[English] 日本語
![](img/lk-miru.gif)
- PDB-6a5p: RNA polymerase II elongation complex stalled at SHL(-5) of the nu... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6a5p | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | RNA polymerase II elongation complex stalled at SHL(-5) of the nucleosome | |||||||||||||||||||||
![]() |
| |||||||||||||||||||||
![]() | TRANSCRIPTION/RNA/DNA / nucleosome / chromatin / RNA polymerase / TRANSCRIPTION / TRANSCRIPTION-RNA-DNA complex | |||||||||||||||||||||
Function / homology | ![]() 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 / transcription initiation at RNA polymerase I promoter / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / RNA polymerase II activity / spermatid development / negative regulation of tumor necrosis factor-mediated signaling pathway / subtelomeric heterochromatin formation / transcription elongation by RNA polymerase I / single fertilization / tRNA transcription by RNA polymerase III / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase I activity / negative regulation of megakaryocyte differentiation / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / transcription-coupled nucleotide-excision repair / protein localization to CENP-A containing chromatin / RNA polymerase II, core complex / pericentric heterochromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / nucleosomal DNA binding / Deposition of new CENPA-containing nucleosomes at the centromere / translation initiation factor binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / embryo implantation / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / innate immune response in mucosa / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Nonhomologous End-Joining (NHEJ) / transcription elongation by RNA polymerase II / Transcriptional regulation by small RNAs / P-body / Formation of the beta-catenin:TCF transactivating complex / 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 / multicellular organism growth / G2/M DNA damage checkpoint / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / heterochromatin formation / DNA Damage/Telomere Stress Induced Senescence / ribonucleoside binding / Metalloprotease DUBs / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / osteoblast differentiation / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / male gonad development / UCH proteinases / antimicrobial humoral immune response mediated by antimicrobial peptide / nucleosome / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() ![]() synthetic construct (others) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7 Å | |||||||||||||||||||||
![]() | Kujirai, T. / Ehara, H. / Fujino, Y. / Shirouzu, M. / Sekine, S. / Kurumizaka, H. | |||||||||||||||||||||
Funding support | ![]()
| |||||||||||||||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 1018.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 800.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 6982MC ![]() 6980C ![]() 6981C ![]() 6983C ![]() 6984C ![]() 6985C ![]() 6986C ![]() 6a5lC ![]() 6a5oC ![]() 6a5rC ![]() 6a5tC ![]() 6a5uC ![]() 6inqC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data | |
EM raw data | ![]() Data size: 1.4 TB Data #1: Unaligned movies of RNA polymerase II transcribing a nucleosome [micrographs - multiframe]) |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
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, DNA-directed RNA polymerase |
---|---|
#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, DNA-directed RNA polymerase |
#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 |
---|---|
#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 |
---|---|
#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 | ||||||
---|---|---|---|---|---|---|---|
#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: 3595.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: produced by in vitro transcription / Source: (synth.) synthetic construct (others) |
---|
-DNA chain , 2 types, 2 molecules TN
#14: DNA chain | Mass: 60869.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
---|---|
#15: DNA chain | Mass: 61381.906 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)
#20: Chemical | ChemComp-ZN / #21: Chemical | ChemComp-MG / | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: RNA polymerase II elongation complex stalled at SHL(-5) of the nucleosome Type: COMPLEX / Entity ID: #1-#19 / Source: MULTIPLE SOURCES |
---|---|
Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
---|---|
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) |
-
Processing
EM software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 91888 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL |