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Yorodumi- EMDB-15127: Structure of mammalian Pol II-DSIF-SPT6-PAF1-TFIIS-hexasome elong... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15127 | ||||||||||||
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Title | Structure of mammalian Pol II-DSIF-SPT6-PAF1-TFIIS-hexasome elongation complex | ||||||||||||
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Keywords | chromatin / rna polymerase II / nucleosome / TFIIS / transcription / elongation | ||||||||||||
Function / homology | Function and homology information blastocyst growth / inner cell mass cell differentiation / Ski complex / positive regulation of mRNA 3'-end processing / mRNA decay by 3' to 5' exoribonuclease / RNA polymerase II C-terminal domain phosphoserine binding / negative regulation of DNA-templated transcription, elongation / Cdc73/Paf1 complex / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / negative regulation of myeloid cell differentiation ...blastocyst growth / inner cell mass cell differentiation / Ski complex / positive regulation of mRNA 3'-end processing / mRNA decay by 3' to 5' exoribonuclease / RNA polymerase II C-terminal domain phosphoserine binding / negative regulation of DNA-templated transcription, elongation / Cdc73/Paf1 complex / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / negative regulation of myeloid cell differentiation / endodermal cell fate commitment / positive regulation of cell cycle G1/S phase transition / DSIF complex / blastocyst hatching / trophectodermal cell differentiation / regulation of transcription elongation by RNA polymerase II / 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 / mRNA 3'-end processing / positive regulation of DNA-templated transcription, elongation / Abortive elongation of HIV-1 transcript in the absence of Tat / stem cell population maintenance / transcription elongation-coupled chromatin remodeling / negative regulation of G1/S transition of mitotic cell cycle / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / interleukin-6-mediated signaling pathway / mRNA Capping / negative regulation of gene expression, epigenetic / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA polymerase III activity / RNA polymerase II complex binding / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / cell surface receptor signaling pathway via JAK-STAT / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / positive regulation of macroautophagy / RNA polymerase II transcribes snRNA genes / RNA polymerase II activity / protein localization to nucleus / positive regulation of Wnt signaling pathway / transcription-coupled nucleotide-excision repair / Tat-mediated elongation of the HIV-1 transcript / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / Formation of HIV-1 elongation complex containing HIV-1 Tat / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase II, core complex / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / negative regulation of fibroblast proliferation / RNA Polymerase II Pre-transcription Events / translation initiation factor binding / SH2 domain binding / rescue of stalled ribosome / TP53 Regulates Transcription of DNA Repair Genes / regulation of cell growth / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / transcription elongation by RNA polymerase II / P-body / Formation of the beta-catenin:TCF transactivating complex / Hedgehog 'on' state / protein destabilization / euchromatin / fibrillar center / ribonucleoside binding / Wnt signaling pathway / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / structural constituent of chromatin / negative regulation of epithelial cell proliferation / nucleosome Similarity search - Function | ||||||||||||
Biological species | Sus scrofa (pig) / Homo sapiens (human) / Xenopus laevis (African clawed frog) / synthetic construct (others) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||
Authors | Farnung L / Ochmann M / Garg G / Vos SM / Cramer P | ||||||||||||
Funding support | European Union, Germany, 3 items
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Citation | Journal: Mol Cell / Year: 2022 Title: Structure of a backtracked hexasomal intermediate of nucleosome transcription. Authors: Lucas Farnung / Moritz Ochmann / Gaurika Garg / Seychelle M Vos / Patrick Cramer / Abstract: During gene transcription, RNA polymerase II (RNA Pol II) passes nucleosomes with the help of various elongation factors. Here, we show that RNA Pol II achieves efficient nucleosome passage when the ...During gene transcription, RNA polymerase II (RNA Pol II) passes nucleosomes with the help of various elongation factors. Here, we show that RNA Pol II achieves efficient nucleosome passage when the human elongation factors DSIF, PAF1 complex (PAF), RTF1, SPT6, and TFIIS are present. The cryo-EM structure of an intermediate of the nucleosome passage shows a partially unraveled hexasome that lacks the proximal H2A-H2B dimer and interacts with the RNA Pol II jaw, DSIF, and the CTR9trestle helix. RNA Pol II adopts a backtracked state with the RNA 3' end dislodged from the active site and bound in the RNA Pol II pore. Additional structures and biochemical data show that human TFIIS enters the RNA Pol II pore and stimulates the cleavage of the backtracked RNA and nucleosome passage. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15127.map.gz | 103.1 MB | EMDB map data format | |
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Header (meta data) | emd-15127-v30.xml emd-15127.xml | 49.8 KB 49.8 KB | Display Display | EMDB header |
Images | emd_15127.png | 72.5 KB | ||
Filedesc metadata | emd-15127.cif.gz | 14.4 KB | ||
Others | emd_15127_half_map_1.map.gz emd_15127_half_map_2.map.gz | 141.4 MB 141.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15127 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15127 | HTTPS FTP |
-Validation report
Summary document | emd_15127_validation.pdf.gz | 989.8 KB | Display | EMDB validaton report |
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Full document | emd_15127_full_validation.pdf.gz | 989.4 KB | Display | |
Data in XML | emd_15127_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | emd_15127_validation.cif.gz | 17.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15127 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15127 | HTTPS FTP |
-Related structure data
Related structure data | 8a3yMC 8a40C C: citing same article (ref.) M: atomic model generated by this map |
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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_15127.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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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
-Half map: Overall
File | emd_15127_half_map_1.map | ||||||||||||
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Annotation | Overall | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Overall
File | emd_15127_half_map_2.map | ||||||||||||
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Annotation | Overall | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Mammalian Pol II-TFIIS elongation complex
+Supramolecule #1: Mammalian Pol II-TFIIS elongation 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 polymerases I, II, and III subunit RPABC2
+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: DNA-directed RNA polymerase II subunit RPB11-a
+Macromolecule #12: RNA polymerase II subunit K
+Macromolecule #13: SPT6
+Macromolecule #16: RNA polymerase-associated protein CTR9 homolog,RNA polymerase-ass...
+Macromolecule #17: RNA polymerase-associated protein RTF1 homolog
+Macromolecule #19: RNA polymerase II-associated factor 1 homolog
+Macromolecule #20: WD repeat-containing protein 61
+Macromolecule #21: Parafibromin
+Macromolecule #22: Transcription elongation factor SPT4
+Macromolecule #23: Transcription elongation factor SPT5
+Macromolecule #24: Histone H3.2
+Macromolecule #25: Histone H4
+Macromolecule #26: Histone H2A
+Macromolecule #27: Histone H2B
+Macromolecule #14: Non-template DNA
+Macromolecule #18: RNA, Template DNA
+Macromolecule #15: RNA, Template DNA
+Macromolecule #28: ZINC ION
+Macromolecule #29: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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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: 50.0 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: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 30000 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |