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Yorodumi- EMDB-32409: RNA polymerase II elongation complex bound with Elf1 and Spt4/5, ... -
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-Basic information
Entry | Database: EMDB / ID: EMD-32409 | ||||||||||||||||||||||||||||||
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Title | RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3) of the nucleosome | ||||||||||||||||||||||||||||||
Map data | RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3) of the nucleosome | ||||||||||||||||||||||||||||||
Sample |
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Keywords | Transcription / RNA / DNA | ||||||||||||||||||||||||||||||
Function / homology | Function and homology information regulation of septum digestion after cytokinesis / regulatory ncRNA-mediated heterochromatin formation / DSIF complex / nuclear DNA-directed RNA polymerase complex / transcription elongation factor activity / RPB4-RPB7 complex / RNA polymerase III activity / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nucleosomal DNA binding / transcription elongation-coupled chromatin remodeling ...regulation of septum digestion after cytokinesis / regulatory ncRNA-mediated heterochromatin formation / DSIF complex / nuclear DNA-directed RNA polymerase complex / transcription elongation factor activity / RPB4-RPB7 complex / RNA polymerase III activity / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nucleosomal DNA binding / transcription elongation-coupled chromatin remodeling / : / termination of RNA polymerase II transcription / termination of RNA polymerase III transcription / RNA polymerase I activity / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / tRNA transcription by RNA polymerase III / transcription initiation at RNA polymerase I promoter / transcription elongation by RNA polymerase I / positive regulation of translational initiation / RNA polymerase II activity / chromosome, centromeric region / negative regulation of tumor necrosis factor-mediated signaling pathway / RNA polymerase II core promoter sequence-specific DNA binding / negative regulation of megakaryocyte differentiation / RNA polymerase I complex / transcription by RNA polymerase I / RNA polymerase III complex / protein localization to CENP-A containing chromatin / transcription by RNA polymerase III / pericentric heterochromatin / RNA polymerase II, core complex / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / translation initiation factor binding / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / 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 / RNA Polymerase I Promoter Opening / SUMOylation of chromatin organization proteins / Assembly of the ORC complex at the origin of replication / DNA methylation / DNA-directed RNA polymerase complex / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / regulation of DNA-templated transcription elongation / innate immune response in mucosa / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / P-body / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / lipopolysaccharide binding / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / ribonucleoside binding / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / DNA-directed 5'-3' RNA polymerase activity / nucleosome assembly / DNA-directed RNA polymerase / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / single-stranded DNA binding / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / HATs acetylate histones / antibacterial humoral response / Senescence-Associated Secretory Phenotype (SASP) Similarity search - Function | ||||||||||||||||||||||||||||||
Biological species | Komagataella pastoris (fungus) / Homo sapiens (human) / Komagataella phaffii (fungus) / synthetic construct (others) | ||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | ||||||||||||||||||||||||||||||
Authors | Osumi K / Kujirai T / Ehara H / Sekine S / Takizawa Y / Kurumizaka H | ||||||||||||||||||||||||||||||
Funding support | Japan, 9 items
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Citation | Journal: J Mol Biol / Year: 2023 Title: Structural Basis of Damaged Nucleotide Recognition by Transcribing RNA Polymerase II in the Nucleosome. Authors: Ken Osumi / Tomoya Kujirai / Haruhiko Ehara / Mitsuo Ogasawara / Chiaki Kinoshita / Mika Saotome / Wataru Kagawa / Shun-Ichi Sekine / Yoshimasa Takizawa / Hitoshi Kurumizaka / Abstract: In transcription-coupled repair (TCR), transcribing RNA polymerase II (RNAPII) stalls at a DNA lesion and recruits TCR proteins to the damaged site. However, the mechanism by which RNAPII recognizes ...In transcription-coupled repair (TCR), transcribing RNA polymerase II (RNAPII) stalls at a DNA lesion and recruits TCR proteins to the damaged site. However, the mechanism by which RNAPII recognizes a DNA lesion in the nucleosome remains enigmatic. In the present study, we inserted an apurinic/apyrimidinic DNA lesion analogue, tetrahydrofuran (THF), in the nucleosomal DNA, where RNAPII stalls at the SHL(-4), SHL(-3.5), and SHL(-3) positions, and determined the structures of these complexes by cryo-electron microscopy. In the RNAPII-nucleosome complex stalled at SHL(-3.5), the nucleosome orientation relative to RNAPII is quite different from those in the SHL(-4) and SHL(-3) complexes, which have nucleosome orientations similar to naturally paused RNAPII-nucleosome complexes. Furthermore, we found that an essential TCR protein, Rad26 (CSB), enhances the RNAPII processivity, and consequently augments the DNA damage recognition efficiency of RNAPII in the nucleosome. The cryo-EM structure of the Rad26-RNAPII-nucleosome complex revealed that Rad26 binds to the stalled RNAPII through a novel interface, which is completely different from those previously reported. These structures may provide important information to understand the mechanism by which RNAPII recognizes the nucleosomal DNA lesion and recruits TCR proteins to the stalled RNAPII on the nucleosome. | ||||||||||||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32409.map.gz | 133.4 MB | EMDB map data format | |
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Header (meta data) | emd-32409-v30.xml emd-32409.xml | 41.5 KB 41.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_32409_fsc.xml | 12 KB | Display | FSC data file |
Images | emd_32409.png | 77.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32409 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32409 | HTTPS FTP |
-Related structure data
Related structure data | 7wbxMC 7wbvC 7wbwC 8he5C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_32409.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3) of the nucleosome | ||||||||||||||||||||
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
-Sample components
+Entire : RNA polymerase II elongation complex bound with Elf1 and Spt4/5, ...
+Supramolecule #1: RNA polymerase II elongation complex bound with Elf1 and Spt4/5, ...
+Supramolecule #2: RNA polymerase II elongation complex bound with Elf1 and Spt4/5
+Supramolecule #3: Histone
+Supramolecule #4: DNA, 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 #13: Transcription elongation factor 1 homolog
+Macromolecule #17: Transcription elongation factor SPT4
+Macromolecule #18: Transcription elongation factor SPT5
+Macromolecule #19: Histone H3.3
+Macromolecule #20: Histone H4
+Macromolecule #21: Histone H2A type 1-B/E
+Macromolecule #22: Histone H2B type 1-J
+Macromolecule #14: DNA (198-MER)
+Macromolecule #16: DNA (198-MER)
+Macromolecule #15: RNA (5'-R(P*UP*CP*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*CP*UP*G)-3')
+Macromolecule #23: ZINC ION
+Macromolecule #24: 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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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 57.6 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |