+データを開く
-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 | |||||||||
マップデータ | Sharpened/masked map for pre-Bact-1 core structure. | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 microfibril / regulation of retinoic acid receptor signaling pathway / WW domain binding / regulation of vitamin D receptor signaling pathway / transcription elongation factor activity / nuclear retinoic acid receptor binding / Prp19 complex / positive regulation of androgen receptor activity / U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions ...microfibril / regulation of retinoic acid receptor signaling pathway / WW domain binding / regulation of vitamin D receptor signaling pathway / transcription elongation factor activity / nuclear retinoic acid receptor binding / Prp19 complex / positive regulation of androgen receptor activity / U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / positive regulation by host of viral transcription / U2-type precatalytic spliceosome / positive regulation of vitamin D receptor signaling pathway / U2-type catalytic step 2 spliceosome / nuclear vitamin D receptor binding / ubiquitin-like protein conjugating enzyme binding / RNA polymerase binding / Notch binding / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / positive regulation of mRNA splicing, via spliceosome / NOTCH4 Intracellular Domain Regulates Transcription / positive regulation of protein targeting to mitochondrion / NOTCH3 Intracellular Domain Regulates Transcription / positive regulation of neurogenesis / K63-linked polyubiquitin modification-dependent protein binding / nuclear androgen receptor binding / precatalytic spliceosome / Notch-HLH transcription pathway / Formation of paraxial mesoderm / mRNA Splicing - Minor Pathway / negative regulation of transcription elongation by RNA polymerase II / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / protein localization to nucleus / spliceosomal tri-snRNP complex assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / retinoic acid receptor signaling pathway / U5 snRNA binding / positive regulation of G1/S transition of mitotic cell cycle / U5 snRNP / U2 snRNA binding / カハール体 / U6 snRNA binding / pre-mRNA intronic binding / cellular response to retinoic acid / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / nuclear receptor coactivator activity / response to cocaine / nuclear receptor binding / positive regulation of transcription elongation by RNA polymerase II / Downregulation of SMAD2/3:SMAD4 transcriptional activity / transcription coregulator activity / spliceosomal complex / protein modification process / NOTCH1 Intracellular Domain Regulates Transcription / 核小体 / 転写後修飾 / Pre-NOTCH Transcription and Translation / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / nuclear matrix / mRNA splicing, via spliceosome / rRNA processing / protein tag activity / transcription corepressor activity / cellular response to xenobiotic stimulus / cellular response to tumor necrosis factor / single-stranded DNA binding / 核膜 / cellular response to lipopolysaccharide / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / nuclear body / nuclear speck / intracellular membrane-bounded organelle / GTPase activity / negative regulation of DNA-templated transcription / 中心体 / クロマチン / regulation of transcription by RNA polymerase II / GTP binding / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / ミトコンドリア / DNA binding / RNA binding / zinc ion binding / 核質 / 生体膜 / identical protein binding / 細胞核 / 細胞質基質 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) / synthetic construct (人工物) / Human (ヒト) | |||||||||
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 | |||||||||
データ登録者 | Townsend C / Kastner B / Leelaram MN / Bertram K / Stark H / Luehrmann R | |||||||||
資金援助 | ドイツ, 1件
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引用 | ジャーナル: Science / 年: 2020 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
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_11694.map.gz | 14.5 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-11694-v30.xml emd-11694.xml | 32.5 KB 32.5 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_11694.png | 33.8 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-11694 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11694 | 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 (文献) |
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類似構造データ | |
電子顕微鏡画像生データ | EMPIAR-10616 (タイトル: Cryo-EM dataset of human pre-Bact spliceosome / Data size: 584.5 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]) |
-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_11694.map.gz / 形式: CCP4 / 大きさ: 216 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Sharpened/masked map for pre-Bact-1 core structure. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-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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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: 7.9 |
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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 |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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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: SPOT SCAN / 撮影モード: BRIGHT FIELDBright-field microscopy |
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 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-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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初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
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 |
-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: |