / cryo-EM | |||||||||
Function / homology | Function and homology information negative regulation of double-strand break repair via nonhomologous end joining / regulation of transcription-coupled nucleotide-excision repair / nucleotide-excision repair complex / B-WICH complex / single strand break repair / regulation of transcription elongation by RNA polymerase II / DNA protection / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape ...negative regulation of double-strand break repair via nonhomologous end joining / regulation of transcription-coupled nucleotide-excision repair / nucleotide-excision repair complex / B-WICH complex / single strand break repair / regulation of transcription elongation by RNA polymerase II / 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 / 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 / ubiquitin ligase complex scaffold activity / Cul4B-RING E3 ubiquitin ligase complex / negative regulation of reproductive process / negative regulation of developmental process / positive regulation of transcription by RNA polymerase I / protein tyrosine kinase activator activity / 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 / viral release from host cell / response to X-ray / RNA polymerase II activity / positive regulation of double-strand break repair via homologous recombination / ectopic germ cell programmed cell death / pyrimidine dimer repair / transcription-coupled nucleotide-excision repair / transcription elongation by RNA polymerase I / positive regulation of transcription initiation by RNA polymerase II / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / ATP-dependent activity, acting on DNA / protein autoubiquitination / proteasomal protein catabolic process / positive regulation of viral genome replication / translation elongation factor activity / RNA polymerase II, core complex / response to UV / JNK cascade / positive regulation of gluconeogenesis / translation initiation factor binding / positive regulation of DNA repair / neurogenesis / transcription elongation factor complex / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / regulation of DNA-templated transcription elongation / DNA damage checkpoint signaling / helicase activity / nucleotide-excision repair / response to gamma radiation / transcription initiation at RNA polymerase II promoter / Recognition of DNA damage by PCNA-containing replication complex / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA Damage Recognition in GG-NER Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Sus scrofa domesticus (domestic pig) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.6 Å | |||||||||
Authors | Kokic G / Cramer P | |||||||||
Funding support | Germany, European Union, 2 items
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Citation | Journal: To Be Published Title: Structure of the Pol II-TCR-ELOF1 complex. Authors: Kokic G / Cramer P | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15825.map.gz | 80.1 MB | EMDB map data format | |
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Header (meta data) | emd-15825-v30.xml emd-15825.xml | 54.1 KB 54.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15825_fsc.xml | 14.8 KB | Display | FSC data file |
Images | emd_15825.png | 73.7 KB | ||
Others | emd_15825_additional_1.map.gz emd_15825_additional_2.map.gz emd_15825_additional_3.map.gz emd_15825_additional_4.map.gz emd_15825_additional_5.map.gz emd_15825_additional_6.map.gz emd_15825_additional_7.map.gz emd_15825_half_map_1.map.gz emd_15825_half_map_2.map.gz | 251.8 MB 227 MB 252 MB 1.7 MB 227 MB 255.1 MB 242.9 MB 258.4 MB 258.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15825 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15825 | HTTPS FTP |
-Validation report
Summary document | emd_15825_validation.pdf.gz | 710 KB | Display | EMDB validaton report |
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Full document | emd_15825_full_validation.pdf.gz | 709.6 KB | Display | |
Data in XML | emd_15825_validation.xml.gz | 22.4 KB | Display | |
Data in CIF | emd_15825_validation.cif.gz | 29.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15825 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15825 | HTTPS FTP |
-Related structure data
Related structure data | 8b3dMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_15825.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Main, composite map. The maps used to make the main map are deposited as additional EM maps. | ||||||||||||||||||||||||||||||||||||
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:
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-Supplemental data
-Additional map: Half map corresponding to the map focused refined on TCR-ELOF1.
File | emd_15825_additional_1.map | ||||||||||||
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Annotation | Half map corresponding to the map focused refined on TCR-ELOF1. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Half map corresponding to the map focused refined on Pol II.
File | emd_15825_additional_2.map | ||||||||||||
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Annotation | Half map corresponding to the map focused refined on Pol II. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Half map corresponding to the map focused refined on TCR-ELOF1.
File | emd_15825_additional_3.map | ||||||||||||
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Annotation | Half map corresponding to the map focused refined on TCR-ELOF1. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Map focused refined on the UVSSA Zn-finger.
File | emd_15825_additional_4.map | ||||||||||||
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Annotation | Map focused refined on the UVSSA Zn-finger. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Half map corresponding to the map focused refined on Pol II.
File | emd_15825_additional_5.map | ||||||||||||
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Annotation | Half map corresponding to the map focused refined on Pol II. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Map focused refined on the UVSSA C-terminus.
File | emd_15825_additional_6.map | ||||||||||||
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Annotation | Map focused refined on the UVSSA C-terminus. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Map focused refined on DDB1-CUL4A-RBX1.
File | emd_15825_additional_7.map | ||||||||||||
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Annotation | Map focused refined on DDB1-CUL4A-RBX1. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map corresponding to the main map.
File | emd_15825_half_map_1.map | ||||||||||||
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Annotation | Half map corresponding to the main map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map corresponding to the main map.
File | emd_15825_half_map_2.map | ||||||||||||
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Annotation | Half map corresponding to the main map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Pol II-TCR-ELOF1 complex.
+Supramolecule #1: Pol II-TCR-ELOF1 complex.
+Macromolecule #1: DNA-directed RNA polymerase subunit
+Macromolecule #2: DNA-directed RNA polymerase subunit beta
+Macromolecule #3: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #4: RNA polymerase II subunit D
+Macromolecule #5: DNA-directed RNA polymerase II subunit E
+Macromolecule #6: DNA-directed RNA polymerase II subunit F
+Macromolecule #7: 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 1 homolog
+Macromolecule #17: DNA excision repair protein ERCC-8
+Macromolecule #18: DNA excision repair protein ERCC-6
+Macromolecule #19: UV-stimulated scaffold protein A
+Macromolecule #20: DNA damage-binding protein 1
+Macromolecule #14: NTS
+Macromolecule #16: TS
+Macromolecule #15: RNA
+Macromolecule #21: ZINC ION
+Macromolecule #22: MAGNESIUM ION
+Macromolecule #23: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #24: BERYLLIUM TRIFLUORIDE ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 42.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.14400000000000002 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |