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Yorodumi- PDB-7xn7: RNA polymerase II elongation complex containing Spt4/5, Elf1, Spt... -
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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 | ||||||||||||||||||||||||
Components |
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Keywords | TRANSCRIPTION / chromatin / nucleosome | ||||||||||||||||||||||||
Function / homology | Function and homology information nuclear DNA-directed RNA polymerase complex / RNA polymerase II C-terminal domain phosphoserine binding / regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / Cdc73/Paf1 complex / DSIF complex / nucleosome organization / regulation of transcription elongation by RNA polymerase II / transcription elongation factor activity / RPB4-RPB7 complex ...nuclear DNA-directed RNA polymerase complex / RNA polymerase II C-terminal domain phosphoserine binding / regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / Cdc73/Paf1 complex / DSIF complex / nucleosome organization / regulation of transcription elongation by RNA polymerase II / transcription elongation factor activity / RPB4-RPB7 complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / transcription elongation-coupled chromatin remodeling / poly(A)+ mRNA export from nucleus / termination of RNA polymerase II transcription / termination of RNA polymerase III transcription / : / : / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / RNA polymerase II complex binding / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / transcription initiation at RNA polymerase I promoter / chromosome, centromeric region / transcription elongation by RNA polymerase I / positive regulation of translational initiation / RNA polymerase I complex / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / RNA polymerase III activity / RNA polymerase II, core complex / pericentric heterochromatin / translation elongation factor activity / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA polymerase II activity / nucleosome binding / translation initiation factor binding / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / single-stranded DNA binding / histone binding / nucleic acid binding / single-stranded RNA binding / protein dimerization activity / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / mRNA binding / chromatin binding / regulation of DNA-templated transcription / nucleolus / regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / nucleus / metal ion binding 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: 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 | 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 | 1.5 MB | Display | |
Data in XML | 7xn7_validation.xml.gz | 184.7 KB | Display | |
Data in CIF | 7xn7_validation.cif.gz | 303 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 (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) / 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: Escherichia coli (E. coli) / References: UniProt: C4R370 |
#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: Escherichia coli (E. coli) / References: UniProt: C4R7L8 |
#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: Escherichia coli (E. coli) / References: UniProt: C4R6B2 |
#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: Escherichia coli (E. coli) / References: UniProt: F2QQ42 |
#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: Escherichia coli (E. coli) / References: UniProt: C4R3K1 |
#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: Escherichia coli (E. coli) / References: UniProt: C4R997 |
#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: 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) / 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: 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) / Strain: GS115 / ATCC 20864 / Gene: PAS_chr2-1_0350 / Production host: Escherichia coli (E. coli) / References: UniProt: C4R0E6 |
#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: 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
#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 |
-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: Escherichia coli (E. coli) |
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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 444232 / Symmetry type: POINT |