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Yorodumi- PDB-7xse: RNA polymerase II elongation complex transcribing a nucleosome (EC42) -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xse | ||||||||||||||||||||||||
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Title | RNA polymerase II elongation complex transcribing a nucleosome (EC42) | ||||||||||||||||||||||||
Components |
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Keywords | TRANSCRIPTION / chromatin / nucleosome | ||||||||||||||||||||||||
Function / homology | Function and homology information RNA polymerase II C-terminal domain phosphoserine binding / regulation of septum digestion after cytokinesis / Cdc73/Paf1 complex / siRNA-mediated pericentric heterochromatin formation / negative regulation of chromosome condensation / DSIF complex / Barr body / regulation of centromere complex assembly / muscle cell differentiation / nucleosome organization ...RNA polymerase II C-terminal domain phosphoserine binding / regulation of septum digestion after cytokinesis / Cdc73/Paf1 complex / siRNA-mediated pericentric heterochromatin formation / negative regulation of chromosome condensation / DSIF complex / Barr body / regulation of centromere complex assembly / muscle cell differentiation / nucleosome organization / regulation of transcription elongation by RNA polymerase II / RPB4-RPB7 complex / pericentric heterochromatin formation / inner kinetochore / transcription elongation factor activity / oocyte maturation / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / poly(A)+ mRNA export from nucleus / transcription elongation-coupled chromatin remodeling / 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 / RNA polymerase II complex binding / 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 / chromosome, centromeric region / 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 / nucleosome binding / Packaging Of Telomere Ends / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / transcription-coupled nucleotide-excision repair / lipoxygenase pathway / translation elongation factor activity / 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 / positive regulation of transcription elongation by RNA polymerase II / 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 / transcription elongation factor complex / Defective pyroptosis / Meiotic recombination / innate immune response in mucosa / DNA Damage/Telomere Stress Induced Senescence / regulation of DNA-templated transcription elongation / 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 Similarity search - Function | ||||||||||||||||||||||||
Biological species | Komagataella phaffii (fungus) Homo sapiens (human) synthetic construct (others) | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||||||||||||||
Authors | Ehara, H. / Kujirai, T. / Shirouzu, M. / Kurumizaka, H. / Sekine, S. | ||||||||||||||||||||||||
Funding support | Japan, 7items
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Citation | Journal: Science / Year: 2022 Title: Structural basis of nucleosome disassembly and reassembly by RNAPII elongation complex with FACT. Authors: Haruhiko Ehara / Tomoya Kujirai / Mikako Shirouzu / Hitoshi Kurumizaka / Shun-Ichi Sekine / Abstract: During gene transcription, RNA polymerase II (RNAPII) traverses nucleosomes in chromatin, but the mechanism has remained elusive. Using cryo-electron microscopy, we obtained structures of the RNAPII ...During gene transcription, RNA polymerase II (RNAPII) traverses nucleosomes in chromatin, but the mechanism has remained elusive. Using cryo-electron microscopy, we obtained structures of the RNAPII elongation complex (EC) passing through a nucleosome in the presence of the transcription elongation factors Spt6, Spn1, Elf1, Spt4/5, and Paf1C and the histone chaperone FACT (facilitates chromatin transcription). The structures show snapshots of EC progression on DNA mediating downstream nucleosome disassembly, followed by its reassembly upstream of the EC, which is facilitated by FACT. FACT dynamically adapts to successively occurring subnucleosome intermediates, forming an interface with the EC. Spt6, Spt4/5, and Paf1C form a "cradle" at the EC DNA-exit site and support the upstream nucleosome reassembly. These structures explain the mechanism by which the EC traverses nucleosomes while maintaining the chromatin structure and epigenetic information. | ||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xse.cif.gz | 1.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7xse.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7xse.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xse_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7xse_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7xse_validation.xml.gz | 194.8 KB | Display | |
Data in CIF | 7xse_validation.cif.gz | 325.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xs/7xse ftp://data.pdbj.org/pub/pdb/validation_reports/xs/7xse | HTTPS FTP |
-Related structure data
Related structure data | 33424MC 7xn7C 7xsxC 7xszC 7xt7C 7xtdC 7xtiC 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 , 11 types, 15 molecules Faebfcgdhnqruvx
#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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#19: Protein | Mass: 15643.262 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B / Production host: Escherichia coli (E. coli) / References: UniProt: P84243 #20: Protein | Mass: 11676.703 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, ...Gene: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4-16, HIST4H4 Production host: Escherichia coli (E. coli) / References: UniProt: P62805 #21: Protein | Mass: 14447.825 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE / Production host: Escherichia coli (E. coli) / References: UniProt: P04908 #22: Protein | Mass: 14217.516 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: H2BC11, H2BFR, HIST1H2BJ / Production host: Escherichia coli (E. coli) / References: UniProt: P06899 #24: Protein | | Mass: 46907.785 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Komagataella phaffii (fungus) / Gene: PAS_chr4_0349 / Production host: Escherichia coli (E. coli) / References: UniProt: C4R7L8 #25: Protein | | Mass: 124979.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Komagataella phaffii (fungus) / Gene: PAS_chr3_1035 / Production host: Escherichia coli (E. coli) / References: UniProt: C4R6B2 #26: Protein | | Mass: 62301.246 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Komagataella phaffii (fungus) / Gene: RTF1, PP7435_Chr1-1405 / Production host: Escherichia coli (E. coli) / References: UniProt: F2QQ42 #27: Protein | | Mass: 52387.715 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Komagataella phaffii (fungus) / Gene: PAS_chr3_1154 / Production host: Escherichia coli (E. coli) / References: UniProt: C4R3K1 #28: Protein | | Mass: 46045.980 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Komagataella phaffii (fungus) / Gene: PAS_chr4_0902 / Production host: Escherichia coli (E. coli) / References: UniProt: C4R997 #29: Protein | | Mass: 44760.652 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Komagataella phaffii (fungus) / Gene: PAS_chr2-1_0674 / Production host: Escherichia coli (E. coli) / References: UniProt: C4R1E6 |
-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 |
-Transcription elongation factor ... , 4 types, 4 molecules MVWm
#13: Protein | Mass: 12606.896 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Komagataella phaffii (fungus) / Gene: PAS_c121_0006 / Production host: Escherichia coli (E. coli) / References: UniProt: C4QZ45 |
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#17: Protein | Mass: 12039.614 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Komagataella phaffii (fungus) / Gene: PAS_chr2-1_0350 / Production host: Escherichia coli (E. coli) / References: UniProt: C4R0E6 |
#18: Protein | Mass: 101459.422 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Komagataella phaffii (fungus) / Gene: PAS_chr3_1136 / Production host: Escherichia coli (E. coli) / References: UniProt: C4R370 |
#23: Protein | Mass: 173241.625 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Komagataella phaffii (fungus) / Gene: PAS_chr4_0308 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: C4R7H2 |
-DNA chain , 2 types, 2 molecules NT
#14: DNA chain | Mass: 61381.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#16: DNA chain | Mass: 60869.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-RNA chain , 1 types, 1 molecules P
#15: RNA chain | Mass: 6081.562 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 2 types, 11 molecules
#30: Chemical | ChemComp-ZN / #31: 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 |
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||
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: TFS 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: 51 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 76913 / Symmetry type: POINT |