- EMDB-36251: RNA polymerase II elongation complex bound with Elf1, Spt4/5 and ... -
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Basic information
Entry
Database: EMDB / ID: EMD-36251
Title
RNA polymerase II elongation complex bound with Elf1, Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome
Map data
Sample
Complex: RNA polymerase II - nucleosome complex
Complex: RNA polymerase II
Complex: Histones
Complex: DNA
Complex: RNA
DNA: x 4 types
Protein or peptide: x 19 types
RNA: x 1 types
Ligand: x 2 types
Keywords
Transcription-DNA-RNA complex / RNAPII / Cryo-EM
Function / homology
Function and homology information
regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / negative regulation of chromosome condensation / Barr body / DSIF complex / : / RPB4-RPB7 complex / inner kinetochore / pericentric heterochromatin formation / chromatin-protein adaptor activity ...regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / negative regulation of chromosome condensation / Barr body / DSIF complex / : / RPB4-RPB7 complex / inner kinetochore / pericentric heterochromatin formation / chromatin-protein adaptor activity / transcription elongation factor activity / muscle cell differentiation / oocyte maturation / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nucleosomal DNA binding / termination of RNA polymerase II transcription / termination of RNA polymerase III transcription / transcription elongation-coupled chromatin remodeling / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / nucleus organization / transcription initiation at RNA polymerase III promoter / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase I promoter / pericentric heterochromatin / RNA polymerase II complex binding / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of translational initiation / chromosome, centromeric region / spermatid development / negative regulation of tumor necrosis factor-mediated signaling pathway / single fertilization / subtelomeric heterochromatin formation / RNA polymerase I complex / negative regulation of megakaryocyte differentiation / transcription elongation by RNA polymerase I / RNA polymerase III complex / RNA polymerase II core promoter sequence-specific DNA binding / protein localization to CENP-A containing chromatin / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / Replacement of protamines by nucleosomes in the male pronucleus / transcription by RNA polymerase I / CENP-A containing nucleosome / Packaging Of Telomere Ends / translation initiation factor binding / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / transcription-coupled nucleotide-excision repair / 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 / embryo implantation / telomere organization / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / innate immune response in mucosa / transcription elongation factor complex / regulation of DNA-templated transcription elongation / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDMs demethylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / transcription elongation by RNA polymerase II / lipopolysaccharide binding / P-body / 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 / G2/M DNA damage checkpoint / Metalloprotease DUBs / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / ribonucleoside binding / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / multicellular organism growth / male gonad development / Transcriptional regulation of granulopoiesis / DNA-directed RNA polymerase / UCH proteinases Similarity search - Function
Transcription elongation factor 1 homolog / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerase II subunit B32 / Transcription elongation factor SPT5 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerase II subunit B12.5 / DNA-directed RNA polymerase subunit ...Transcription elongation factor 1 homolog / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerase II subunit B32 / Transcription elongation factor SPT5 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerase II subunit B12.5 / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase subunit / RNA polymerase subunit ABC10-alpha / DNA-directed RNA polymerase subunit / Transcription elongation factor SPT4 / Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H4 / Histone H3.3 Similarity search - Component
Japan Agency for Medical Research and Development (AMED)
JP22ama121009
Japan
Japan Science and Technology
JPMJER1901
Japan
Citation
Journal: J Biol Chem / Year: 2023 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.
Macromolecule #12: RNA polymerase subunit ABC10-beta, common to RNA polymerases I, I...
Macromolecule
Name: RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
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