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Yorodumi- PDB-8jh3: RNA polymerase II elongation complex containing 40 bp upstream DN... -
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-Basic information
Entry | Database: PDB / ID: 8jh3 | |||||||||||||||||||||||||||||||||
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Title | RNA polymerase II elongation complex containing 40 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome | |||||||||||||||||||||||||||||||||
Components |
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Keywords | Transcription/DNA/RNA / Transcription-DNA-RNA complex / RNAPII | |||||||||||||||||||||||||||||||||
Function / homology | Function and homology information regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / muscle cell differentiation / RPB4-RPB7 complex / pericentric heterochromatin formation / inner kinetochore / oocyte maturation ...regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / muscle cell differentiation / RPB4-RPB7 complex / pericentric heterochromatin formation / inner kinetochore / oocyte maturation / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / termination of RNA polymerase II transcription / termination of RNA polymerase III transcription / nucleus organization / termination of RNA polymerase I transcription / RNA polymerase III activity / transcription initiation at RNA polymerase III promoter / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / protein localization to CENP-A containing chromatin / transcription initiation at RNA polymerase I promoter / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / CENP-A containing nucleosome / RNA polymerase II activity / spermatid development / negative regulation of tumor necrosis factor-mediated signaling pathway / subtelomeric heterochromatin formation / Replacement of protamines by nucleosomes in the male pronucleus / transcription elongation by RNA polymerase I / single fertilization / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / tRNA transcription by RNA polymerase III / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase I activity / Packaging Of Telomere Ends / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / transcription-coupled nucleotide-excision repair / lipoxygenase pathway / RNA polymerase II, core complex / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / pericentric heterochromatin / telomere organization / arachidonate metabolic process / lipid oxidation / Deposition of new CENPA-containing nucleosomes at the centromere / hepoxilin biosynthetic process / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / linoleic acid metabolic process / Meiotic synapsis / Inhibition of DNA recombination at telomere / nucleosomal DNA binding / translation initiation factor binding / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / embryo implantation / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / Meiotic recombination / innate immune response in mucosa / DNA Damage/Telomere Stress Induced Senescence / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / transcription initiation at RNA polymerase II promoter / lipopolysaccharide binding / Transcriptional regulation of granulopoiesis / transcription elongation by RNA polymerase II / Formation of the beta-catenin:TCF transactivating complex / HCMV Early Events / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / P-body / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / multicellular organism growth / heterochromatin formation / RMTs methylate histone arginines / ribonucleoside binding / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / Activation of anterior HOX genes in hindbrain development during early embryogenesis / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / osteoblast differentiation / structural constituent of chromatin / male gonad development / UCH proteinases / nucleosome Similarity search - Function | |||||||||||||||||||||||||||||||||
Biological species | synthetic construct (others) Homo sapiens (human) Komagataella phaffii (fungus) | |||||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||||||||||||||||||||||||||
Authors | Akatsu, M. / Fujita, R. / Ogasawara, M. / Ehara, H. / Kujirai, T. / Takizawa, Y. / Sekine, S. / Kurumizaka, H. | |||||||||||||||||||||||||||||||||
Funding support | Japan, 10items
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Citation | Journal: J Biol Chem / Year: 2023 Title: Cryo-EM structures of RNA polymerase II-nucleosome complexes rewrapping transcribed DNA. Authors: Munetaka Akatsu / Haruhiko Ehara / Tomoya Kujirai / Risa Fujita / Tomoko Ito / Ken Osumi / Mitsuo Ogasawara / Yoshimasa Takizawa / Shun-Ichi Sekine / Hitoshi Kurumizaka / Abstract: RNA polymerase II (RNAPII) transcribes DNA wrapped in the nucleosome by stepwise pausing, especially at nucleosomal superhelical locations -5 and -1 [SHL(-5) and SHL(-1), respectively]. In the ...RNA polymerase II (RNAPII) transcribes DNA wrapped in the nucleosome by stepwise pausing, especially at nucleosomal superhelical locations -5 and -1 [SHL(-5) and SHL(-1), respectively]. In the present study, we performed cryo-electron microscopy analyses of RNAPII-nucleosome complexes paused at a major nucleosomal pausing site, SHL(-1). We determined two previously undetected structures, in which the transcribed DNA behind RNAPII is sharply kinked at the RNAPII exit tunnel and rewrapped around the nucleosomal histones in front of RNAPII by DNA looping. This DNA kink shifts the DNA orientation toward the nucleosome, and the transcribed DNA region interacts with basic amino acid residues of histones H2A, H2B, and H3 exposed by the RNAPII-mediated nucleosomal DNA peeling. The DNA loop structure was not observed in the presence of the transcription elongation factors Spt4/5 and Elf1. These RNAPII-nucleosome structures provide important information for understanding the functional relevance of DNA looping during transcription elongation in the nucleosome. | |||||||||||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jh3.cif.gz | 1012 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jh3.ent.gz | 797 KB | Display | PDB format |
PDBx/mmJSON format | 8jh3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jh3_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8jh3_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8jh3_validation.xml.gz | 117.4 KB | Display | |
Data in CIF | 8jh3_validation.cif.gz | 188.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jh/8jh3 ftp://data.pdbj.org/pub/pdb/validation_reports/jh/8jh3 | HTTPS FTP |
-Related structure data
Related structure data | 36252MC 8jh2C 8jh4C 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 ... , 3 types, 3 molecules ABI
#1: Protein | Mass: 194107.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii (fungus) / References: UniProt: C4R4Y0, DNA-directed RNA polymerase |
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#2: Protein | Mass: 139746.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii (fungus) / References: UniProt: C4QZQ7, DNA-directed RNA polymerase |
#9: Protein | Mass: 13612.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii (fungus) / References: UniProt: F2QPE6 |
-RNA polymerase II ... , 4 types, 4 molecules CDGK
#3: Protein | Mass: 34216.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii (fungus) / References: UniProt: C4R7L2 |
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#4: Protein | Mass: 20622.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii (fungus) / References: UniProt: C4R2U9 |
#7: Protein | Mass: 18802.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii (fungus) / References: UniProt: C4R9A1 |
#11: Protein | Mass: 13832.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii (fungus) / References: UniProt: C4R3Z5 |
-DNA-directed RNA polymerases I, II, and III subunit ... , 2 types, 2 molecules EH
#5: Protein | Mass: 24962.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii (fungus) / References: UniProt: C4R3P8 |
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#8: Protein | Mass: 16249.220 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii (fungus) / References: UniProt: C4R273 |
-Protein , 5 types, 9 molecules Faebfcgdh
#6: Protein | Mass: 17803.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii (fungus) / References: UniProt: C4R1V1 | ||||||
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#16: Protein | Mass: 15360.983 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: H3-3A, H3.3A, H3F3, H3F3A, PP781, H3-3B, H3.3B, H3F3B / Production host: Escherichia coli (E. coli) / References: UniProt: P84243 #17: Protein | Mass: 11394.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P62805 #18: Protein | Mass: 14165.551 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P04908 #19: Protein | Mass: 13935.239 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2BJ, H2BFR / Production host: Escherichia coli (E. coli) / References: UniProt: P06899 |
-RNA polymerase subunit ABC10- ... , 2 types, 2 molecules JL
#10: Protein | Mass: 8554.064 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii (fungus) / References: UniProt: C4R009 |
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#12: Protein | Mass: 7862.048 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii (fungus) / References: UniProt: F2QMI1 |
-DNA chain , 2 types, 2 molecules NT
#13: DNA chain | Mass: 61381.906 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
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#15: DNA chain | Mass: 60869.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
-RNA chain , 1 types, 1 molecules P
#14: RNA chain | Mass: 4207.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 2 types, 9 molecules
#20: Chemical | ChemComp-ZN / #21: Chemical | ChemComp-MG / | |
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-Details
Has ligand of interest | Y |
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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 |
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Molecular weight |
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 Details: 20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl | ||||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.09144 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: dsDNA concentration is 0.09144 mg/mL. This sample contains 0.005% Tween20. | ||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-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: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 59.84 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: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 51652 / Symmetry type: POINT |