+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 / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / chromosome condensation / 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 / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / chromosome condensation / 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 / transcription initiation at RNA polymerase III promoter / 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 / negative regulation of tumor necrosis factor-mediated signaling pathway / transcription elongation by RNA polymerase I / negative regulation of megakaryocyte differentiation / positive regulation of translational initiation / RNA polymerase I complex / RNA polymerase III complex / protein localization to CENP-A containing chromatin / transcription-coupled nucleotide-excision repair / RNA polymerase III activity / RNA polymerase II, core complex / Chromatin modifying enzymes / pericentric heterochromatin / tRNA transcription by RNA polymerase III / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / RNA polymerase I activity / heterochromatin organization / epigenetic regulation of gene expression / Packaging Of Telomere Ends / RNA polymerase II activity / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / nucleosomal DNA binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / translation initiation factor binding / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / innate immune response in mucosa / Defective pyroptosis / HDACs deacetylate histones / transcription elongation by RNA polymerase II / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / transcription initiation at RNA polymerase II promoter / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / P-body / euchromatin / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / ribonucleoside binding / chromatin DNA binding / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / antimicrobial humoral immune response mediated by antimicrobial peptide / UCH proteinases / nucleosome / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / single-stranded DNA binding / Factors involved in megakaryocyte development and platelet production 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 |