+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34415 | |||||||||||||||||||||
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Title | RNA polymerase II transcribing a chromatosome (type I) | |||||||||||||||||||||
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Sample |
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Keywords | chromatin / nucleosome / TRANSCRIPTION | |||||||||||||||||||||
Function / homology | Function and homology information regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / negative regulation of DNA recombination / RPB4-RPB7 complex / Apoptosis induced DNA fragmentation / chromosome condensation / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / termination of RNA polymerase II transcription / termination of RNA polymerase III transcription ...regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / negative regulation of DNA recombination / RPB4-RPB7 complex / Apoptosis induced DNA fragmentation / chromosome condensation / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / termination of RNA polymerase II transcription / termination of RNA polymerase III transcription / 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 / negative regulation of tumor necrosis factor-mediated signaling pathway / Replacement of protamines by nucleosomes in the male pronucleus / transcription elongation by RNA polymerase I / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / tRNA transcription by RNA polymerase III / 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 / Chromatin modifying enzymes / 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 / Interleukin-7 signaling / epigenetic regulation of gene expression / 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 / HDMs demethylate histones / 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 / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / euchromatin / heterochromatin formation / chromatin DNA binding / 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 / structural constituent of chromatin / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks Similarity search - Function | |||||||||||||||||||||
Biological species | Komagataella phaffii (fungus) / Homo sapiens (human) / synthetic construct (others) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||||||||||||||
Authors | Hirano R / Ehara H / Tomoya K / Takizawa Y / Sekine S / Kurumizaka H | |||||||||||||||||||||
Funding support | Japan, 6 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structural basis of RNA polymerase II transcription on the chromatosome containing linker histone H1. Authors: Rina Hirano / Haruhiko Ehara / Tomoya Kujirai / Tamami Uejima / Yoshimasa Takizawa / Shun-Ichi Sekine / Hitoshi Kurumizaka / Abstract: In chromatin, linker histone H1 binds to nucleosomes, forming chromatosomes, and changes the transcription status. However, the mechanism by which RNA polymerase II (RNAPII) transcribes the DNA in ...In chromatin, linker histone H1 binds to nucleosomes, forming chromatosomes, and changes the transcription status. However, the mechanism by which RNA polymerase II (RNAPII) transcribes the DNA in the chromatosome has remained enigmatic. Here we report the cryo-electron microscopy (cryo-EM) structures of transcribing RNAPII-chromatosome complexes (forms I and II), in which RNAPII is paused at the entry linker DNA region of the chromatosome due to H1 binding. In the form I complex, the H1 bound to the nucleosome restricts the linker DNA orientation, and the exit linker DNA is captured by the RNAPII DNA binding cleft. In the form II complex, the RNAPII progresses a few bases ahead by releasing the exit linker DNA from the RNAPII cleft, and directly clashes with the H1 bound to the nucleosome. The transcription elongation factor Spt4/5 masks the RNAPII DNA binding region, and drastically reduces the H1-mediated RNAPII pausing. | |||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34415.map.gz | 40.7 MB | EMDB map data format | |
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Header (meta data) | emd-34415-v30.xml emd-34415.xml | 46.3 KB 46.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_34415_fsc.xml | 8.5 KB | Display | FSC data file |
Images | emd_34415.png | 63.7 KB | ||
Filedesc metadata | emd-34415.cif.gz | 10.7 KB | ||
Others | emd_34415_additional_1.map.gz emd_34415_additional_2.map.gz emd_34415_half_map_1.map.gz emd_34415_half_map_2.map.gz | 40.8 MB 40.7 MB 40.8 MB 40.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34415 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34415 | HTTPS FTP |
-Validation report
Summary document | emd_34415_validation.pdf.gz | 915.1 KB | Display | EMDB validaton report |
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Full document | emd_34415_full_validation.pdf.gz | 914.7 KB | Display | |
Data in XML | emd_34415_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | emd_34415_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34415 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34415 | HTTPS FTP |
-Related structure data
Related structure data | 8h0vMC 8h0wC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_34415.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.49 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: RNAP reconstruction
File | emd_34415_additional_1.map | ||||||||||||
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Annotation | RNAP reconstruction | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Nucleosome reconstruction
File | emd_34415_additional_2.map | ||||||||||||
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Annotation | Nucleosome reconstruction | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34415_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34415_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : RNA polymerase II transcribing a chromatosome (type I)
+Supramolecule #1: RNA polymerase II transcribing a chromatosome (type I)
+Supramolecule #2: RNA polymerase II
+Supramolecule #3: DNA,RNA
+Supramolecule #4: Histone
+Macromolecule #1: DNA-directed RNA polymerase subunit
+Macromolecule #2: DNA-directed RNA polymerase subunit beta
+Macromolecule #3: RNA polymerase II third largest subunit B44, part of central core
+Macromolecule #4: RNA polymerase II subunit B32
+Macromolecule #5: DNA-directed RNA polymerases I, II, and III subunit RPABC1
+Macromolecule #6: RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
+Macromolecule #7: RNA polymerase II subunit
+Macromolecule #8: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #9: DNA-directed RNA polymerase subunit
+Macromolecule #10: RNA polymerase subunit ABC10-beta, common to RNA polymerases I, I...
+Macromolecule #11: RNA polymerase II subunit B12.5
+Macromolecule #12: RNA polymerase subunit ABC10-alpha
+Macromolecule #16: Histone H3.1
+Macromolecule #17: Histone H4
+Macromolecule #18: Histone H2A type 1-B/E
+Macromolecule #19: Histone H2B type 1-J
+Macromolecule #20: Histone H1.2
+Macromolecule #13: RNA (5'-R(P*AP*GP*CP*AP*AP*UP*AP*GP*GP*AP*GP*CP*UP*U)-3')
+Macromolecule #14: DNA (261-MER)
+Macromolecule #15: DNA (261-MER)
+Macromolecule #21: ZINC ION
+Macromolecule #22: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 56.2 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |