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基本情報
登録情報 | データベース: EMDB / ID: EMD-11694 | |||||||||
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タイトル | Human pre-Bact-1 spliceosome core structure | |||||||||
![]() | Sharpened/masked map for pre-Bact-1 core structure. | |||||||||
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![]() | Complex / spliceosome / catalytic activation / splicing | |||||||||
機能・相同性 | ![]() microfibril / regulation of retinoic acid receptor signaling pathway / regulation of vitamin D receptor signaling pathway / nuclear retinoic acid receptor binding / transcription elongation factor activity / RNA splicing, via transesterification reactions / U2-type catalytic step 1 spliceosome / positive regulation of mRNA splicing, via spliceosome / host-mediated activation of viral transcription / U2-type precatalytic spliceosome ...microfibril / regulation of retinoic acid receptor signaling pathway / regulation of vitamin D receptor signaling pathway / nuclear retinoic acid receptor binding / transcription elongation factor activity / RNA splicing, via transesterification reactions / U2-type catalytic step 1 spliceosome / positive regulation of mRNA splicing, via spliceosome / host-mediated activation of viral transcription / U2-type precatalytic spliceosome / U2-type spliceosomal complex / positive regulation of vitamin D receptor signaling pathway / mRNA cis splicing, via spliceosome / nuclear vitamin D receptor binding / RNA polymerase binding / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / Notch binding / positive regulation of neurogenesis / RUNX3 regulates NOTCH signaling / U2-type catalytic step 2 spliceosome / NOTCH4 Intracellular Domain Regulates Transcription / positive regulation of protein targeting to mitochondrion / NOTCH3 Intracellular Domain Regulates Transcription / ubiquitin-like protein conjugating enzyme binding / WW domain binding / nuclear androgen receptor binding / K63-linked polyubiquitin modification-dependent protein binding / precatalytic spliceosome / Notch-HLH transcription pathway / Formation of paraxial mesoderm / SMAD binding / positive regulation of transforming growth factor beta receptor signaling pathway / mRNA Splicing - Minor Pathway / negative regulation of transcription elongation by RNA polymerase II / spliceosomal tri-snRNP complex assembly / Prp19 complex / U5 snRNA binding / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / U5 snRNP / protein localization to nucleus / positive regulation of G1/S transition of mitotic cell cycle / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / Cajal body / U1 snRNA binding / retinoic acid receptor signaling pathway / U4/U6 x U5 tri-snRNP complex / cellular response to retinoic acid / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / nuclear receptor binding / transcription coregulator activity / spliceosomal complex / response to cocaine / positive regulation of transcription elongation by RNA polymerase II / Downregulation of SMAD2/3:SMAD4 transcriptional activity / protein modification process / mRNA splicing, via spliceosome / NOTCH1 Intracellular Domain Regulates Transcription / Pre-NOTCH Transcription and Translation / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / protein tag activity / nuclear matrix / fibrillar center / mRNA processing / rRNA processing / transcription corepressor activity / cellular response to xenobiotic stimulus / cellular response to tumor necrosis factor / single-stranded DNA binding / cellular response to lipopolysaccharide / microtubule cytoskeleton / nuclear membrane / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / nuclear speck / nuclear body / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / GTPase activity / centrosome / regulation of transcription by RNA polymerase II / chromatin / GTP binding / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / membrane / cytosol / cytoplasm 類似検索 - 分子機能 | |||||||||
生物種 | ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.9 Å | |||||||||
![]() | Townsend C / Kastner B | |||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Mechanism of protein-guided folding of the active site U2/U6 RNA during spliceosome activation. 著者: Cole Townsend / Majety N Leelaram / Dmitry E Agafonov / Olexandr Dybkov / Cindy L Will / Karl Bertram / Henning Urlaub / Berthold Kastner / Holger Stark / Reinhard Lührmann / ![]() 要旨: Spliceosome activation involves extensive protein and RNA rearrangements that lead to formation of a catalytically active U2/U6 RNA structure. At present, little is known about the assembly pathway ...Spliceosome activation involves extensive protein and RNA rearrangements that lead to formation of a catalytically active U2/U6 RNA structure. At present, little is known about the assembly pathway of the latter and the mechanism whereby proteins aid its proper folding. Here, we report the cryo-electron microscopy structures of two human, activated spliceosome precursors (that is, pre-B complexes) at core resolutions of 3.9 and 4.2 angstroms. These structures elucidate the order of the numerous protein exchanges that occur during activation, the mutually exclusive interactions that ensure the correct order of ribonucleoprotein rearrangements needed to form the U2/U6 catalytic RNA, and the stepwise folding pathway of the latter. Structural comparisons with mature B complexes reveal the molecular mechanism whereby a conformational change in the scaffold protein PRP8 facilitates final three-dimensional folding of the U2/U6 catalytic RNA. | |||||||||
履歴 |
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構造の表示
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構造ビューア | EMマップ: ![]() ![]() ![]() |
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ダウンロードとリンク
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マップデータ | ![]() | 14.5 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 35.4 KB 35.4 KB | 表示 表示 | ![]() |
画像 | ![]() | 33.8 KB | ||
Filedesc metadata | ![]() | 12 KB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 363.8 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 363.4 KB | 表示 | |
XML形式データ | ![]() | 7 KB | 表示 | |
CIF形式データ | ![]() | 8.1 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 7abfMC ![]() 7aavC ![]() 7abgC ![]() 7abhC ![]() 7abiC 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 ( |
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類似構造データ | |
電子顕微鏡画像生データ | ![]() Data #1: Motion-corrected micrographs (without dose-weighting) of human pre-Bact spliceosome [micrographs - single frame] Data #2: Motion-corrected micrographs (with dose-weighting) of human pre-Bact spliceosome [micrographs - single frame]) |
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Sharpened/masked map for pre-Bact-1 core structure. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.16 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
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試料の構成要素
+全体 : pre-Bact-1 spliceosomal complex
+超分子 #1: pre-Bact-1 spliceosomal complex
+超分子 #2: pre-Bact-1 spliceosomal complex
+超分子 #3: MINX M3 RNA
+分子 #1: Protein BUD31 homolog
+分子 #2: Pre-mRNA-splicing factor 38A
+分子 #3: Pre-mRNA-processing-splicing factor 8
+分子 #4: 116 kDa U5 small nuclear ribonucleoprotein component
+分子 #5: Zinc finger matrin-type protein 2
+分子 #6: Ubiquitin-like protein 5
+分子 #7: Spliceosome-associated protein CWC15 homolog
+分子 #10: WW domain-binding protein 11
+分子 #11: SNW domain-containing protein 1
+分子 #12: Pleiotropic regulator 1
+分子 #14: Microfibrillar-associated protein 1
+分子 #15: Transcription elongation regulator 1
+分子 #8: U5 small nuclear RNA
+分子 #9: U6 small nuclear RNA
+分子 #13: MINX M3 RNA
+分子 #16: INOSITOL HEXAKISPHOSPHATE
+分子 #17: GUANOSINE-5'-TRIPHOSPHATE
+分子 #18: 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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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
緩衝液 | pH: 7.9 |
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グリッド | モデル: Quantifoil R3.5/1 / 材質: COPPER / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: CONTINUOUS |
凍結 | 凍結剤: ETHANE / 装置: FEI VITROBOT MARK IV |
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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: FEI FALCON III (4k x 4k) 検出モード: INTEGRATING / デジタル化 - サイズ - 横: 4096 pixel / デジタル化 - サイズ - 縦: 4096 pixel / 平均露光時間: 1.0 sec. / 平均電子線量: 2.25 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 照射モード: SPOT SCAN / 撮影モード: BRIGHT FIELD |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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画像解析
初期モデル | モデルのタイプ: OTHER / 詳細: cryoSPARC ab initio reconstruction |
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最終 再構成 | 想定した対称性 - 点群: C1 (非対称) / 解像度のタイプ: BY AUTHOR / 解像度: 3.9 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: RELION (ver. 3.0) / 使用した粒子像数: 84539 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
-原子モデル構築 1
精密化 | 空間: REAL / プロトコル: RIGID BODY FIT |
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得られたモデル | ![]() PDB-7abf: |