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Yorodumi- EMDB-32409: RNA polymerase II elongation complex bound with Elf1 and Spt4/5, ... -
+Open data
-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 / siRNA-mediated pericentric heterochromatin formation / DSIF complex / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / muscle cell differentiation / regulation of transcription elongation by RNA polymerase II / transcription elongation factor activity / pericentric heterochromatin formation ...regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / DSIF complex / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / muscle cell differentiation / regulation of transcription elongation by RNA polymerase II / transcription elongation factor activity / pericentric heterochromatin formation / RPB4-RPB7 complex / inner kinetochore / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / oocyte maturation / transcription elongation-coupled chromatin remodeling / termination of RNA polymerase II transcription / termination of RNA polymerase III transcription / nucleus organization / : / : / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / RNA polymerase II complex binding / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / transcription initiation at RNA polymerase I promoter / chromosome, centromeric region / spermatid development / negative regulation of tumor necrosis factor-mediated signaling pathway / subtelomeric heterochromatin formation / single fertilization / transcription elongation by RNA polymerase I / negative regulation of megakaryocyte differentiation / RNA polymerase II core promoter sequence-specific DNA binding / positive regulation of translational initiation / RNA polymerase I complex / RNA polymerase III complex / protein localization to CENP-A containing chromatin / transcription-coupled nucleotide-excision repair / RNA polymerase III activity / RNA polymerase II, core complex / pericentric heterochromatin / tRNA transcription by RNA polymerase III / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / RNA polymerase I activity / heterochromatin organization / Packaging Of Telomere Ends / RNA polymerase II activity / 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 / nucleosomal DNA binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / translation initiation factor binding / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / embryo implantation / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / transcription elongation factor complex / PRC2 methylates histones and DNA / innate immune response in mucosa / regulation of DNA-templated transcription elongation / Defective pyroptosis / HDACs deacetylate histones / transcription elongation by RNA polymerase II / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / transcription initiation at RNA polymerase II promoter / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / P-body / 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 / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / HDMs demethylate histones / multicellular organism growth / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / ribonucleoside binding / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / Activation of anterior HOX genes in hindbrain development during early embryogenesis 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 | ||||||||||||||||||||||||||||||
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 | 42.8 KB 42.8 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 | ||
Filedesc metadata | emd-32409.cif.gz | 11.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32409 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32409 | HTTPS FTP |
-Validation report
Summary document | emd_32409_validation.pdf.gz | 598.6 KB | Display | EMDB validaton report |
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Full document | emd_32409_full_validation.pdf.gz | 598.2 KB | Display | |
Data in XML | emd_32409_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | emd_32409_validation.cif.gz | 16.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32409 ftp://ftp.pdbj.org/pub/emdb/validation_reports/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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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 57.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
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 |