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データを開く
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基本情報
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タイトル | The cryo-EM map of the human 17S U2 snRNP core region | |||||||||
![]() | The EM map of U2 snRNP | |||||||||
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![]() | U2 snRNP / PRP5 / SF3B1 / Splicing | |||||||||
機能・相同性 | ![]() U11/U12 snRNP / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / B-WICH complex / chromatin-protein adaptor activity / histone pre-mRNA 3'end processing complex / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs ...U11/U12 snRNP / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / B-WICH complex / chromatin-protein adaptor activity / histone pre-mRNA 3'end processing complex / 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 / U1 snRNP binding / protein localization to site of double-strand break / poly-ADP-D-ribose modification-dependent protein binding / pICln-Sm protein complex / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / P granule / telomerase holoenzyme complex / 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 / U2 snRNP / SAGA complex / positive regulation of mRNA splicing, via spliceosome / RNA Polymerase II Transcription Termination / positive regulation of transcription by RNA polymerase III / U1 snRNP / U2-type prespliceosome / positive regulation of transcription by RNA polymerase I / precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / regulation of alternative mRNA splicing, via spliceosome / regulation of RNA splicing / mRNA 3'-splice site recognition / U5 snRNP / U2 snRNA binding / regulation of DNA repair / spliceosomal snRNP assembly / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / catalytic step 2 spliceosome / 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 / negative regulation of protein catabolic process / mRNA processing / fibrillar center / nuclear matrix / positive regulation of neuron projection development / mRNA splicing, via spliceosome / cytoplasmic ribonucleoprotein granule / site of double-strand break / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / spermatogenesis / nucleic acid binding / RNA helicase activity / nuclear body / RNA helicase / nuclear speck / chromatin remodeling / mRNA binding / protein-containing complex binding / nucleolus / positive regulation of DNA-templated transcription / enzyme binding / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.5 Å | |||||||||
![]() | Zhang X / Zhan X | |||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Structural insights into branch site proofreading by human spliceosome. 著者: Xiaofeng Zhang / Xiechao Zhan / Tong Bian / Fenghua Yang / Pan Li / Yichen Lu / Zhihan Xing / Rongyan Fan / Qiangfeng Cliff Zhang / Yigong Shi / ![]() 要旨: Selection of the pre-mRNA branch site (BS) by the U2 small nuclear ribonucleoprotein (snRNP) is crucial to prespliceosome (A complex) assembly. The RNA helicase PRP5 proofreads BS selection but the ...Selection of the pre-mRNA branch site (BS) by the U2 small nuclear ribonucleoprotein (snRNP) is crucial to prespliceosome (A complex) assembly. The RNA helicase PRP5 proofreads BS selection but the underlying mechanism remains unclear. Here we report the atomic structures of two sequential complexes leading to prespliceosome assembly: human 17S U2 snRNP and a cross-exon pre-A complex. PRP5 is anchored on 17S U2 snRNP mainly through occupation of the RNA path of SF3B1 by an acidic loop of PRP5; the helicase domain of PRP5 associates with U2 snRNA; the BS-interacting stem-loop (BSL) of U2 snRNA is shielded by TAT-SF1, unable to engage the BS. In the pre-A complex, an initial U2-BS duplex is formed; the translocated helicase domain of PRP5 stays with U2 snRNA and the acidic loop still occupies the RNA path. The pre-A conformation is specifically stabilized by the splicing factors SF1, DNAJC8 and SF3A2. Cancer-derived mutations in SF3B1 damage its association with PRP5, compromising BS proofreading. Together, these findings reveal key insights into prespliceosome assembly and BS selection or proofreading by PRP5. | |||||||||
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構造の表示
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ダウンロードとリンク
-EMDBアーカイブ
マップデータ | ![]() | 116.7 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 36.4 KB 36.4 KB | 表示 表示 | ![]() |
画像 | ![]() | 35.5 KB | ||
Filedesc metadata | ![]() | 12.2 KB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 547.7 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 547.3 KB | 表示 | |
XML形式データ | ![]() | 6.4 KB | 表示 | |
CIF形式データ | ![]() | 7.2 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 7evoMC ![]() 7vpxC 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 ( |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||
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注釈 | The EM map of U2 snRNP | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.087 Å | ||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
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試料の構成要素
+全体 : The human U2 snRNP
+超分子 #1: The human U2 snRNP
+分子 #1: U2 snRNA
+分子 #2: Splicing factor 3B subunit 1
+分子 #3: Splicing factor 3B subunit 2
+分子 #4: Splicing factor 3B subunit 3
+分子 #5: Splicing factor 3B subunit 4
+分子 #6: Splicing factor 3B subunit 5
+分子 #7: PHD finger-like domain-containing protein 5A
+分子 #8: Splicing factor 3A subunit 1
+分子 #9: Splicing factor 3A subunit 2
+分子 #10: Splicing factor 3A subunit 3
+分子 #11: HIV Tat-specific factor 1
+分子 #12: RNA helicase
+分子 #13: U2 small nuclear ribonucleoprotein A'
+分子 #14: U2 small nuclear ribonucleoprotein B''
+分子 #15: Small nuclear ribonucleoprotein Sm D2
+分子 #16: Small nuclear ribonucleoprotein F
+分子 #17: Small nuclear ribonucleoprotein E
+分子 #18: Small nuclear ribonucleoprotein G
+分子 #19: Small nuclear ribonucleoprotein Sm D3
+分子 #20: Small nuclear ribonucleoprotein-associated proteins B and B'
+分子 #21: Small nuclear ribonucleoprotein Sm D1
+分子 #22: [(2~{S},3~{S},4~{E},6~{S},7~{R},10~{R})-3,7-dimethyl-2-[(2~{E},4~...
+分子 #23: 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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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
濃度 | 0.5 mg/mL |
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緩衝液 | pH: 7.9 |
グリッド | モデル: Quantifoil R1.2/1.3 / 材質: GOLD / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY / 前処理 - タイプ: GLOW DISCHARGE |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / 装置: FEI VITROBOT MARK IV |
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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: GATAN K3 (6k x 4k) / 平均電子線量: 50.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 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 |
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画像解析
初期モデル | モデルのタイプ: OTHER / 詳細: Initial model from CryoSparc |
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最終 再構成 | アルゴリズム: FOURIER SPACE / 解像度のタイプ: BY AUTHOR / 解像度: 2.5 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 485418 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |