+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-18718 | |||||||||
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タイトル | Cryo-EM structure of the cross-exon pre-B complex | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | spliceosome / SPLICING | |||||||||
機能・相同性 | 機能・相同性情報 Lsm2-8 complex / U6 snRNA 3'-end binding / spliceosomal snRNP complex / ribonucleoprotein complex localization / U4atac snRNP / positive regulation of cytotoxic T cell differentiation / maturation of 5S rRNA / positive regulation of hippo signaling / RNA localization / R-loop processing ...Lsm2-8 complex / U6 snRNA 3'-end binding / spliceosomal snRNP complex / ribonucleoprotein complex localization / U4atac snRNP / positive regulation of cytotoxic T cell differentiation / maturation of 5S rRNA / positive regulation of hippo signaling / RNA localization / R-loop processing / U4atac snRNA binding / mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / regulation of mitotic cell cycle spindle assembly checkpoint / U6 snRNP / box C/D sno(s)RNA binding / U11/U12 snRNP / PH domain binding / dense fibrillar component / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / 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 / U4/U6 snRNP / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / protein methylation / U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / snRNP binding / U1 snRNP binding / P-body assembly / blastocyst formation / pICln-Sm protein complex / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / U2-type catalytic step 1 spliceosome / U4 snRNA binding / sno(s)RNA-containing ribonucleoprotein complex / box C/D methylation guide snoRNP complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / P granule / telomerase holoenzyme complex / mRNA cis splicing, via spliceosome / telomerase RNA binding / U2-type precatalytic spliceosome / U2-type spliceosomal complex / commitment complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / positive regulation of mRNA splicing, via spliceosome / box C/D snoRNP assembly / U4 snRNP / rRNA modification in the nucleus and cytosol / U2 snRNP / RNA Polymerase II Transcription Termination / SAGA complex / U3 snoRNA binding / positive regulation of transcription by RNA polymerase III / U1 snRNP / tRNA processing / Cajal body / U2-type prespliceosome / K63-linked polyubiquitin modification-dependent protein binding / precatalytic spliceosome / positive regulation of transcription by RNA polymerase I / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / regulation of RNA splicing / negative regulation of mRNA splicing, via spliceosome / mRNA catabolic process / nuclear-transcribed mRNA catabolic process / 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 / U2 snRNA binding / RNA processing / U6 snRNA binding / ribonucleoprotein complex binding / spliceosomal snRNP assembly / regulation of DNA repair / pre-mRNA intronic binding / 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 / positive regulation of protein export from nucleus 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: 9.6 Å | |||||||||
データ登録者 | Zhang Z / Kumar V / Dybkov O / Will CL / Zhong J / Ludwig S / Urlaub H / Kastner B / Stark H / Luehrmann R | |||||||||
資金援助 | ドイツ, 1件
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引用 | ジャーナル: Nature / 年: 2024 タイトル: Structural insights into the cross-exon to cross-intron spliceosome switch. 著者: Zhenwei Zhang / Vinay Kumar / Olexandr Dybkov / Cindy L Will / Jiayun Zhong / Sebastian E J Ludwig / Henning Urlaub / Berthold Kastner / Holger Stark / Reinhard Lührmann / 要旨: Early spliceosome assembly can occur through an intron-defined pathway, whereby U1 and U2 small nuclear ribonucleoprotein particles (snRNPs) assemble across the intron. Alternatively, it can occur ...Early spliceosome assembly can occur through an intron-defined pathway, whereby U1 and U2 small nuclear ribonucleoprotein particles (snRNPs) assemble across the intron. Alternatively, it can occur through an exon-defined pathway, whereby U2 binds the branch site located upstream of the defined exon and U1 snRNP interacts with the 5' splice site located directly downstream of it. The U4/U6.U5 tri-snRNP subsequently binds to produce a cross-intron (CI) or cross-exon (CE) pre-B complex, which is then converted to the spliceosomal B complex. Exon definition promotes the splicing of upstream introns and plays a key part in alternative splicing regulation. However, the three-dimensional structure of exon-defined spliceosomal complexes and the molecular mechanism of the conversion from a CE-organized to a CI-organized spliceosome, a pre-requisite for splicing catalysis, remain poorly understood. Here cryo-electron microscopy analyses of human CE pre-B complex and B-like complexes reveal extensive structural similarities with their CI counterparts. The results indicate that the CE and CI spliceosome assembly pathways converge already at the pre-B stage. Add-back experiments using purified CE pre-B complexes, coupled with cryo-electron microscopy, elucidate the order of the extensive remodelling events that accompany the formation of B complexes and B-like complexes. The molecular triggers and roles of B-specific proteins in these rearrangements are also identified. We show that CE pre-B complexes can productively bind in trans to a U1 snRNP-bound 5' splice site. Together, our studies provide new mechanistic insights into the CE to CI switch during spliceosome assembly and its effect on pre-mRNA splice site pairing at this stage. | |||||||||
履歴 |
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-構造の表示
添付画像 |
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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 | emd_18718.map.gz | 40.3 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-18718-v30.xml emd-18718.xml | 75.5 KB 75.5 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_18718.png | 37.1 KB | ||
Filedesc metadata | emd-18718.cif.gz | 20.7 KB | ||
その他 | emd_18718_half_map_1.map.gz emd_18718_half_map_2.map.gz | 40.7 MB 40.6 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-18718 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18718 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_18718_validation.pdf.gz | 767 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_18718_full_validation.pdf.gz | 766.6 KB | 表示 | |
XML形式データ | emd_18718_validation.xml.gz | 11.8 KB | 表示 | |
CIF形式データ | emd_18718_validation.cif.gz | 13.9 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18718 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18718 | HTTPS FTP |
-関連構造データ
関連構造データ | 8qxdMC 8qozC 8qp8C 8qp9C 8qpaC 8qpbC 8qpeC 8qpkC 8qzsC 8r08C 8r09C 8r0aC 8r0bC 8rm5C 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 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-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_18718.map.gz / 形式: CCP4 / 大きさ: 52.7 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: 2.7 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
-ハーフマップ: #2
ファイル | emd_18718_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_18718_half_map_2.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
+全体 : cross-exon pre-B complex
+超分子 #1: cross-exon pre-B complex
+分子 #1: Pre-mRNA-processing-splicing factor 8
+分子 #2: U5 small nuclear ribonucleoprotein 200 kDa helicase
+分子 #7: Splicing factor 3A subunit 1
+分子 #8: Splicing factor 3A subunit 2
+分子 #9: 116 kDa U5 small nuclear ribonucleoprotein component
+分子 #10: Thioredoxin-like protein 4A
+分子 #11: U5 small nuclear ribonucleoprotein 40 kDa protein
+分子 #12: U4/U6 small nuclear ribonucleoprotein Prp4
+分子 #13: NHP2-like protein 1, N-terminally processed
+分子 #14: RNA-binding protein 42
+分子 #15: Ubiquitin carboxyl-terminal hydrolase 39
+分子 #16: U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein
+分子 #18: U4/U6.U5 tri-snRNP-associated protein 1
+分子 #19: U4/U6 small nuclear ribonucleoprotein Prp3
+分子 #20: Serine/threonine-protein kinase PRP4 homolog
+分子 #21: Pre-mRNA-processing factor 6
+分子 #22: Probable ATP-dependent RNA helicase DDX23
+分子 #23: U4/U6 small nuclear ribonucleoprotein Prp31
+分子 #24: Splicing factor 3B subunit 4
+分子 #25: Splicing factor 3A subunit 3
+分子 #26: Splicing factor 3B subunit 2
+分子 #27: Splicing factor 3B subunit 5
+分子 #28: Splicing factor 3B subunit 3
+分子 #29: PHD finger-like domain-containing protein 5A
+分子 #30: Splicing factor 3B subunit 1
+分子 #31: Splicing factor 3B subunit 6
+分子 #32: Small nuclear ribonucleoprotein Sm D2
+分子 #33: U2 small nuclear ribonucleoprotein B''
+分子 #34: Small nuclear ribonucleoprotein F
+分子 #35: Small nuclear ribonucleoprotein-associated proteins B and B'
+分子 #36: Small nuclear ribonucleoprotein Sm D3
+分子 #37: Small nuclear ribonucleoprotein G
+分子 #38: Small nuclear ribonucleoprotein E
+分子 #39: Small nuclear ribonucleoprotein Sm D1
+分子 #40: U2 small nuclear ribonucleoprotein A'
+分子 #41: Small nuclear ribonucleoprotein-associated proteins B and B'
+分子 #42: Small nuclear ribonucleoprotein G
+分子 #43: Small nuclear ribonucleoprotein-associated proteins B and B'
+分子 #44: Small nuclear ribonucleoprotein Sm D1
+分子 #45: U6 snRNA-associated Sm-like protein LSm6
+分子 #46: U6 snRNA-associated Sm-like protein LSm7
+分子 #47: U6 snRNA-associated Sm-like protein LSm2
+分子 #48: U6 snRNA-associated Sm-like protein LSm3
+分子 #49: U6 snRNA-associated Sm-like protein LSm8
+分子 #50: U6 snRNA-associated Sm-like protein LSm4
+分子 #51: U6 snRNA-associated Sm-like protein LSm5
+分子 #3: U2 snRNA
+分子 #4: U4 snRNA
+分子 #5: U5 snRNA
+分子 #6: U6 snRNA
+分子 #17: pre-mRNA
-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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凍結 | 凍結剤: ETHANE |
-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) 平均電子線量: 45.0 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 / 最大 デフォーカス(公称値): 5.0 µm / 最小 デフォーカス(公称値): 1.5 µm |
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: ab initio |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 9.6 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 279781 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |