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Yorodumi- EMDB-26621: Pol II-DSIF-SPT6-PAF1c-TFIIS-nucleosome complex (stalled at +38) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26621 | |||||||||
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Title | Pol II-DSIF-SPT6-PAF1c-TFIIS-nucleosome complex (stalled at +38) | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information blastocyst growth / inner cell mass cell differentiation / Ski complex / RNA polymerase II C-terminal domain phosphoserine binding / positive regulation of mRNA 3'-end processing / mRNA decay by 3' to 5' exoribonuclease / negative regulation of DNA-templated transcription, elongation / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / Cdc73/Paf1 complex / regulation of isotype switching ...blastocyst growth / inner cell mass cell differentiation / Ski complex / RNA polymerase II C-terminal domain phosphoserine binding / positive regulation of mRNA 3'-end processing / mRNA decay by 3' to 5' exoribonuclease / negative regulation of DNA-templated transcription, elongation / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / Cdc73/Paf1 complex / regulation of isotype switching / regulation of mRNA export from nucleus / regulation of muscle cell differentiation / endodermal cell fate commitment / negative regulation of myeloid cell differentiation / blastocyst hatching / positive regulation of cell cycle G1/S phase transition / DSIF complex / regulation of transcription elongation by RNA polymerase II / nucleosome organization / trophectodermal cell differentiation / regulation of mRNA processing / nuclear DNA-directed RNA polymerase complex / mRNA 3'-end processing / 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 / blastocyst formation / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / nuclear lumen / Abortive elongation of HIV-1 transcript in the absence of Tat / positive regulation of DNA-templated transcription, elongation / : / transcription elongation-coupled chromatin remodeling / negative regulation of gene expression, epigenetic / negative regulation of G1/S transition of mitotic cell cycle / stem cell population maintenance / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / transcription factor TFIID complex / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / interleukin-6-mediated signaling pathway / RNA polymerase II complex binding / negative regulation of transcription elongation by RNA polymerase II / 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 macroautophagy / organelle membrane / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / protein localization to nucleus / positive regulation of Wnt signaling pathway / nucleosome binding / mRNA transport / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / RNA polymerase I complex / RNA polymerase III complex / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase II, core complex / rescue of stalled ribosome / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / negative regulation of fibroblast proliferation / RNA Polymerase II Pre-transcription Events / SH2 domain binding / transcription elongation factor complex / DNA-directed RNA polymerase complex / RNA splicing / regulation of cell growth / transcription elongation by RNA polymerase II / DNA-templated transcription initiation / TP53 Regulates Transcription of DNA Repair Genes Similarity search - Function | |||||||||
Biological species | pig (pig) / Sus scrofa (pig) / Homo sapiens (human) / Xenopus laevis (African clawed frog) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Filipovski M / Vos SM / Farnung L | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Science / Year: 2022 Title: Structural basis of nucleosome retention during transcription elongation. Authors: Martin Filipovski / Jelly H M Soffers / Seychelle M Vos / Lucas Farnung / Abstract: In eukaryotes, RNA polymerase (Pol) II transcribes chromatin and must move past nucleosomes, often resulting in nucleosome displacement. How Pol II unwraps the DNA from nucleosomes to allow ...In eukaryotes, RNA polymerase (Pol) II transcribes chromatin and must move past nucleosomes, often resulting in nucleosome displacement. How Pol II unwraps the DNA from nucleosomes to allow transcription and how DNA rewraps to retain nucleosomes has been unclear. Here, we report the 3.0-angstrom cryo-electron microscopy structure of a mammalian Pol II-DSIF-SPT6-PAF1c-TFIIS-nucleosome complex stalled 54 base pairs within the nucleosome. The structure provides a mechanistic basis for nucleosome retention during transcription elongation where upstream DNA emerging from the Pol II cleft has rewrapped the proximal side of the nucleosome. The structure uncovers a direct role for Pol II and transcription elongation factors in nucleosome retention and explains how nucleosomes are retained to prevent the disruption of chromatin structure across actively transcribed genes. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26621.map.gz | 318.1 MB | EMDB map data format | |
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Header (meta data) | emd-26621-v30.xml emd-26621.xml | 83.3 KB 83.3 KB | Display Display | EMDB header |
Images | emd_26621.png | 62.6 KB | ||
Masks | emd_26621_msk_1.map emd_26621_msk_2.map emd_26621_msk_3.map | 347.6 MB 347.6 MB 347.6 MB | Mask map | |
Others | emd_26621_additional_1.map.gz emd_26621_additional_10.map.gz emd_26621_additional_11.map.gz emd_26621_additional_12.map.gz emd_26621_additional_13.map.gz emd_26621_additional_14.map.gz emd_26621_additional_15.map.gz emd_26621_additional_16.map.gz emd_26621_additional_2.map.gz emd_26621_additional_3.map.gz emd_26621_additional_4.map.gz emd_26621_additional_5.map.gz emd_26621_additional_6.map.gz emd_26621_additional_7.map.gz emd_26621_additional_8.map.gz emd_26621_additional_9.map.gz | 328.2 MB 328.2 MB 322.3 MB 322.3 MB 322.3 MB 328.5 MB 173.1 MB 322.3 MB 322.6 MB 322.6 MB 173.1 MB 322.8 MB 327.5 MB 322.7 MB 168.6 MB 173.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26621 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26621 | HTTPS FTP |
-Related structure data
Related structure data | 7undMC 7uncC 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_26621.map.gz / Format: CCP4 / Size: 347.6 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: 0.83 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
+Mask #1
+Mask #2
+Mask #3
+Additional map: Map I, 38 complex, SPT4/5 local refinement, sharp
+Additional map: Map G, 38 complex, Pol II (active site) local refinement, sharp
+Additional map: Map G, 38 complex, Pol II (active site) local refinement, half B
+Additional map: Map G, 38 complex, Pol II (active site) local refinement, half A
+Additional map: Map F, 38 complex, overall, half B
+Additional map: Map F, 38 complex, overall, sharp
+Additional map: Map F, 38 complex, overall, consensus
+Additional map: Map F, 38 complex, overall, half A
+Additional map: Map I, 38 complex, SPT4/5 local refinement, half A
+Additional map: Map I, 38 complex, SPT4/5 local refinement, half B
+Additional map: Map I, 38 complex, SPT4/5 local refinement, consensus
+Additional map: Map H, 38 complex, nucleosome local refinement, half A
+Additional map: Map H, 38 complex, nucleosome local refinement, sharp
+Additional map: Map H, 38 complex, nucleosome local refinement, half B
+Additional map: Map H, 38 complex, nucleosome local refinement, consensus
+Additional map: Map G, 38 complex, Pol II (active site) local refinement, consensus
-Sample components
+Entire : Pol II-DSIF-SPT6-PAF1c-TFIIS complex (stalled at +38)
+Supramolecule #1: Pol II-DSIF-SPT6-PAF1c-TFIIS complex (stalled at +38)
+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: RPOL4c domain-containing protein
+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: RPB8
+Macromolecule #9: RPB9
+Macromolecule #10: RPB10
+Macromolecule #11: RPB11
+Macromolecule #12: RNA polymerase II subunit K
+Macromolecule #13: Transcription elongation factor SPT6
+Macromolecule #15: Transcription elongation factor A protein 1
+Macromolecule #17: RNA polymerase-associated protein CTR9 homolog
+Macromolecule #18: RNA polymerase-associated protein RTF1 homolog
+Macromolecule #20: RNA polymerase-associated protein LEO1
+Macromolecule #21: RNA polymerase II-associated factor 1 homolog
+Macromolecule #22: WDR61
+Macromolecule #23: Parafibromin
+Macromolecule #24: Transcription elongation factor SPT4
+Macromolecule #25: Transcription elongation factor SPT5
+Macromolecule #26: Histone H3.2
+Macromolecule #27: Histone H4
+Macromolecule #28: Histone H2A
+Macromolecule #29: Histone H2B 1.1
+Macromolecule #14: Non-template DNA
+Macromolecule #19: Template DNA
+Macromolecule #16: RNA
+Macromolecule #30: ZINC ION
+Macromolecule #31: 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 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Details: 15 mA with 10 s hold time | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / 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: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000 |
Specialist optics | Phase plate: VOLTA PHASE PLATE / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 52.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER / Details: Ab initio |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Number classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 105420 |