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Yorodumi- EMDB-6985: RNA polymerase II elongation complex stalled at SHL(-1) of the nu... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6985 | |||||||||||||||||||||
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Title | RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA, tilt conformation | |||||||||||||||||||||
Map data | whole, postprocessed | |||||||||||||||||||||
Sample |
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Keywords | nucleosome / chromatin / RNA polymerase / TRANSCRIPTION / TRANSCRIPTION-RNA-DNA complex | |||||||||||||||||||||
Function / homology | Function and homology information regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / muscle cell differentiation / RPB4-RPB7 complex / pericentric heterochromatin formation / inner kinetochore / oocyte maturation ...regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / muscle cell differentiation / RPB4-RPB7 complex / pericentric heterochromatin formation / inner kinetochore / oocyte maturation / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 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 / 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 / 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 / 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 / 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 / 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 / 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 / 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 / B-WICH complex positively regulates rRNA expression / multicellular organism growth / heterochromatin formation / 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 / osteoblast differentiation / structural constituent of chromatin / male gonad development / UCH proteinases / nucleosome Similarity search - Function | |||||||||||||||||||||
Biological species | Komagataella phaffii (fungus) / Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) / Homo sapiens (human) / synthetic construct (others) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.6 Å | |||||||||||||||||||||
Authors | Kujirai T / Ehara H / Fujino Y / Shirouzu M / Sekine S / Kurumizaka H | |||||||||||||||||||||
Funding support | Japan, 6 items
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Citation | Journal: Science / Year: 2018 Title: Structural basis of the nucleosome transition during RNA polymerase II passage. Authors: Tomoya Kujirai / Haruhiko Ehara / Yuka Fujino / Mikako Shirouzu / Shun-Ichi Sekine / Hitoshi Kurumizaka / Abstract: Genomic DNA forms chromatin, in which the nucleosome is the repeating unit. The mechanism by which RNA polymerase II (RNAPII) transcribes the nucleosomal DNA remains unclear. Here we report the cryo- ...Genomic DNA forms chromatin, in which the nucleosome is the repeating unit. The mechanism by which RNA polymerase II (RNAPII) transcribes the nucleosomal DNA remains unclear. Here we report the cryo-electron microscopy structures of RNAPII-nucleosome complexes in which RNAPII pauses at the superhelical locations SHL(-6), SHL(-5), SHL(-2), and SHL(-1) of the nucleosome. RNAPII pauses at the major histone-DNA contact sites, and the nucleosome interactions with the RNAPII subunits stabilize the pause. These structures reveal snapshots of nucleosomal transcription, in which RNAPII gradually tears DNA from the histone surface while preserving the histone octamer. The nucleosomes in the SHL(-1) complexes are bound to a "foreign" DNA segment, which might explain the histone transfer mechanism. These results provide the foundations for understanding chromatin transcription and epigenetic regulation. | |||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6985.map.gz | 48.1 MB | EMDB map data format | |
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Header (meta data) | emd-6985-v30.xml emd-6985.xml | 40.2 KB 40.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_6985_fsc.xml | 8.6 KB | Display | FSC data file |
Images | emd_6985.png | 89.6 KB | ||
Filedesc metadata | emd-6985.cif.gz | 10.7 KB | ||
Others | emd_6985_additional.map.gz | 49.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6985 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6985 | HTTPS FTP |
-Validation report
Summary document | emd_6985_validation.pdf.gz | 539.5 KB | Display | EMDB validaton report |
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Full document | emd_6985_full_validation.pdf.gz | 539.1 KB | Display | |
Data in XML | emd_6985_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | emd_6985_validation.cif.gz | 13.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6985 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6985 | HTTPS FTP |
-Related structure data
Related structure data | 6a5uMC 6980C 6981C 6982C 6983C 6984C 6986C 6a5lC 6a5oC 6a5pC 6a5rC 6a5tC 6inqC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_6985.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | whole, postprocessed | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.49 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: nucleosome, postprocessed
File | emd_6985_additional.map | ||||||||||||
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Annotation | nucleosome, postprocessed | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : RNA polymerase II elongation complex stalled at SHL(-1) of the nu...
+Supramolecule #1: RNA polymerase II elongation complex stalled at SHL(-1) of the nu...
+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: RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III
+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 H3.3
+Macromolecule #17: Histone H4
+Macromolecule #18: Histone H2A, Histone H2A type 1-B/E
+Macromolecule #19: Histone H2B, Histone H2B type 1-J
+Macromolecule #13: RNA (5'-R(P*GP*GP*UP*GP*UP*CP*UP*UP*GP*GP*G)-3')
+Macromolecule #14: DNA (198-MER)
+Macromolecule #15: DNA (198-MER)
+Macromolecule #20: DNA (40-MER)
+Macromolecule #21: DNA (40-MER)
+Macromolecule #22: ZINC ION
+Macromolecule #23: 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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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-6a5u: |