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- EMDB-36252: RNA polymerase II elongation complex containing 40 bp upstream DN... -
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Open data
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Basic information
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Title | RNA polymerase II elongation complex containing 40 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome | |||||||||||||||||||||||||||||||||
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![]() | Transcription-DNA-RNA complex / RNAPII | |||||||||||||||||||||||||||||||||
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 | ![]() ![]() | |||||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||||||||||||||||||||||||||
![]() | Akatsu M / Fujita R / Ogasawara M / Ehara H / Kujirai T / Takizawa Y / Sekine S / Kurumizaka H | |||||||||||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structures of RNA polymerase II-nucleosome complexes rewrapping transcribed DNA. Authors: Munetaka Akatsu / Haruhiko Ehara / Tomoya Kujirai / Risa Fujita / Tomoko Ito / Ken Osumi / Mitsuo Ogasawara / Yoshimasa Takizawa / Shun-Ichi Sekine / Hitoshi Kurumizaka / ![]() Abstract: RNA polymerase II (RNAPII) transcribes DNA wrapped in the nucleosome by stepwise pausing, especially at nucleosomal superhelical locations -5 and -1 [SHL(-5) and SHL(-1), respectively]. In the ...RNA polymerase II (RNAPII) transcribes DNA wrapped in the nucleosome by stepwise pausing, especially at nucleosomal superhelical locations -5 and -1 [SHL(-5) and SHL(-1), respectively]. In the present study, we performed cryo-electron microscopy analyses of RNAPII-nucleosome complexes paused at a major nucleosomal pausing site, SHL(-1). We determined two previously undetected structures, in which the transcribed DNA behind RNAPII is sharply kinked at the RNAPII exit tunnel and rewrapped around the nucleosomal histones in front of RNAPII by DNA looping. This DNA kink shifts the DNA orientation toward the nucleosome, and the transcribed DNA region interacts with basic amino acid residues of histones H2A, H2B, and H3 exposed by the RNAPII-mediated nucleosomal DNA peeling. The DNA loop structure was not observed in the presence of the transcription elongation factors Spt4/5 and Elf1. These RNAPII-nucleosome structures provide important information for understanding the functional relevance of DNA looping during transcription elongation in the nucleosome. | |||||||||||||||||||||||||||||||||
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Structure visualization
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Downloads & links
-EMDB archive
Map data | ![]() | 13.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 46.8 KB 46.8 KB | Display Display | ![]() |
Images | ![]() | 113.1 KB | ||
Filedesc metadata | ![]() | 11 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() | 6.3 MB 11.2 MB 163.3 MB 140.7 MB 140.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8jh3MC ![]() 8jh2C ![]() 8jh4C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #3
File | emd_36252_additional_1.map | ||||||||||||
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Density Histograms |
-Additional map: #2
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-Additional map: #1
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-Half map: #2
File | emd_36252_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_36252_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
+Entire : RNA polymerase II - nucleosome complex
+Supramolecule #1: RNA polymerase II - nucleosome complex
+Supramolecule #2: RNA polymerase II
+Supramolecule #3: Histones
+Supramolecule #4: DNA
+Supramolecule #5: RNA
+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 #16: Histone H3.3
+Macromolecule #17: Histone H4
+Macromolecule #18: Histone H2A type 1-B/E
+Macromolecule #19: Histone H2B type 1-J
+Macromolecule #13: DNA (198-MER)
+Macromolecule #15: DNA (198-MER)
+Macromolecule #14: RNA (5'-R(P*GP*GP*UP*GP*UP*CP*UP*UP*GP*GP*GP*UP*GP)-3')
+Macromolecule #20: ZINC ION
+Macromolecule #21: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.09144 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
Details: 20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III | |||||||||||||||
Details | dsDNA concentration is 0.09144 mg/mL. This sample contains 0.005% Tween20. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 59.84 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
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 |
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Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 51652 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |