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Yorodumi- EMDB-33436: RNA polymerase II elongation complex transcribing a nucleosome (EC49) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33436 | ||||||||||||||||||||||||
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Title | RNA polymerase II elongation complex transcribing a nucleosome (EC49) | ||||||||||||||||||||||||
Map data | |||||||||||||||||||||||||
Sample |
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Keywords | chromatin / nucleosome / TRANSCRIPTION | ||||||||||||||||||||||||
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 / siRNA-mediated pericentric heterochromatin formation / histone chaperone activity / Cdc73/Paf1 complex / regulation of chromatin organization / DSIF complex / negative regulation of chromosome condensation ...constitutive heterochromatin formation / FACT complex / RNA polymerase II C-terminal domain phosphoserine binding / regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / histone chaperone activity / Cdc73/Paf1 complex / regulation of chromatin organization / DSIF complex / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / nucleosome organization / muscle cell differentiation / regulation of transcription elongation by RNA polymerase II / transcription elongation factor activity / pericentric heterochromatin formation / RPB4-RPB7 complex / inner kinetochore / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / oocyte maturation / transcription elongation-coupled chromatin remodeling / poly(A)+ mRNA export from nucleus / termination of RNA polymerase II transcription / termination of RNA polymerase III transcription / nucleus organization / : / : / 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 / spermatid development / negative regulation of tumor necrosis factor-mediated signaling pathway / subtelomeric heterochromatin formation / single fertilization / transcription elongation by RNA polymerase I / negative regulation of megakaryocyte differentiation / RNA polymerase II core promoter sequence-specific DNA binding / 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 / pericentric heterochromatin / translation elongation factor activity / 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 / 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 / nucleosome binding / 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 / embryo implantation / 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 / transcription elongation factor complex / PRC2 methylates histones and DNA / innate immune response in mucosa / regulation of DNA-templated transcription elongation / 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 / positive regulation of transcription elongation by RNA polymerase II / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / P-body / 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 Similarity search - Function | ||||||||||||||||||||||||
Biological species | Komagataella phaffii (fungus) / synthetic construct (others) / Homo sapiens (human) | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 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_33436.map.gz | 40.8 MB | EMDB map data format | |
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Header (meta data) | emd-33436-v30.xml emd-33436.xml | 66.7 KB 66.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33436_fsc.xml | 8.5 KB | Display | FSC data file |
Images | emd_33436.png | 118.3 KB | ||
Filedesc metadata | emd-33436.cif.gz | 16 KB | ||
Others | emd_33436_additional_1.map.gz emd_33436_additional_2.map.gz emd_33436_half_map_1.map.gz emd_33436_half_map_2.map.gz | 40.8 MB 40.3 MB 40.9 MB 40.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33436 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33436 | HTTPS FTP |
-Validation report
Summary document | emd_33436_validation.pdf.gz | 983.7 KB | Display | EMDB validaton report |
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Full document | emd_33436_full_validation.pdf.gz | 983.3 KB | Display | |
Data in XML | emd_33436_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | emd_33436_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33436 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33436 | HTTPS FTP |
-Related structure data
Related structure data | 7xsxMC 7xn7C 7xseC 7xszC 7xt7C 7xtdC 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_33436.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: EC reconstruction
File | emd_33436_additional_1.map | ||||||||||||
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Annotation | EC reconstruction | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: nucleosome reconstruction
File | emd_33436_additional_2.map | ||||||||||||
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Annotation | nucleosome reconstruction | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33436_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33436_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 (EC49)
+Supramolecule #1: RNA polymerase II elongation complex transcribing a nucleosome (EC49)
+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 #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*GP*AP*CP*CP*CP*GP*GP*GP*UP*GP*UP*CP*UP*UP*CP*CP*CP*CP...
+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 |