+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-0672 | ||||||||||||||||||
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タイトル | RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1A) | ||||||||||||||||||
マップデータ | overall reconstruction (before postprocessing) | ||||||||||||||||||
試料 |
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キーワード | nucleosome / chromatin / RNA polymerase / TRANSCRIPTION / TRANSCRIPTION-RNA-DNA complex | ||||||||||||||||||
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 / transcription elongation factor activity / 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 類似検索 - 分子機能 | ||||||||||||||||||
生物種 | Komagataella phaffii (菌類) / Komagataella phaffii (strain GS115 / ATCC 20864) (菌類) / Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1) (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: 4.3 Å | ||||||||||||||||||
データ登録者 | Ehara H / Kujirai T | ||||||||||||||||||
資金援助 | 日本, 5件
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引用 | ジャーナル: Science / 年: 2019 タイトル: Structural insight into nucleosome transcription by RNA polymerase II with elongation factors. 著者: Haruhiko Ehara / Tomoya Kujirai / Yuka Fujino / Mikako Shirouzu / Hitoshi Kurumizaka / Shun-Ichi Sekine / 要旨: RNA polymerase II (RNAPII) transcribes chromosomal DNA that contains multiple nucleosomes. The nucleosome forms transcriptional barriers, and nucleosomal transcription requires several additional ...RNA polymerase II (RNAPII) transcribes chromosomal DNA that contains multiple nucleosomes. The nucleosome forms transcriptional barriers, and nucleosomal transcription requires several additional factors in vivo. We demonstrate that the transcription elongation factors Elf1 and Spt4/5 cooperatively lower the barriers and increase the RNAPII processivity in the nucleosome. The cryo-electron microscopy structures of the nucleosome-transcribing RNAPII elongation complexes (ECs) reveal that Elf1 and Spt4/5 reshape the EC downstream edge and intervene between RNAPII and the nucleosome. They facilitate RNAPII progression through superhelical location SHL(-1) by adjusting the nucleosome in favor of the forward progression. They suppress pausing at SHL(-5) by preventing the stable RNAPII-nucleosome interaction. Thus, the EC overcomes the nucleosomal barriers while providing a platform for various chromatin functions. | ||||||||||||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_0672.map.gz | 40.7 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-0672-v30.xml emd-0672.xml | 43.6 KB 43.6 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_0672_fsc.xml | 8.6 KB | 表示 | FSCデータファイル |
画像 | emd_0672.png | 121.8 KB | ||
Filedesc metadata | emd-0672.cif.gz | 11.8 KB | ||
その他 | emd_0672_additional_1.map.gz emd_0672_additional_2.map.gz | 40.7 MB 48.3 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-0672 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0672 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_0672_validation.pdf.gz | 570.6 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_0672_full_validation.pdf.gz | 570.2 KB | 表示 | |
XML形式データ | emd_0672_validation.xml.gz | 10.6 KB | 表示 | |
CIF形式データ | emd_0672_validation.cif.gz | 13.8 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0672 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0672 | HTTPS FTP |
-関連構造データ
関連構造データ | 6j4xMC 0671C 0673C 0674C 0675C 0676C 9713C 6ir9C 6j4wC 6j4yC 6j4zC 6j50C 6j51C M: このマップから作成された原子モデル C: 同じ文献を引用 (文献) |
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類似構造データ |
-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_0672.map.gz / 形式: CCP4 / 大きさ: 52.7 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | overall reconstruction (before postprocessing) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.49 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-追加マップ: RNAPII reconstruction
ファイル | emd_0672_additional_1.map | ||||||||||||
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注釈 | RNAPII reconstruction | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Nucleosome reconstruction (postprocessed)
ファイル | emd_0672_additional_2.map | ||||||||||||
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注釈 | Nucleosome reconstruction (postprocessed) | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-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, ...
+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: RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III
+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 #16: Transcription elongation factor 1 homolog
+分子 #17: Transcription elongation factor SPT4
+分子 #18: Protein that forms a complex with Spt4p
+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 #13: RNA (5'-R(P*CP*CP*UP*GP*GP*UP*GP*UP*CP*UP*UP*GP*GP*GP*UP*G)-3')
+分子 #14: DNA (198-MER)
+分子 #15: DNA (198-MER)
+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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グリッド | モデル: Quantifoil R1.2/1.3 / 材質: COPPER |
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TECNAI ARCTICA |
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撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: SUPER-RESOLUTION / 平均電子線量: 50.0 e/Å2 |
電子線 | 加速電圧: 200 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 |
実験機器 | モデル: Talos Arctica / 画像提供: FEI Company |