+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-32407 | ||||||||||||||||||||||||||||||
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タイトル | RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-4) of the nucleosome | ||||||||||||||||||||||||||||||
マップデータ | RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-4) of the nucleosome | ||||||||||||||||||||||||||||||
試料 |
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キーワード | Transcription / RNA / DNA | ||||||||||||||||||||||||||||||
機能・相同性 | 機能・相同性情報 regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / negative regulation of chromosome condensation / DSIF complex / Barr body / regulation of centromere complex assembly / muscle cell differentiation / regulation of transcription elongation by RNA polymerase II / RPB4-RPB7 complex / pericentric heterochromatin formation ...regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / negative regulation of chromosome condensation / DSIF complex / Barr body / regulation of centromere complex assembly / muscle cell differentiation / regulation of transcription elongation by RNA polymerase II / RPB4-RPB7 complex / pericentric heterochromatin formation / inner kinetochore / oocyte maturation / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 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 / RNA polymerase III activity / transcription initiation at RNA polymerase III promoter / RNA polymerase II complex binding / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / protein localization to CENP-A containing chromatin / transcription initiation at RNA polymerase I promoter / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / CENP-A containing nucleosome / chromosome, centromeric region / RNA polymerase II activity / spermatid development / negative regulation of tumor necrosis factor-mediated signaling pathway / subtelomeric heterochromatin formation / Replacement of protamines by nucleosomes in the male pronucleus / transcription elongation by RNA polymerase I / single fertilization / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / tRNA transcription by RNA polymerase III / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase I activity / Packaging Of Telomere Ends / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / transcription-coupled nucleotide-excision repair / lipoxygenase pathway / RNA polymerase II, core complex / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / pericentric heterochromatin / telomere organization / arachidonate metabolic process / lipid oxidation / Deposition of new CENPA-containing nucleosomes at the centromere / hepoxilin biosynthetic process / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / linoleic acid metabolic process / Meiotic synapsis / Inhibition of DNA recombination at telomere / nucleosomal DNA binding / translation initiation factor binding / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / embryo implantation / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / transcription elongation factor complex / Defective pyroptosis / Meiotic recombination / innate immune response in mucosa / DNA Damage/Telomere Stress Induced Senescence / regulation of DNA-templated transcription elongation / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / transcription initiation at RNA polymerase II promoter / lipopolysaccharide binding / Transcriptional regulation of granulopoiesis / transcription elongation by RNA polymerase II / Formation of the beta-catenin:TCF transactivating complex / HCMV Early Events / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / P-body / G2/M DNA damage checkpoint / 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 / multicellular organism growth / heterochromatin formation / RMTs methylate histone arginines / ribonucleoside binding / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / Activation of anterior HOX genes in hindbrain development during early embryogenesis 類似検索 - 分子機能 | ||||||||||||||||||||||||||||||
生物種 | Komagataella phaffii (菌類) / Homo sapiens (ヒト) / synthetic construct (人工物) | ||||||||||||||||||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.1 Å | ||||||||||||||||||||||||||||||
データ登録者 | Osumi K / Kujirai T | ||||||||||||||||||||||||||||||
資金援助 | 日本, 9件
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引用 | ジャーナル: J Mol Biol / 年: 2023 タイトル: Structural Basis of Damaged Nucleotide Recognition by Transcribing RNA Polymerase II in the Nucleosome. 著者: Ken Osumi / Tomoya Kujirai / Haruhiko Ehara / Mitsuo Ogasawara / Chiaki Kinoshita / Mika Saotome / Wataru Kagawa / Shun-Ichi Sekine / Yoshimasa Takizawa / Hitoshi Kurumizaka / 要旨: 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. | ||||||||||||||||||||||||||||||
履歴 |
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-構造の表示
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_32407.map.gz | 133.9 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-32407-v30.xml emd-32407.xml | 42.5 KB 42.5 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_32407_fsc.xml | 12 KB | 表示 | FSCデータファイル |
画像 | emd_32407.png | 81.4 KB | ||
Filedesc metadata | emd-32407.cif.gz | 11.3 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-32407 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32407 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_32407_validation.pdf.gz | 593.3 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_32407_full_validation.pdf.gz | 592.9 KB | 表示 | |
XML形式データ | emd_32407_validation.xml.gz | 12.5 KB | 表示 | |
CIF形式データ | emd_32407_validation.cif.gz | 16.8 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32407 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32407 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_32407.map.gz / 形式: CCP4 / 大きさ: 144.7 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-4) of the nucleosome | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.06 Å | ||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-試料の構成要素
+全体 : RNA polymerase II elongation complex bound with Elf1 and Spt4/5, ...
+超分子 #1: RNA polymerase II elongation complex bound with Elf1 and Spt4/5, ...
+超分子 #2: RNA polymerase II elongation complex bound with Elf1 and Spt4/5
+超分子 #3: Histone
+超分子 #4: DNA, RNA
+分子 #1: DNA-directed RNA polymerase subunit
+分子 #2: DNA-directed RNA polymerase subunit beta
+分子 #3: RNA polymerase II third largest subunit B44, part of central core
+分子 #4: RNA polymerase II subunit B32
+分子 #5: DNA-directed RNA polymerases I, II, and III subunit RPABC1
+分子 #6: RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
+分子 #7: RNA polymerase II subunit
+分子 #8: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+分子 #9: DNA-directed RNA polymerase subunit
+分子 #10: RNA polymerase subunit ABC10-beta, common to RNA polymerases I, I...
+分子 #11: RNA polymerase II subunit B12.5
+分子 #12: RNA polymerase subunit ABC10-alpha
+分子 #13: Transcription elongation factor 1 homolog
+分子 #17: Transcription elongation factor SPT4
+分子 #18: Transcription elongation factor SPT5
+分子 #19: Histone H3.3
+分子 #20: Histone H4
+分子 #21: Histone H2A type 1-B/E
+分子 #22: Histone H2B type 1-J
+分子 #14: DNA (198-MER)
+分子 #16: DNA (159-MER)
+分子 #15: RNA (5'-R(P*UP*GP*GP*CP*CP*GP*UP*UP*UP*UP*CP*GP*UP*UP*GP*U)-3')
+分子 #23: ZINC ION
+分子 #24: MAGNESIUM ION
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
緩衝液 | pH: 7.5 |
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凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 平均電子線量: 57.3 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2.5 µm / 最小 デフォーカス(公称値): 1.0 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |