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Yorodumi- PDB-8a3y: Structure of mammalian Pol II-DSIF-SPT6-PAF1-TFIIS-hexasome elong... -
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-Basic information
Entry | Database: PDB / ID: 8a3y | ||||||||||||
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Title | Structure of mammalian Pol II-DSIF-SPT6-PAF1-TFIIS-hexasome elongation complex | ||||||||||||
Components |
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Keywords | TRANSCRIPTION / chromatin / rna polymerase II / nucleosome / TFIIS / 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 / endodermal cell fate commitment ...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 / endodermal cell fate commitment / negative regulation of myeloid cell differentiation / blastocyst hatching / positive regulation of cell cycle G1/S phase transition / DSIF complex / 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 / transcription elongation-coupled chromatin remodeling / 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 / interleukin-6-mediated signaling pathway / negative regulation of gene expression, epigenetic / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / RNA polymerase III activity / RNA polymerase II complex binding / maintenance of transcriptional fidelity during 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 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 elongation by RNA polymerase I / Tat-mediated elongation of the HIV-1 transcript / tRNA transcription by RNA polymerase III / RNA polymerase I activity / Formation of HIV-1 elongation complex containing HIV-1 Tat / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / Formation of HIV elongation complex in the absence of HIV Tat / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / positive regulation of transcription elongation by RNA polymerase II / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / negative regulation of fibroblast proliferation / translation initiation factor binding / RNA Polymerase II Pre-transcription Events / rescue of stalled ribosome / SH2 domain binding / regulation of cell growth / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / transcription elongation by RNA polymerase II / Formation of the beta-catenin:TCF transactivating complex / Hedgehog 'on' state / P-body / protein destabilization / euchromatin / ribonucleoside binding / Wnt signaling pathway / fibrillar center / 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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||
Authors | Farnung, L. / Ochmann, M. / Garg, G. / Vos, S.M. / Cramer, P. | ||||||||||||
Funding support | European Union, Germany, 3items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8a3y.cif.gz | 2.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8a3y.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8a3y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/8a3y ftp://data.pdbj.org/pub/pdb/validation_reports/a3/8a3y | HTTPS FTP |
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-Related structure data
Related structure data | 15127MC 8a40C 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 ABCEGIK
#1: Protein | Mass: 219049.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A7M4DUC2 |
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#2: Protein | Mass: 142426.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LGP4, DNA-directed RNA polymerase |
#3: Protein | Mass: 30898.428 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: POLR2C / Production host: Trichoplusia ni (cabbage looper) / 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 |
#7: Protein | Mass: 19314.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VKG7 |
#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 |
#11: Protein | Mass: 13310.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RKE4 |
-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 (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 (pig) / References: UniProt: A0A8D0JYF1 |
-DNA-directed RNA polymerases I, II, and III subunit ... , 3 types, 3 molecules FHJ
#6: Protein | Mass: 14477.001 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1KNW4 |
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#8: Protein | Mass: 17162.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LCB2 |
#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 |
-Protein , 8 types, 10 molecules MVWXaebfcd
#13: Protein | Mass: 117027.672 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) | ||||||
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#19: Protein | Mass: 36450.977 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 | ||||||
#20: 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 | ||||||
#21: 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 | ||||||
#24: Protein | Mass: 15435.126 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233 #25: Protein | Mass: 11394.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799 #26: Protein | | Mass: 11294.136 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) Gene: LOC494591, h2ac14.L, hist1h2aj, hist1h2aj.L, XELAEV_18003602mg Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6AZJ8 #27: Protein | | Mass: 10607.212 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC108704302 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8J1LZU9 |
-DNA chain , 1 types, 1 molecules N
#14: DNA chain | Mass: 39557.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-RNA, Template ... , 2 types, 2 molecules PT
#15: RNA chain | Mass: 9054.556 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#18: DNA chain | Mass: 42305.887 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-RNA polymerase-associated protein ... , 2 types, 3 molecules QUR
#16: Protein | Mass: 210005.672 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTR9, KIAA0155, SH2BP1, LEO1, RDL / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6PD62, UniProt: Q8WVC0 #17: Protein | | Mass: 29128.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RTF1, KIAA0252 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q92541 |
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-Transcription elongation factor ... , 2 types, 2 molecules YZ
#22: Protein | Mass: 13508.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SUPT4H1, QtsA-10763 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q4R941 |
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#23: Protein | Mass: 121225.477 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SUPT5H, SPT5, SPT5H / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O00267 |
-Non-polymers , 2 types, 10 molecules
#28: Chemical | ChemComp-ZN / #29: 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: Mammalian Pol II-TFIIS elongation complex / Type: COMPLEX / Entity ID: #1-#17, #20-#27 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Sus scrofa (pig) |
Buffer solution | pH: 7.4 |
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: 1200 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30000 / Symmetry type: POINT |