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- PDB-6inq: 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: PDB / ID: 6inq | |||||||||||||||||||||
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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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![]() | TRANSCRIPTION/RNA/DNA / ![]() ![]() ![]() ![]() | |||||||||||||||||||||
Function / homology | ![]() regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / negative regulation of chromosome condensation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() ![]() ![]() synthetic construct (others) | |||||||||||||||||||||
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. | |||||||||||||||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1012.6 KB | Display | ![]() |
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PDB format | ![]() | 794.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6986MC ![]() 6980C ![]() 6981C ![]() 6982C ![]() 6983C ![]() 6984C ![]() 6985C ![]() 6a5lC ![]() 6a5oC ![]() 6a5pC ![]() 6a5rC ![]() 6a5tC ![]() 6a5uC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-DNA-directed RNA polymerase ... , 3 types, 3 molecules ABI
#1: Protein | ![]() Mass: 194107.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: GS115 / ATCC 20864 / References: UniProt: C4R4Y0, ![]() |
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#2: Protein | ![]() Mass: 139746.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: GS115 / ATCC 20864 / References: UniProt: C4QZQ7, ![]() |
#9: Protein | ![]() Mass: 13612.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: GS115 / ATCC 20864 / References: UniProt: F2QPE6 |
-RNA polymerase II ... , 4 types, 4 molecules CDGK
#3: Protein | Mass: 34216.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: GS115 / ATCC 20864 / References: UniProt: C4R7L2 |
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#4: Protein | ![]() Mass: 20622.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: GS115 / ATCC 20864 / References: UniProt: C4R2U9 |
#7: Protein | ![]() Mass: 18802.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: GS115 / ATCC 20864 / References: UniProt: C4R9A1 |
#11: Protein | ![]() Mass: 13832.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: GS115 / ATCC 20864 / References: UniProt: C4R3Z5 |
-RNA polymerase subunit ... , 4 types, 4 molecules EFJL
#5: Protein | ![]() Mass: 24962.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: GS115 / ATCC 20864 / References: UniProt: C4R3P8 |
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#6: Protein | ![]() Mass: 17803.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: GS115 / ATCC 20864 / References: UniProt: C4R1V1 |
#10: Protein | ![]() Mass: 8554.064 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: GS115 / ATCC 20864 / References: UniProt: C4R009 |
#12: Protein | ![]() Mass: 7862.048 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: GS115 / ATCC 20864 / References: UniProt: F2QMI1 |
-Protein , 5 types, 9 molecules Haebfcgdh
#8: Protein | ![]() Mass: 16249.220 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: GS115 / ATCC 20864 / References: UniProt: C4R273 | ||||||
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#16: Protein | ![]() Mass: 15643.262 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #17: Protein | ![]() Mass: 11676.703 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, ...Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4 Production host: ![]() ![]() ![]() #18: Protein | Mass: 14447.825 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #19: Protein | Mass: 14217.516 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
-RNA chain , 1 types, 1 molecules P
#13: RNA chain | Mass: 3517.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-DNA chain , 4 types, 4 molecules TN01
#14: DNA chain | Mass: 60869.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#15: DNA chain | Mass: 61381.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#20: DNA chain | Mass: 9544.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#21: DNA chain | Mass: 9520.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 2 types, 9 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MG.gif)
#22: Chemical | ChemComp-ZN / #23: Chemical | ChemComp-MG / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position) Type: COMPLEX / Entity ID: #1-#21 / Source: MULTIPLE SOURCES |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() |
Vitrification![]() | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI ARCTICA |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Image recording | Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
EM software |
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CTF correction![]() | Type: NONE | ||||||||||||
Symmetry | Point symmetry![]() | ||||||||||||
3D reconstruction![]() | Resolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28961 / Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL |