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- EMDB-6986: RNA polymerase II elongation complex stalled at SHL(-1) of the nu... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-6986 | |||||||||||||||||||||
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Title | RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position) | |||||||||||||||||||||
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![]() | RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position)
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Function / homology | ![]() regulation of septum digestion after cytokinesis / telomeric repeat-containing RNA transcription by RNA polymerase II / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||||||||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||||||||||||||
Method | ![]() ![]() | |||||||||||||||||||||
![]() | Kujirai T / Ehara H / Fujino Y / Shirouzu M / Sekine S / Kurumizaka H | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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. | |||||||||||||||||||||
Validation Report | ![]() ![]() ![]() ![]() | |||||||||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
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Download
FSC (resolution estimation) |
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Header (meta data in XML format) |
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Images |
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Others |
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Archive directory |
-Related structure data
Related structure data | ![]() 6inqCM ![]() 6980C ![]() 6981C ![]() 6982C ![]() 6983C ![]() 6984C ![]() 6985C ![]() 6a5lC ![]() 6a5oC ![]() 6a5pC ![]() 6a5rC ![]() 6a5tC ![]() 6a5uC C: citing same article ( M: atomic model generated by this map |
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Similar-shape strucutres |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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_6986_additional.map | ||||||||||||
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Annotation | nucleosome, postprocessed | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire RNA polymerase II elongation complex stalled at SHL(-1) of the nu...
+Component #1: protein, RNA polymerase II elongation complex stalled at SHL(-1) ...
+Component #2: protein, DNA-directed RNA polymerase subunit
+Component #3: protein, DNA-directed RNA polymerase subunit beta
+Component #4: protein, RNA polymerase II third largest subunit B44, part of cen...
+Component #5: protein, RNA polymerase II subunit B32
+Component #6: protein, RNA polymerase subunit ABC27, common to RNA polymerases ...
+Component #7: protein, RNA polymerase subunit ABC23, common to RNA polymerases ...
+Component #8: protein, RNA polymerase II subunit
+Component #9: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Component #10: protein, DNA-directed RNA polymerase subunit
+Component #11: protein, RNA polymerase subunit ABC10-beta, common to RNA polymer...
+Component #12: protein, RNA polymerase II subunit B12.5
+Component #13: protein, RNA polymerase subunit ABC10-alpha
+Component #14: nucleic-acid, RNA (5'-R(P*GP*UP*GP*UP*CP*UP*UP*GP*GP*GP*U)-3')
+Component #15: nucleic-acid, DNA (198-MER)
+Component #16: nucleic-acid, DNA (198-MER)
+Component #17: protein, Histone H3.3
+Component #18: protein, Histone H4
+Component #19: protein, Histone H2A, Histone H2A type 1-B/E
+Component #20: protein, Histone H2B, Histone H2B type 1-J
+Component #21: nucleic-acid, DNA (31-MER)
+Component #22: nucleic-acid, DNA (31-MER)
+Component #23: ligand, ZINC ION
+Component #24: ligand, MAGNESIUM ION
-Experimental details
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Sample preparation
Specimen | Specimen state: Particle / Method: ![]() |
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Sample solution | pH: 7.5 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 100 % |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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![]() | Microscope: FEI TECNAI ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN![]() |
Lens | Imaging mode: BRIGHT FIELD![]() |
Specimen Holder | Model: OTHER |
Camera | Detector: GATAN K2 SUMMIT (4k x 4k) |
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Image processing
-Atomic model buiding
Modeling #1 | Refinement protocol: rigid body / Refinement space: REAL |
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Output model |