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Open data
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Basic information
Entry | Database: PDB / ID: 7nky | |||||||||||||||
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Title | RNA Polymerase II-Spt4/5-nucleosome-FACT structure | |||||||||||||||
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![]() | TRANSCRIPTION / Chromatin / nucleosome / elongation / histone chaperone | |||||||||||||||
Function / homology | ![]() Regulation of TP53 Activity through Phosphorylation / regulation of sister chromatid cohesion / FACT complex / regulation of chromatin organization / DSIF complex / nucleosome organization / regulation of transcription elongation by RNA polymerase II / RPB4-RPB7 complex / replication fork protection complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay ...Regulation of TP53 Activity through Phosphorylation / regulation of sister chromatid cohesion / FACT complex / regulation of chromatin organization / DSIF complex / nucleosome organization / regulation of transcription elongation by RNA polymerase II / RPB4-RPB7 complex / replication fork protection complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / transcription elongation-coupled chromatin remodeling / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / termination of RNA polymerase II transcription / RNA-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / : / Formation of TC-NER Pre-Incision Complex / : / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / RNA polymerase II complex binding / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / 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 / transcription by RNA polymerase I / Estrogen-dependent gene expression / transcription by RNA polymerase III / chromosome, centromeric region / Dual incision in TC-NER / transcription elongation by RNA polymerase I / positive regulation of transcription initiation by RNA polymerase II / positive regulation of translational initiation / RNA polymerase I complex / RNA polymerase III complex / positive regulation of RNA polymerase II transcription preinitiation complex assembly / transcription-coupled nucleotide-excision repair / RNA polymerase III activity / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / RNA polymerase I activity / translesion synthesis / RNA polymerase II activity / nucleosome binding / translation initiation factor binding / regulation of DNA-templated transcription elongation / DNA-templated transcription initiation / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / P-body / ribonucleoside binding / DNA-templated DNA replication / mRNA processing / DNA-directed 5'-3' RNA polymerase activity / cytoplasmic stress granule / DNA-directed RNA polymerase / structural constituent of chromatin / peroxisome / nucleosome / nucleosome assembly / ribosome biogenesis / chromatin organization / chromosome / single-stranded DNA binding / DNA replication / transcription by RNA polymerase II / nucleic acid binding / single-stranded RNA binding / protein dimerization activity / protein heterodimerization activity / DNA repair / nucleotide binding / mRNA binding / chromatin / nucleolus / regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() synthetic RNA (others) synthetic construct (others) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||||||||
![]() | Farnung, L. / Ochmann, M. / Engeholm, M. / Cramer, P. | |||||||||||||||
Funding support | European Union, ![]()
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![]() | ![]() Title: Structural basis of nucleosome transcription mediated by Chd1 and FACT. Authors: Lucas Farnung / Moritz Ochmann / Maik Engeholm / Patrick Cramer / ![]() Abstract: Efficient transcription of RNA polymerase II (Pol II) through nucleosomes requires the help of various factors. Here we show biochemically that Pol II transcription through a nucleosome is ...Efficient transcription of RNA polymerase II (Pol II) through nucleosomes requires the help of various factors. Here we show biochemically that Pol II transcription through a nucleosome is facilitated by the chromatin remodeler Chd1 and the histone chaperone FACT when the elongation factors Spt4/5 and TFIIS are present. We report cryo-EM structures of transcribing Saccharomyces cerevisiae Pol II-Spt4/5-nucleosome complexes with bound Chd1 or FACT. In the first structure, Pol II transcription exposes the proximal histone H2A-H2B dimer that is bound by Spt5. Pol II has also released the inhibitory DNA-binding region of Chd1 that is poised to pump DNA toward Pol II. In the second structure, Pol II has generated a partially unraveled nucleosome that binds FACT, which excludes Chd1 and Spt5. These results suggest that Pol II progression through a nucleosome activates Chd1, enables FACT binding and eventually triggers transfer of FACT together with histones to upstream DNA. | |||||||||||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Download
PDBx/mmCIF format | ![]() | 1.2 MB | Display | ![]() |
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PDB format | ![]() | 939.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 989.3 KB | Display | ![]() |
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Full document | ![]() | 992.5 KB | Display | |
Data in XML | ![]() | 129.4 KB | Display | |
Data in CIF | ![]() | 218.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 12450MC ![]() 7nkxC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-RNA chain , 1 types, 1 molecules P
#1: RNA chain | Mass: 4913.807 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic RNA (others) |
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-DNA chain , 2 types, 2 molecules NT
#2: DNA chain | Mass: 42792.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 45537.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-DNA-directed RNA polymerase II subunit ... , 7 types, 7 molecules ABCIKDG
#4: Protein | Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#5: Protein | Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#6: Protein | Mass: 35330.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#10: Protein | Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#12: Protein | Mass: 13633.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#16: Protein | Mass: 25451.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#17: Protein | Mass: 19081.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 5 molecules EFHJL
#7: Protein | Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#8: Protein | Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#9: Protein | Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#11: Protein | Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#13: Protein | Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein , 6 types, 10 molecules YZaebfcgdh
#14: Protein | Mass: 11168.772 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: BJ5464 Gene: PACBIOSEQ_LOCUS2707, PACBIOSEQ_LOCUS2757, SCNYR20_0003027800, SCP684_0002027900 Cell line (production host): Hi5 / Production host: ![]() | ||||||
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#15: Protein | Mass: 115929.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: PACBIOSEQ_LOCUS4816 / Production host: ![]() | ||||||
#20: Protein | Mass: 15435.126 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #21: Protein | Mass: 11394.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #22: Protein | Mass: 14109.436 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #23: Protein | Mass: 13655.948 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-FACT complex subunit ... , 2 types, 2 molecules OQ
#18: Protein | Mass: 63068.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: BJ5464 Gene: PACBIOSEQ_LOCUS4754, SCNYR20_0006005900, SCP684_0006005800 Cell line (production host): Hi5 / Production host: ![]() |
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#19: Protein | Mass: 118776.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: BJ5464 / Gene: SPT16, CDC68, SSF1, YGL207W / Cell line (production host): Hi5 / Production host: ![]() |
-Non-polymers , 2 types, 10 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MG.gif)
#24: Chemical | ChemComp-ZN / #25: Chemical | ChemComp-MG / | |
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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
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