+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-11569 | |||||||||
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タイトル | Human C Complex Spliceosome - High-resolution CORE | |||||||||
マップデータ | ||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 striated muscle dense body / post-spliceosomal complex / post-mRNA release spliceosomal complex / regulation of retinoic acid receptor signaling pathway / 3'-5' RNA helicase activity / generation of catalytic spliceosome for first transesterification step / regulation of vitamin D receptor signaling pathway / embryonic brain development / nuclear retinoic acid receptor binding / Prp19 complex ...striated muscle dense body / post-spliceosomal complex / post-mRNA release spliceosomal complex / regulation of retinoic acid receptor signaling pathway / 3'-5' RNA helicase activity / generation of catalytic spliceosome for first transesterification step / regulation of vitamin D receptor signaling pathway / embryonic brain development / nuclear retinoic acid receptor binding / Prp19 complex / positive regulation of androgen receptor activity / mRNA 3'-end processing / RNA splicing, via transesterification reactions / pre-mRNA binding / U2-type catalytic step 1 spliceosome / sno(s)RNA-containing ribonucleoprotein complex / C2H2 zinc finger domain binding / regulation of mRNA splicing, via spliceosome / positive regulation by host of viral transcription / U2-type precatalytic spliceosome / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / Transport of Mature mRNA derived from an Intron-Containing Transcript / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / U2-type catalytic step 2 spliceosome / 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 / RNA Polymerase II Transcription Termination / NOTCH4 Intracellular Domain Regulates Transcription / muscle organ development / WD40-repeat domain binding / NOTCH3 Intracellular Domain Regulates Transcription / positive regulation of neurogenesis / K63-linked polyubiquitin modification-dependent protein binding / cyclosporin A binding / nuclear androgen receptor binding / Notch-HLH transcription pathway / generation of catalytic spliceosome for second transesterification step / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / SMAD binding / negative regulation of DNA damage response, signal transduction by p53 class mediator / mRNA 3'-splice site recognition / 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 / RNA processing / U2 snRNA binding / U6 snRNA binding / protein peptidyl-prolyl isomerization / Cajal body / 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 / positive regulation of RNA splicing / positive regulation of protein export from nucleus / nuclear receptor coactivator activity / DNA damage checkpoint signaling / response to cocaine / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Downregulation of SMAD2/3:SMAD4 transcriptional activity / spliceosomal complex / NOTCH1 Intracellular Domain Regulates Transcription / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / fibrillar center / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Pre-NOTCH Transcription and Translation / histone deacetylase binding / nuclear matrix / Z disc / mRNA splicing, via spliceosome / positive regulation of protein import into nucleus / mRNA processing / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / rRNA processing / transcription corepressor activity / calcium-dependent protein binding / disordered domain specific binding / actin filament binding / cellular response to xenobiotic stimulus / protein folding 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) / 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: 3.4 Å | |||||||||
データ登録者 | Bertram K / Kastner B | |||||||||
資金援助 | ドイツ, 2件
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引用 | ジャーナル: Mol Cell / 年: 2020 タイトル: Structural Insights into the Roles of Metazoan-Specific Splicing Factors in the Human Step 1 Spliceosome. 著者: Karl Bertram / Leyla El Ayoubi / Olexandr Dybkov / Dmitry E Agafonov / Cindy L Will / Klaus Hartmuth / Henning Urlaub / Berthold Kastner / Holger Stark / Reinhard Lührmann / 要旨: Human spliceosomes contain numerous proteins absent in yeast, whose functions remain largely unknown. Here we report a 3D cryo-EM structure of the human spliceosomal C complex at 3.4 Å core ...Human spliceosomes contain numerous proteins absent in yeast, whose functions remain largely unknown. Here we report a 3D cryo-EM structure of the human spliceosomal C complex at 3.4 Å core resolution and 4.5-5.7 Å at its periphery, and aided by protein crosslinking we determine its molecular architecture. Our structure provides additional insights into the spliceosome's architecture between the catalytic steps of splicing, and how proteins aid formation of the spliceosome's catalytically active RNP (ribonucleoprotein) conformation. It reveals the spatial organization of the metazoan-specific proteins PPWD1, WDR70, FRG1, and CIR1 in human C complexes, indicating they stabilize functionally important protein domains and RNA structures rearranged/repositioned during the B to C transition. Structural comparisons with human B, C, and P complexes reveal an intricate cascade of RNP rearrangements during splicing catalysis, with intermediate RNP conformations not found in yeast, and additionally elucidate the structural basis for the sequential recruitment of metazoan-specific spliceosomal proteins. | |||||||||
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_11569.map.gz | 300.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-11569-v30.xml emd-11569.xml | 45.8 KB 45.8 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_11569.png | 181.2 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-11569 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11569 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_11569_validation.pdf.gz | 261.5 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_11569_full_validation.pdf.gz | 260.6 KB | 表示 | |
XML形式データ | emd_11569_validation.xml.gz | 7.1 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11569 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11569 | 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_11569.map.gz / 形式: CCP4 / 大きさ: 325 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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:
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 : Human C complex Spliceosome - High resolution core
+超分子 #1: Human C complex Spliceosome - High resolution core
+分子 #1: U2 snRNA
+分子 #2: U5 snRNA
+分子 #3: U6 snRNA
+分子 #19: pre-mRNA
+分子 #4: Corepressor interacting with RBPJ 1
+分子 #5: Pre-mRNA-processing-splicing factor 8
+分子 #6: 116 kDa U5 small nuclear ribonucleoprotein component
+分子 #7: SNW domain-containing protein 1
+分子 #8: Pleiotropic regulator 1
+分子 #9: Pre-mRNA-processing factor 17
+分子 #10: U5 small nuclear ribonucleoprotein 40 kDa protein
+分子 #11: Cell division cycle 5-like protein
+分子 #12: Crooked neck-like protein 1
+分子 #13: Pre-mRNA-splicing factor RBM22
+分子 #14: Protein BUD31 homolog
+分子 #15: Spliceosome-associated protein CWC15 homolog
+分子 #16: Serine/arginine repetitive matrix protein 2
+分子 #17: Pre-mRNA-splicing factor CWC22 homolog
+分子 #18: Peptidyl-prolyl cis-trans isomerase-like 1
+分子 #20: WD repeat-containing protein 70
+分子 #21: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16
+分子 #22: Pre-mRNA-splicing factor ISY1 homolog
+分子 #23: Pre-mRNA-splicing factor CWC25 homolog
+分子 #24: Splicing factor YJU2
+分子 #25: Protein FRG1
+分子 #26: MAGNESIUM ION
+分子 #27: INOSITOL HEXAKISPHOSPHATE
+分子 #28: GUANOSINE-5'-TRIPHOSPHATE
+分子 #29: ZINC 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
濃度 | 0.1 mg/mL | ||||||||||||
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緩衝液 | pH: 7.9 構成要素:
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グリッド | モデル: Quantifoil / 材質: COPPER / メッシュ: 200 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY ARRAY | ||||||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK II | ||||||||||||
詳細 | Monodisperse particle distribution |
-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 / 撮影したグリッド数: 2 / 実像数: 28279 / 平均露光時間: 1.0 sec. / 平均電子線量: 120.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 70.0 µm / 照射モード: SPOT SCAN / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス(公称値): -0.003 µm / 最小 デフォーカス(公称値): -0.001 µm / 倍率(公称値): 132000 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
粒子像選択 | 選択した数: 1751359 |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.4 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 411539 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |