+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-10689 | |||||||||
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タイトル | human 17S U2 snRNP | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | 17S U2 snRNP / SPLICING | |||||||||
機能・相同性 | 機能・相同性情報 U11/U12 snRNP / poly-ADP-D-ribose modification-dependent protein binding / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / B-WICH complex / histone pre-mRNA 3'end processing complex / chromatin-protein adaptor activity / SLBP independent Processing of Histone Pre-mRNAs ...U11/U12 snRNP / poly-ADP-D-ribose modification-dependent protein binding / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / B-WICH complex / histone pre-mRNA 3'end processing complex / chromatin-protein adaptor activity / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / splicing factor binding / protein methylation / U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / protein localization to site of double-strand break / U1 snRNP binding / blastocyst formation / pICln-Sm protein complex / snRNP binding / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / telomerase RNA binding / spliceosomal tri-snRNP complex / telomerase holoenzyme complex / P granule / U2-type spliceosomal complex / U2-type precatalytic spliceosome / mRNA cis splicing, via spliceosome / commitment complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / SAGA complex / U4 snRNP / positive regulation of mRNA splicing, via spliceosome / U2 snRNP / RNA Polymerase II Transcription Termination / positive regulation of transcription by RNA polymerase III / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / positive regulation of transcription by RNA polymerase I / mRNA Splicing - Minor Pathway / spliceosomal complex assembly / regulation of RNA splicing / mRNA 3'-splice site recognition / U5 snRNP / U2 snRNA binding / spliceosomal snRNP assembly / Cajal body / regulation of DNA repair / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / mRNA Splicing - Major Pathway / RNA splicing / stem cell differentiation / spliceosomal complex / double-strand break repair via homologous recombination / B-WICH complex positively regulates rRNA expression / fibrillar center / mRNA splicing, via spliceosome / positive regulation of neuron projection development / nuclear matrix / cytoplasmic ribonucleoprotein granule / mRNA processing / site of double-strand break / snRNP Assembly / spermatogenesis / SARS-CoV-2 modulates host translation machinery / RNA helicase activity / nuclear body / RNA helicase / nuclear speck / chromatin remodeling / mRNA binding / nucleolus / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / RNA binding / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 7.1 Å | |||||||||
データ登録者 | Zhang Z / Will CL | |||||||||
資金援助 | ドイツ, 1件
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引用 | ジャーナル: Nature / 年: 2020 タイトル: Molecular architecture of the human 17S U2 snRNP. 著者: Zhenwei Zhang / Cindy L Will / Karl Bertram / Olexandr Dybkov / Klaus Hartmuth / Dmitry E Agafonov / Romina Hofele / Henning Urlaub / Berthold Kastner / Reinhard Lührmann / Holger Stark / 要旨: The U2 small nuclear ribonucleoprotein (snRNP) has an essential role in the selection of the precursor mRNA branch-site adenosine, the nucleophile for the first step of splicing. Stable addition of ...The U2 small nuclear ribonucleoprotein (snRNP) has an essential role in the selection of the precursor mRNA branch-site adenosine, the nucleophile for the first step of splicing. Stable addition of U2 during early spliceosome formation requires the DEAD-box ATPase PRP5. Yeast U2 small nuclear RNA (snRNA) nucleotides that form base pairs with the branch site are initially sequestered in a branchpoint-interacting stem-loop (BSL), but whether the human U2 snRNA folds in a similar manner is unknown. The U2 SF3B1 protein, a common mutational target in haematopoietic cancers, contains a HEAT domain (SF3B1) with an open conformation in isolated SF3b, but a closed conformation in spliceosomes, which is required for stable interaction between U2 and the branch site. Here we report a 3D cryo-electron microscopy structure of the human 17S U2 snRNP at a core resolution of 4.1 Å and combine it with protein crosslinking data to determine the molecular architecture of this snRNP. Our structure reveals that SF3B1 interacts with PRP5 and TAT-SF1, and maintains its open conformation in U2 snRNP, and that U2 snRNA forms a BSL that is sandwiched between PRP5, TAT-SF1 and SF3B1. Thus, substantial remodelling of the BSL and displacement of BSL-interacting proteins must occur to allow formation of the U2-branch-site helix. Our studies provide a structural explanation of why TAT-SF1 must be displaced before the stable addition of U2 to the spliceosome, and identify RNP rearrangements facilitated by PRP5 that are required for stable interaction between U2 and the branch site. | |||||||||
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_10689.map.gz | 80.1 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-10689-v30.xml emd-10689.xml | 33.6 KB 33.6 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_10689.png | 33.7 KB | ||
Filedesc metadata | emd-10689.cif.gz | 10.5 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-10689 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10689 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_10689_validation.pdf.gz | 222.6 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_10689_full_validation.pdf.gz | 221.7 KB | 表示 | |
XML形式データ | emd_10689_validation.xml.gz | 6.4 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10689 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10689 | 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_10689.map.gz / 形式: CCP4 / 大きさ: 103 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
-試料の構成要素
+全体 : human 17S U2 snRNP
+超分子 #1: human 17S U2 snRNP
+分子 #1: U2 small nuclear ribonucleoprotein A'
+分子 #2: U2 small nuclear ribonucleoprotein B''
+分子 #3: Splicing factor 3B subunit 6
+分子 #4: Probable ATP-dependent RNA helicase DDX46
+分子 #5: Splicing factor 3A subunit 1
+分子 #6: Splicing factor 3A subunit 2
+分子 #7: Splicing factor 3A subunit 3
+分子 #8: Splicing factor 3B subunit 4
+分子 #9: Small nuclear ribonucleoprotein-associated proteins B and B'
+分子 #10: Small nuclear ribonucleoprotein G
+分子 #11: Small nuclear ribonucleoprotein Sm D1
+分子 #12: Small nuclear ribonucleoprotein Sm D2
+分子 #13: Small nuclear ribonucleoprotein Sm D3
+分子 #14: Small nuclear ribonucleoprotein E
+分子 #15: Small nuclear ribonucleoprotein F
+分子 #16: HIV Tat-specific factor 1
+分子 #17: Splicing factor 3B subunit 2
+分子 #18: Splicing factor 3B subunit 1
+分子 #19: U2 snRNA
-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 / チャンバー内湿度: 100 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK I |
-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 / 平均露光時間: 1.0 sec. / 平均電子線量: 72.0 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: SPOT SCAN / 撮影モード: BRIGHT FIELD / Cs: 0.01 mm |
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
初期モデル | モデルのタイプ: OTHER |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 7.1 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: 120070 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD / ソフトウェア - 名称: RELION (ver. 3.0) |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD / ソフトウェア - 名称: RELION (ver. 3.0) |