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Yorodumi- EMDB-33447: RNA polymerase II elongation complex transcribing a nucleosome (E... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33447 | ||||||||||||||||||||||||
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Title | RNA polymerase II elongation complex transcribing a nucleosome (EC58oct) | ||||||||||||||||||||||||
Map data | |||||||||||||||||||||||||
Sample |
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Keywords | chromatin / nucleosome / TRANSCRIPTION / TRANSCRIPTION-DNA-RNA complex | ||||||||||||||||||||||||
Function / homology | Function and homology information constitutive heterochromatin formation / FACT complex / RNA polymerase II C-terminal domain phosphoserine binding / regulation of septum digestion after cytokinesis / Cdc73/Paf1 complex / siRNA-mediated pericentric heterochromatin formation / histone chaperone activity / regulation of chromatin organization / negative regulation of chromosome condensation / DSIF complex ...constitutive heterochromatin formation / FACT complex / RNA polymerase II C-terminal domain phosphoserine binding / regulation of septum digestion after cytokinesis / Cdc73/Paf1 complex / siRNA-mediated pericentric heterochromatin formation / histone chaperone activity / regulation of chromatin organization / negative regulation of chromosome condensation / DSIF complex / Barr body / regulation of centromere complex assembly / muscle cell differentiation / nucleosome organization / regulation of transcription elongation by RNA polymerase II / RPB4-RPB7 complex / pericentric heterochromatin formation / inner kinetochore / transcription elongation factor activity / oocyte maturation / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / poly(A)+ mRNA export from nucleus / transcription elongation-coupled chromatin remodeling / termination of RNA polymerase II transcription / termination of RNA polymerase III transcription / nucleus organization / termination of RNA polymerase I transcription / RNA polymerase III activity / transcription initiation at RNA polymerase III promoter / RNA polymerase II complex binding / 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 / chromosome, centromeric region / RNA polymerase II activity / spermatid development / negative regulation of tumor necrosis factor-mediated signaling pathway / subtelomeric heterochromatin formation / Replacement of protamines by nucleosomes in the male pronucleus / transcription elongation by RNA polymerase I / single fertilization / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / tRNA transcription by RNA polymerase III / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase I activity / nucleosome binding / Packaging Of Telomere Ends / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / transcription-coupled nucleotide-excision repair / lipoxygenase pathway / translation elongation factor activity / 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 / lipid oxidation / positive regulation of transcription elongation by RNA polymerase II / 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 / embryo implantation / 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 / transcription elongation factor complex / Defective pyroptosis / Meiotic recombination / innate immune response in mucosa / DNA Damage/Telomere Stress Induced Senescence / regulation of DNA-templated transcription elongation / 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 / Formation of the beta-catenin:TCF transactivating complex / HCMV Early Events / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function Similarity search - Function | ||||||||||||||||||||||||
Biological species | Komagataella phaffii (fungus) / Homo sapiens (human) / synthetic construct (others) | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||||||||||||||||||||
Authors | Ehara H / Kujirai T / Shirouzu M / Kurumizaka H / Sekine S | ||||||||||||||||||||||||
Funding support | Japan, 7 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33447.map.gz | 40.9 MB | EMDB map data format | |
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Header (meta data) | emd-33447-v30.xml emd-33447.xml | 67.7 KB 67.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33447_fsc.xml | 8.5 KB | Display | FSC data file |
Images | emd_33447.png | 102.8 KB | ||
Filedesc metadata | emd-33447.cif.gz | 16.4 KB | ||
Others | emd_33447_additional_1.map.gz emd_33447_additional_2.map.gz emd_33447_half_map_1.map.gz emd_33447_half_map_2.map.gz | 40.6 MB 40.8 MB 40.9 MB 40.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33447 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33447 | HTTPS FTP |
-Validation report
Summary document | emd_33447_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_33447_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_33447_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | emd_33447_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33447 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33447 | HTTPS FTP |
-Related structure data
Related structure data | 7xtdMC 7xn7C 7xseC 7xsxC 7xszC 7xt7C 7xtiC 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_33447.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: 1.484 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: nucleosome reconstruction
File | emd_33447_additional_1.map | ||||||||||||
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Annotation | nucleosome reconstruction | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: EC reconstruction
File | emd_33447_additional_2.map | ||||||||||||
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Annotation | EC reconstruction | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33447_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33447_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : RNA polymerase II elongation complex transcribing a nucleosome (E...
+Supramolecule #1: RNA polymerase II elongation complex transcribing a nucleosome (E...
+Supramolecule #2: RNA polymerase II
+Supramolecule #3: Elf1,Spt4/5,Spn1 and Paf1C
+Supramolecule #4: DNA,RNA
+Supramolecule #5: histone, FACT complex subunit
+Supramolecule #6: Spt6
+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 #13: Transcription elongation factor 1 homolog
+Macromolecule #17: Transcription elongation factor SPT4
+Macromolecule #18: Transcription elongation factor SPT5
+Macromolecule #19: Transcription elongation factor Spt6
+Macromolecule #20: Protein that interacts with Spt6p and copurifies with Spt5p and R...
+Macromolecule #21: Component of the Paf1p complex
+Macromolecule #22: RNAPII-associated chromatin remodeling Paf1 complex subunit
+Macromolecule #23: Leo1
+Macromolecule #24: RNAP II-associated protein
+Macromolecule #25: Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p,...
+Macromolecule #26: Histone H3.3
+Macromolecule #27: Histone H4
+Macromolecule #28: Histone H2A type 1-B/E
+Macromolecule #29: Histone H2B type 1-J
+Macromolecule #30: FACT complex subunit
+Macromolecule #31: FACT complex subunit POB3
+Macromolecule #14: DNA (198-MER)
+Macromolecule #16: DNA (198-MER)
+Macromolecule #15: RNA (5'-R(P*UP*GP*UP*AP*AP*UP*CP*CP*CP*CP*UP*UP*GP*GP*CP*GP*GP*UP...
+Macromolecule #32: ZINC ION
+Macromolecule #33: 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 | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 51.0 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: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |