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Yorodumi- PDB-7xn7: RNA polymerase II elongation complex containing Spt4/5, Elf1, Spt... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 7xn7 | ||||||||||||||||||||||||
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| Title | RNA polymerase II elongation complex containing Spt4/5, Elf1, Spt6, Spn1 and Paf1C | ||||||||||||||||||||||||
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Keywords | TRANSCRIPTION / chromatin / nucleosome | ||||||||||||||||||||||||
| Function / homology | Function and homology informationregulation of septum digestion after cytokinesis / RNA polymerase II C-terminal domain phosphoserine binding / Cdc73/Paf1 complex / siRNA-mediated pericentric heterochromatin formation / DSIF complex / RPB4-RPB7 complex / nucleosome organization / transcription elongation factor activity / chromatin-protein adaptor activity / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay ...regulation of septum digestion after cytokinesis / RNA polymerase II C-terminal domain phosphoserine binding / Cdc73/Paf1 complex / siRNA-mediated pericentric heterochromatin formation / DSIF complex / RPB4-RPB7 complex / nucleosome organization / transcription elongation factor activity / chromatin-protein adaptor activity / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / termination of RNA polymerase II transcription / poly(A)+ mRNA export from nucleus / termination of RNA polymerase III transcription / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / transcription elongation-coupled chromatin remodeling / transcription initiation at RNA polymerase III promoter / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase I promoter / RNA polymerase II complex binding / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of translational initiation / chromosome, centromeric region / translation elongation factor activity / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / pericentric heterochromatin / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / nucleosome binding / transcription by RNA polymerase I / translation initiation factor binding / transcription-coupled nucleotide-excision repair / regulation of DNA-templated transcription elongation / transcription elongation factor complex / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / P-body / positive regulation of transcription elongation by RNA polymerase II / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / single-stranded DNA binding / histone binding / nucleic acid binding / transcription by RNA polymerase II / single-stranded RNA binding / protein dimerization activity / nucleotide binding / RNA-directed RNA polymerase activity / mRNA binding / DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / nucleolus / mitochondrion / DNA binding / RNA binding / zinc ion binding / metal ion binding / nucleus Similarity search - Function | ||||||||||||||||||||||||
| Biological species | Komagataella phaffii (fungus)synthetic construct (others) | ||||||||||||||||||||||||
| Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||||||||||||||
Authors | Ehara, H. / Kujirai, T. / Shirouzu, M. / Kurumizaka, H. / Sekine, S. | ||||||||||||||||||||||||
| Funding support | Japan, 7items
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Citation | Journal: Science / Year: 2022Title: 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. | ||||||||||||||||||||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 7xn7.cif.gz | 1.7 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb7xn7.ent.gz | Display | PDB format | |
| PDBx/mmJSON format | 7xn7.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 7xn7_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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| Full document | 7xn7_full_validation.pdf.gz | 1.4 MB | Display | |
| Data in XML | 7xn7_validation.xml.gz | 184.7 KB | Display | |
| Data in CIF | 7xn7_validation.cif.gz | 303.2 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xn/7xn7 ftp://data.pdbj.org/pub/pdb/validation_reports/xn/7xn7 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 33313MC ![]() 7xseC ![]() 7xsxC ![]() 7xszC ![]() 7xt7C ![]() 7xtdC ![]() 7xtiC M: map data used to model this data C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
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Assembly
| Deposited unit | ![]()
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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) / Strain: GS115 / ATCC 20864 / 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) / Strain: GS115 / ATCC 20864 / 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) / Strain: GS115 / ATCC 20864 / 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) / Strain: GS115 / ATCC 20864 / 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) / Strain: GS115 / ATCC 20864 / 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: F2QX94 |
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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) / Strain: GS115 / ATCC 20864 / References: UniProt: C4R273 |
-Protein , 8 types, 8 molecules FWnqruvx
| #6: Protein | Mass: 17803.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii (fungus) / Strain: GS115 / ATCC 20864 / References: UniProt: C4R1V1 |
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| #18: Protein | Mass: 101459.422 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Komagataella phaffii (fungus) / Strain: GS115 / ATCC 20864 / Gene: PAS_chr3_1136 / Production host: ![]() |
| #20: Protein | Mass: 46907.785 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Komagataella phaffii (fungus) / Strain: GS115 / ATCC 20864 / Gene: PAS_chr4_0349 / Production host: ![]() |
| #21: 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: ![]() |
| #22: 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: ![]() |
| #23: Protein | Mass: 52387.715 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Komagataella phaffii (fungus) / Strain: GS115 / ATCC 20864 / Gene: PAS_chr3_1154 / Production host: ![]() |
| #24: Protein | Mass: 46045.980 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Komagataella phaffii (fungus) / Strain: GS115 / ATCC 20864 / Gene: PAS_chr4_0902 / Production host: ![]() |
| #25: Protein | Mass: 44760.652 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Komagataella phaffii (fungus) / Strain: GS115 / ATCC 20864 / Gene: PAS_chr2-1_0674 / Production host: ![]() |
-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) / Strain: GS115 / ATCC 20864 / 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 ... , 3 types, 3 molecules MVm
| #13: Protein | Mass: 12606.896 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Komagataella phaffii (fungus) / Strain: GS115 / ATCC 20864 / Gene: PAS_c121_0006 / Production host: ![]() |
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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) / Strain: GS115 / ATCC 20864 / Gene: PAS_chr2-1_0350 / Production host: ![]() |
| #19: Protein | Mass: 173241.625 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Komagataella phaffii (fungus) / Strain: GS115 / ATCC 20864 / Gene: PAS_chr4_0308 / Production host: ![]() |
-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 


| #26: Chemical | ChemComp-ZN / #27: 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 |
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Sample preparation
| Component | Name: RNA polymerase II elongation complex containing Spt4/5, Elf1, Spt6, Spn1 and Paf1C Type: COMPLEX / Entity ID: #1-#25 / Source: RECOMBINANT |
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| Molecular weight | Experimental value: NO |
| Source (natural) | Organism: Komagataella phaffii (fungus) |
| Source (recombinant) | Organism: ![]() |
| Buffer solution | pH: 7.5 |
| Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
| Vitrification | Cryogen name: ETHANE |
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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) |
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Processing
| CTF correction | Type: NONE |
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| 3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 444232 / Symmetry type: POINT |
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About Yorodumi



Komagataella phaffii (fungus)
Japan, 7items
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FIELD EMISSION GUN