+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-11695 | |||||||||
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タイトル | Human pre-Bact-1 spliceosome | |||||||||
マップデータ | Unmasked/unsharpened map of the pre-Bact-1 complex. | |||||||||
試料 |
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キーワード | Complex / spliceosome (スプライセオソーム) / catalytic activation / splicing | |||||||||
機能・相同性 | 機能・相同性情報 snRNA export from nucleus / nuclear cap binding complex / DNA topoisomerase binding / mRNA metabolic process / RNA cap binding complex / histone mRNA metabolic process / microfibril / positive regulation of mRNA 3'-end processing / Lsm2-8 complex / U6 snRNA 3'-end binding ...snRNA export from nucleus / nuclear cap binding complex / DNA topoisomerase binding / mRNA metabolic process / RNA cap binding complex / histone mRNA metabolic process / microfibril / positive regulation of mRNA 3'-end processing / Lsm2-8 complex / U6 snRNA 3'-end binding / positive regulation of RNA export from nucleus / cap-dependent translational initiation / protein kinase B binding / mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / U11/U12 snRNP / U6 snRNP / Processing of Intronless Pre-mRNAs / regulation of retinoic acid receptor signaling pathway / PH domain binding / snRNP binding / snRNA binding / U2 snRNP binding / positive regulation of RNA binding / U7 snRNA binding / histone pre-mRNA DCP binding / RNA cap binding / U7 snRNP / WW domain binding / alternative mRNA splicing, via spliceosome / regulation of vitamin D receptor signaling pathway / B-WICH complex / histone pre-mRNA 3'end processing complex / cis assembly of pre-catalytic spliceosome / regulation of mRNA processing / SLBP independent Processing of Histone Pre-mRNAs / miRNA-mediated post-transcriptional gene silencing / primary miRNA processing / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / regulatory ncRNA-mediated post-transcriptional gene silencing / mRNA splice site recognition / splicing factor binding / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / transcription elongation factor activity / protein methylation / miRNA processing / U12-type spliceosomal complex / methylosome / mRNA 3'-end processing / Transport of the SLBP independent Mature mRNA / RNA 7-methylguanosine cap binding / P-body assembly / nuclear retinoic acid receptor binding / Transport of the SLBP Dependant Mature mRNA / Prp19 complex / 7-methylguanosine cap hypermethylation / positive regulation of androgen receptor activity / U1 snRNP binding / pICln-Sm protein complex / mRNA 3'-end processing / : / blastocyst formation / pre-mRNA binding / Transport of Mature mRNA Derived from an Intronless Transcript / U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / sno(s)RNA-containing ribonucleoprotein complex / P granule / SMN-Sm protein complex / regulation of mRNA splicing, via spliceosome / spliceosomal tri-snRNP complex / telomerase holoenzyme complex / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / positive regulation by host of viral transcription / telomerase RNA binding / U2-type precatalytic spliceosome / commitment complex / RNA catabolic process / positive regulation of vitamin D receptor signaling pathway / Transport of Mature mRNA derived from an Intron-Containing Transcript / transcription regulator inhibitor activity / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / Abortive elongation of HIV-1 transcript in the absence of Tat / nuclear vitamin D receptor binding / ubiquitin-like protein conjugating enzyme binding / RNA polymerase binding / U4 snRNP / regulation of translational initiation / Notch binding / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / SAGA complex / positive regulation of mRNA splicing, via spliceosome / U2 snRNP / RNA Polymerase II Transcription Termination / NOTCH4 Intracellular Domain Regulates Transcription / nuclear-transcribed mRNA catabolic process 類似検索 - 分子機能 | |||||||||
生物種 | 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: 7.8 Å | |||||||||
データ登録者 | Townsend C / Kastner B | |||||||||
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_11695.map.gz | 170.7 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-11695-v30.xml emd-11695.xml | 83.8 KB 83.8 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_11695.png | 41.1 KB | ||
Filedesc metadata | emd-11695.cif.gz | 22 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-11695 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11695 | HTTPS FTP |
-関連構造データ
関連構造データ | 7abgMC 7aavC 7abfC 7abhC 7abiC C: 同じ文献を引用 (文献) M: このマップから作成された原子モデル |
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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_11695.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 | Unmasked/unsharpened map of the pre-Bact-1 complex. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
+分子 #1: Nuclear cap-binding protein subunit 1
+分子 #2: U6 snRNA-associated Sm-like protein LSm7
+分子 #3: Splicing factor 3B subunit 6
+分子 #4: Splicing factor 3A subunit 2
+分子 #5: U5 small nuclear ribonucleoprotein 40 kDa protein
+分子 #6: U2 small nuclear ribonucleoprotein A'
+分子 #7: U2 small nuclear ribonucleoprotein B''
+分子 #8: U5 small nuclear ribonucleoprotein 200 kDa helicase
+分子 #9: Protein BUD31 homolog
+分子 #10: Nuclear cap-binding protein subunit 2
+分子 #12: Cell division cycle 5-like protein
+分子 #13: Spliceosome-associated protein CWC15 homolog
+分子 #14: U6 snRNA-associated Sm-like protein LSm2
+分子 #15: U6 snRNA-associated Sm-like protein LSm3
+分子 #16: U6 snRNA-associated Sm-like protein LSm4
+分子 #17: U6 snRNA-associated Sm-like protein LSm5
+分子 #18: U6 snRNA-associated Sm-like protein LSm6
+分子 #20: U6 snRNA-associated Sm-like protein LSm8
+分子 #21: Microfibrillar-associated protein 1
+分子 #22: PHD finger-like domain-containing protein 5A
+分子 #23: Pleiotropic regulator 1
+分子 #25: Pre-mRNA-processing-splicing factor 8
+分子 #26: Pre-mRNA-splicing factor 38A
+分子 #27: Pre-mRNA-splicing factor RBM22
+分子 #28: Splicing factor 3A subunit 1
+分子 #29: Splicing factor 3A subunit 3
+分子 #30: Transcription elongation regulator 1
+分子 #31: Splicing factor 3B subunit 1
+分子 #32: Splicing factor 3B subunit 2
+分子 #33: Splicing factor 3B subunit 3
+分子 #34: Splicing factor 3B subunit 4
+分子 #35: Splicing factor 3B subunit 5
+分子 #36: SNW domain-containing protein 1
+分子 #37: Smad nuclear-interacting protein 1
+分子 #38: Zinc finger matrin-type protein 2
+分子 #39: 116 kDa U5 small nuclear ribonucleoprotein component
+分子 #40: Serine/arginine repetitive matrix protein 1
+分子 #42: Serine/arginine-rich splicing factor 1
+分子 #43: Small nuclear ribonucleoprotein Sm D2
+分子 #44: Small nuclear ribonucleoprotein F
+分子 #45: Small nuclear ribonucleoprotein-associated proteins B and B'
+分子 #46: Small nuclear ribonucleoprotein Sm D3
+分子 #47: Small nuclear ribonucleoprotein G
+分子 #48: Small nuclear ribonucleoprotein E
+分子 #49: Small nuclear ribonucleoprotein Sm D1
+分子 #50: Ubiquitin-like protein 5
+分子 #51: WW domain-binding protein 11
+分子 #11: U5 snRNA
+分子 #19: U2 snRNA
+分子 #24: MINX M3 pre-mRNA
+分子 #41: U6 snRNA
+分子 #52: INOSITOL HEXAKISPHOSPHATE
+分子 #53: GUANOSINE-5'-TRIPHOSPHATE
+分子 #54: MAGNESIUM ION
+分子 #55: 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE
-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 | 解像度のタイプ: BY AUTHOR / 解像度: 7.8 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-7abg: |