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Yorodumi- PDB-7wbv: RNA polymerase II elongation complex bound with Elf1 and Spt4/5, ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wbv | ||||||||||||||||||||||||||||||
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Title | RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-4) of the nucleosome | ||||||||||||||||||||||||||||||
Components |
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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 / 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 / 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) / positive regulation of cell growth Similarity search - Function | ||||||||||||||||||||||||||||||
Biological species | Komagataella phaffii (fungus) Homo sapiens (human) synthetic construct (others) | ||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||||||||||||||||||||||||||
Authors | Osumi, K. / Kujirai, T. / Ehara, H. / Sekine, S. / Takizawa, Y. / Kurumizaka, H. | ||||||||||||||||||||||||||||||
Funding support | Japan, 9items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wbv.cif.gz | 1.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7wbv.ent.gz | 1.6 MB | Display | PDB format |
PDBx/mmJSON format | 7wbv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/7wbv ftp://data.pdbj.org/pub/pdb/validation_reports/wb/7wbv | HTTPS FTP |
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-Related structure data
Related structure data | 32407MC 7wbwC 7wbxC 8he5C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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) Komagataella phaffii (fungus) / References: UniProt: C4R4Y0, DNA-directed RNA polymerase |
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#2: Protein | Mass: 139746.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Komagataella phaffii (fungus) / Gene: PAS_chr2-1_0125 / Production host: Komagataella pastoris (fungus) / 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) Komagataella phaffii (fungus) / 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 genetically manipulated source Source: (gene. exp.) Komagataella phaffii (fungus) / Gene: PAS_chr4_0344 / Production host: Komagataella pastoris (fungus) / 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) Komagataella phaffii (fungus) / References: UniProt: C4R2U9 |
#7: Protein | Mass: 18802.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii (fungus) / References: UniProt: C4R9A1 |
#11: Protein | Mass: 13832.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii (fungus) / References: UniProt: C4R3Z5 |
-DNA-directed RNA polymerases I, II, and III subunit ... , 2 types, 2 molecules EH
#5: Protein | Mass: 24962.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii (fungus) / References: UniProt: C4R3P8 |
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#8: Protein | Mass: 16249.220 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii (fungus) / References: UniProt: C4R273 |
-Protein , 5 types, 9 molecules Faebfcgdh
#6: Protein | Mass: 17803.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii (fungus) / References: UniProt: C4R1V1 | ||||||
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#19: Protein | Mass: 15643.262 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B / Production host: Escherichia coli (E. coli) / References: UniProt: P84243 #20: Protein | Mass: 11676.703 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, ...Gene: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4-16, HIST4H4 Production host: Escherichia coli (E. coli) / References: UniProt: P62805 #21: Protein | Mass: 14447.825 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE / Production host: Escherichia coli (E. coli) / References: UniProt: P04908 #22: Protein | Mass: 14217.516 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: H2BC11, H2BFR, HIST1H2BJ / Production host: Escherichia coli (E. coli) / References: UniProt: P06899 |
-RNA polymerase subunit ABC10- ... , 2 types, 2 molecules JL
#10: Protein | Mass: 8554.064 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii (fungus) / References: UniProt: C4R009 |
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#12: Protein | Mass: 7862.048 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii (fungus) / References: UniProt: F2QMI1 |
-Transcription elongation factor ... , 3 types, 3 molecules MVW
#13: Protein | Mass: 12606.896 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Komagataella phaffii (fungus) / Gene: PAS_c121_0006 / Production host: Escherichia coli (E. coli) / References: UniProt: C4QZ45 |
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#17: Protein | Mass: 12039.614 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Komagataella phaffii (fungus) / Gene: PAS_chr2-1_0350 / Production host: Escherichia coli (E. coli) / References: UniProt: C4R0E6 |
#18: Protein | Mass: 91353.367 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Komagataella phaffii (fungus) / Gene: SPT5 / Production host: Escherichia coli (E. coli) / References: UniProt: F2QUC3 |
-DNA chain , 2 types, 2 molecules NT
#14: DNA chain | Mass: 61381.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#16: DNA chain | Mass: 60845.949 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-RNA chain , 1 types, 1 molecules P
#15: RNA chain | Mass: 5045.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 2 types, 11 molecules
#23: Chemical | ChemComp-ZN / #24: Chemical | ChemComp-MG / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Source (natural) |
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Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 57.3 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55012 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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