+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-4665 | |||||||||
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タイトル | Structure of a human fully-assembled precatalytic spliceosome (pre-B complex). | |||||||||
マップデータ | None | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 mRNA Splicing - Minor Pathway / negative regulation of protein refolding / mRNA Splicing - Major Pathway / Lsm2-8 complex / U6 snRNA 3'-end binding / spliceosomal snRNP complex / ribonucleoprotein complex localization / snRNP binding / U4atac snRNP / positive regulation of cytotoxic T cell differentiation ...mRNA Splicing - Minor Pathway / negative regulation of protein refolding / mRNA Splicing - Major Pathway / Lsm2-8 complex / U6 snRNA 3'-end binding / spliceosomal snRNP complex / ribonucleoprotein complex localization / snRNP binding / U4atac snRNP / positive regulation of cytotoxic T cell differentiation / maturation of 5S rRNA / RNA localization / R-loop processing / U4atac snRNA binding / regulation of ATP-dependent activity / mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / regulation of mitotic cell cycle spindle assembly checkpoint / U11/U12 snRNP / U6 snRNP / box C/D sno(s)RNA binding / PH domain binding / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / dense fibrillar component / B-WICH complex / histone pre-mRNA 3'end processing complex / cis assembly of pre-catalytic spliceosome / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / splicing factor binding / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / protein methylation / U12-type spliceosomal complex / methylosome / P-body assembly / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / U1 snRNP binding / pICln-Sm protein complex / U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / sno(s)RNA-containing ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / P granule / U4 snRNA binding / telomerase holoenzyme complex / box C/D methylation guide snoRNP complex / negative regulation of chaperone-mediated autophagy / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / U2-type precatalytic spliceosome / commitment complex / telomerase RNA binding / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / box C/D snoRNP assembly / U2 snRNP / SAGA complex / positive regulation of mRNA splicing, via spliceosome / rRNA modification in the nucleus and cytosol / RNA Polymerase II Transcription Termination / positive regulation of transcription by RNA polymerase III / tRNA processing / U1 snRNP / U3 snoRNA binding / pre-mRNA 5'-splice site binding / nuclear-transcribed mRNA catabolic process / U2-type prespliceosome / K63-linked polyubiquitin modification-dependent protein binding / nuclear androgen receptor binding / positive regulation of transcription by RNA polymerase I / precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / regulation of alternative mRNA splicing, via spliceosome / mRNA catabolic process / negative regulation of mRNA splicing, via spliceosome / mRNA 5'-splice site recognition / regulation of RNA splicing / mRNA 3'-splice site recognition / MLL1 complex / spliceosomal tri-snRNP complex assembly / single fertilization / Major pathway of rRNA processing in the nucleolus and cytosol / U5 snRNA binding / U5 snRNP / RNA processing / U2 snRNA binding / U6 snRNA binding / regulation of DNA repair / spliceosomal snRNP assembly / Cajal body / ribonucleoprotein complex binding / pre-mRNA intronic binding 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) / Human adenovirus 2 (ヒトアデノウイルス) / 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: 3.28 Å | |||||||||
データ登録者 | Charenton C / Wilkinson ME / Nagai K | |||||||||
資金援助 | 英国, 2件
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引用 | ジャーナル: Science / 年: 2019 タイトル: Mechanism of 5' splice site transfer for human spliceosome activation. 著者: Clément Charenton / Max E Wilkinson / Kiyoshi Nagai / 要旨: The prespliceosome, comprising U1 and U2 small nuclear ribonucleoproteins (snRNPs) bound to the precursor messenger RNA 5' splice site (5'SS) and branch point sequence, associates with the U4/U6.U5 ...The prespliceosome, comprising U1 and U2 small nuclear ribonucleoproteins (snRNPs) bound to the precursor messenger RNA 5' splice site (5'SS) and branch point sequence, associates with the U4/U6.U5 tri-snRNP to form the fully assembled precatalytic pre-B spliceosome. Here, we report cryo-electron microscopy structures of the human pre-B complex captured before U1 snRNP dissociation at 3.3-angstrom core resolution and the human tri-snRNP at 2.9-angstrom resolution. U1 snRNP inserts the 5'SS-U1 snRNA helix between the two RecA domains of the Prp28 DEAD-box helicase. Adenosine 5'-triphosphate-dependent closure of the Prp28 RecA domains releases the 5'SS to pair with the nearby U6 ACAGAGA-box sequence presented as a mobile loop. The structures suggest that formation of the 5'SS-ACAGAGA helix triggers remodeling of an intricate protein-RNA network to induce Brr2 helicase relocation to its loading sequence in U4 snRNA, enabling Brr2 to unwind the U4/U6 snRNA duplex to allow U6 snRNA to form the catalytic center of the spliceosome. | |||||||||
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_4665.map.gz | 260.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-4665-v30.xml emd-4665.xml | 80.9 KB 80.9 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_4665_fsc.xml | 14.9 KB | 表示 | FSCデータファイル |
画像 | emd_4665.png | 125.9 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-4665 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4665 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_4665_validation.pdf.gz | 331.9 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_4665_full_validation.pdf.gz | 331 KB | 表示 | |
XML形式データ | emd_4665_validation.xml.gz | 14 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4665 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4665 | HTTPS FTP |
-関連構造データ
関連構造データ | 6qx9MC 4658C 4672C 4673C 4674C 4675C 4676C 4686C 4687C 4688C 4689C 4690C 6qw6C 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-10307 (タイトル: Human pre-B spliceosome and U4/U6.U5 tri-snRNP Data size: 2.3 TB Data #1: Dataset 1 of human pre-B spliceosome; motion-corrected micrographs [micrographs - single frame] Data #2: Dataset 2 of human pre-B spliceosome; motion-corrected micrographs [micrographs - single frame] Data #3: Dataset 3 of human pre-B spliceosome; motion-corrected micrographs [micrographs - single frame] Data #4: Dataset 4 of human pre-B spliceosome; motion-corrected micrographs [micrographs - single frame] Data #5: Dataset 5 of human pre-B spliceosome; motion-corrected micrographs [micrographs - single frame] Data #6: Selected U4/U6.U5 tri-snRNP particles after Bayesian polishing [picked particles - single frame - processed] Data #7: Crude shifted preB particles [picked particles - single frame - unprocessed]) |
-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_4665.map.gz / 形式: CCP4 / 大きさ: 282.6 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.022 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 : Fully-assembled precatalytic spliceosome (pre-B complex).
+超分子 #1: Fully-assembled precatalytic spliceosome (pre-B complex).
+超分子 #2: Fully-assembled precatalytic spliceosome (pre-B complex).
+超分子 #3: Probable ATP-dependent RNA helicase DDX23
+超分子 #4: AdML pre-mRNA
+分子 #1: U1 snRNA
+分子 #2: U6 snRNA
+分子 #8: AdML pre-mRNA
+分子 #17: U5 snRNA
+分子 #32: U2 snRNA
+分子 #45: U4 snRNA
+分子 #3: U5 small nuclear ribonucleoprotein 40 kDa protein
+分子 #4: Splicing factor 3B subunit 4
+分子 #5: Small nuclear ribonucleoprotein Sm D3
+分子 #6: U4/U6 small nuclear ribonucleoprotein Prp4
+分子 #7: Small nuclear ribonucleoprotein E
+分子 #9: U1 small nuclear ribonucleoprotein 70 kDa
+分子 #10: U4/U6 small nuclear ribonucleoprotein Prp31
+分子 #11: Small nuclear ribonucleoprotein Sm D1
+分子 #12: RNA-binding protein 42
+分子 #13: Small nuclear ribonucleoprotein F
+分子 #14: U6 snRNA-associated Sm-like protein LSm6
+分子 #15: U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein
+分子 #16: Small nuclear ribonucleoprotein Sm D2
+分子 #18: U6 snRNA-associated Sm-like protein LSm7
+分子 #19: U6 snRNA-associated Sm-like protein LSm2
+分子 #20: U2 small nuclear ribonucleoprotein B''
+分子 #21: Splicing factor 3A subunit 2
+分子 #22: Splicing factor 3B subunit 2
+分子 #23: 116 kDa U5 small nuclear ribonucleoprotein component
+分子 #24: Probable ATP-dependent RNA helicase DDX23
+分子 #25: Small nuclear ribonucleoprotein-associated proteins B and B'
+分子 #26: Splicing factor 3B subunit 5
+分子 #27: U1 small nuclear ribonucleoprotein A
+分子 #28: U4/U6.U5 tri-snRNP-associated protein 1
+分子 #29: Pre-mRNA-processing factor 6
+分子 #30: NHP2-like protein 1
+分子 #31: U6 snRNA-associated Sm-like protein LSm3
+分子 #33: Splicing factor 3B subunit 3
+分子 #34: Small nuclear ribonucleoprotein G
+分子 #35: U6 snRNA-associated Sm-like protein LSm8
+分子 #36: Pre-mRNA-processing-splicing factor 8
+分子 #37: Splicing factor 3A subunit 3
+分子 #38: U4/U6.U5 tri-snRNP-associated protein 2
+分子 #39: Thioredoxin-like protein 4A
+分子 #40: U6 snRNA-associated Sm-like protein LSm4
+分子 #41: PHD finger-like domain-containing protein 5A
+分子 #42: U1 small nuclear ribonucleoprotein C
+分子 #43: Serine/threonine-protein kinase PRP4 homolog
+分子 #44: U4/U6 small nuclear ribonucleoprotein Prp3
+分子 #46: U2 small nuclear ribonucleoprotein A'
+分子 #47: Splicing factor 3A subunit 1,Splicing factor 3A subunit 1,Splicin...
+分子 #48: U6 snRNA-associated Sm-like protein LSm5
+分子 #49: U5 small nuclear ribonucleoprotein 200 kDa helicase
+分子 #50: Splicing factor 3B subunit 1
+分子 #51: ZINC ION
+分子 #52: MAGNESIUM ION
+分子 #53: GUANOSINE-5'-TRIPHOSPHATE
+分子 #54: INOSITOL HEXAKISPHOSPHATE
-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 | 1.4 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 R2/2 / 材質: COPPER / メッシュ: 400 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: CONTINUOUS / 支持フィルム - Film thickness: 6.0 nm / 前処理 - タイプ: GLOW DISCHARGE | ||||||||||
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 III |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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特殊光学系 | エネルギーフィルター - 名称: GIF Bioquantum / エネルギーフィルター - スリット幅: 20 eV |
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: COUNTING / デジタル化 - 画像ごとのフレーム数: 1-40 / 平均露光時間: 6.0 sec. / 平均電子線量: 50.0 e/Å2 |
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: FLOOD BEAM / 撮影モード: BRIGHT FIELD |
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 |