+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-12106 | |||||||||
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タイトル | Yeast C complex spliceosome at 2.8 Angstrom resolution with Prp18/Slu7 bound, composite map | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | splicing / spliceosome / RNA / ribozyme | |||||||||
機能・相同性 | 機能・相同性情報 second spliceosomal transesterification activity / pre-mRNA 3'-splice site binding / post-mRNA release spliceosomal complex / splicing factor binding / U4/U6 snRNP / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / 7-methylguanosine cap hypermethylation / Prp19 complex / pICln-Sm protein complex / snRNP binding ...second spliceosomal transesterification activity / pre-mRNA 3'-splice site binding / post-mRNA release spliceosomal complex / splicing factor binding / U4/U6 snRNP / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / 7-methylguanosine cap hypermethylation / Prp19 complex / pICln-Sm protein complex / snRNP binding / U2-type catalytic step 1 spliceosome / small nuclear ribonucleoprotein complex / pre-mRNA binding / SMN-Sm protein complex / spliceosomal tri-snRNP complex / poly(U) RNA binding / commitment complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / generation of catalytic spliceosome for second transesterification step / spliceosomal complex assembly / regulation of RNA splicing / mRNA 5'-splice site recognition / mRNA 3'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / RNA splicing / helicase activity / spliceosomal complex / mRNA splicing, via spliceosome / mRNA processing / metallopeptidase activity / nucleic acid binding / RNA helicase activity / RNA helicase / GTPase activity / mRNA binding / GTP binding / ATP hydrolysis activity / RNA binding / zinc ion binding / ATP binding / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm 類似検索 - 分子機能 | |||||||||
生物種 | Saccharomyces cerevisiae (パン酵母) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.8 Å | |||||||||
データ登録者 | Wilkinson ME / Fica SM | |||||||||
資金援助 | 英国, 2件
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引用 | ジャーナル: Mol Cell / 年: 2021 タイトル: Structural basis for conformational equilibrium of the catalytic spliceosome. 著者: Max E Wilkinson / Sebastian M Fica / Wojciech P Galej / Kiyoshi Nagai / 要旨: The ATPase Prp16 governs equilibrium between the branching (B/C) and exon ligation (C/P) conformations of the spliceosome. Here, we present the electron cryomicroscopy reconstruction of the ...The ATPase Prp16 governs equilibrium between the branching (B/C) and exon ligation (C/P) conformations of the spliceosome. Here, we present the electron cryomicroscopy reconstruction of the Saccharomyces cerevisiae C-complex spliceosome at 2.8 Å resolution and identify a novel C-complex intermediate (C) that elucidates the molecular basis for this equilibrium. The exon-ligation factors Prp18 and Slu7 bind to C before ATP hydrolysis by Prp16 can destabilize the branching conformation. Biochemical assays suggest that these pre-bound factors prime the C complex for conversion to C by Prp16. A complete model of the Prp19 complex (NTC) reveals how the branching factors Yju2 and Isy1 are recruited by the NTC before branching. Prp16 remodels Yju2 binding after branching, allowing Yju2 to remain tethered to the NTC in the C complex to promote exon ligation. Our results explain how Prp16 action modulates the dynamic binding of step-specific factors to alternatively stabilize the C or C conformation and establish equilibrium of the catalytic 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_12106.map.gz | 128 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-12106-v30.xml emd-12106.xml | 62 KB 62 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_12106.png | 202.5 KB | ||
Filedesc metadata | emd-12106.cif.gz | 17.9 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-12106 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12106 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_12106_validation.pdf.gz | 440.8 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_12106_full_validation.pdf.gz | 440.4 KB | 表示 | |
XML形式データ | emd_12106_validation.xml.gz | 7.5 KB | 表示 | |
CIF形式データ | emd_12106_validation.cif.gz | 8.6 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12106 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12106 | HTTPS FTP |
-関連構造データ
関連構造データ | 7b9vMC 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 | |
電子顕微鏡画像生データ | EMPIAR-10687 (タイトル: Yeast C, Ci, C*, and P complex spliceosomes / Data size: 8.9 TB Data #1: Unaligned movies of C-complex spliceosome with 3' splice site AG to AC mutation (Dataset 1) [micrographs - multiframe] Data #2: Unaligned movies of C and C*-complex spliceosomes with 3' splice site AG to AdG mutation (Dataset 2) [micrographs - multiframe] Data #3: Unaligned movies of C and C*-complex spliceosomes with 3' splice site AG to AdG mutation (Dataset 3) [micrographs - multiframe] Data #4: Aligned movies of C-complex spliceosomes with cold-sensitive prp16-302 mutation, purified with Cwc25 (Dataset 4) [micrographs - multiframe] Data #5: Unaligned movies of C-complex spliceosomes with cold-sensitive prp16-302 mutation, purified with Cwc25 and incubated with ATP and Mg (Dataset 5) [micrographs - multiframe] Data #6: Unaligned movies of C, C*, and P-complex spliceosomes with dominant-negative Prp22 mutation K512A, purified with Slu7 (Dataset 6) [micrographs - multiframe] Data #7: Unaligned movies of P-complex spliceosomes with dominant-negative Prp22 mutation K512A, treated with anti-3'exon RNaseH oligo, purified in presence of Mg (Dataset 9) [micrographs - single frame] Data #8: Selected C-complex particles after polishing [picked particles - single frame - processed] Data #9: Selected P-complex particles after polishing [picked particles - single frame - processed] Data #10: Various signal subtractions for C- and P-complex spliceosomes [picked particles - single frame - processed]) |
-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_12106.map.gz / 形式: CCP4 / 大きさ: 244.1 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: 1.145 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 : Yeast C complex spliceosome with Prp18/Slu7 bound
+超分子 #1: Yeast C complex spliceosome with Prp18/Slu7 bound
+分子 #1: U2 snRNA
+分子 #2: U5 snRNA
+分子 #3: U6 snRNA
+分子 #8: 5' exon of UBC4 mRNA
+分子 #12: Branched intron and 3' exon of UBC4 pre-mRNA
+分子 #4: Pre-mRNA-splicing factor 8
+分子 #5: Pre-mRNA-splicing helicase BRR2
+分子 #6: Pre-mRNA-splicing factor SNU114
+分子 #7: Splicing factor YJU2
+分子 #9: Pre-mRNA-splicing factor CWC25
+分子 #10: Pre-mRNA-splicing factor ISY1
+分子 #11: CWC22 isoform 1
+分子 #13: BJ4_G0054360.mRNA.1.CDS.1
+分子 #14: Pre-mRNA-processing protein 45
+分子 #15: BUD31 isoform 1
+分子 #16: Pre-mRNA-splicing factor CWC2
+分子 #17: Pre-mRNA-splicing factor SLT11
+分子 #18: Y55_G0042700.mRNA.1.CDS.1
+分子 #19: Pre-mRNA-splicing factor CWC15
+分子 #20: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16
+分子 #21: Pre-mRNA-splicing factor CWC21
+分子 #22: CLF1 isoform 1
+分子 #23: SYF1 isoform 1
+分子 #24: HLJ1_G0053790.mRNA.1.CDS.1
+分子 #25: Unassigned structure
+分子 #26: BJ4_G0027490.mRNA.1.CDS.1
+分子 #27: NTC20 isoform 1
+分子 #28: Pre-mRNA-splicing factor 18
+分子 #29: Small nuclear ribonucleoprotein-associated protein B
+分子 #30: Pre-mRNA-splicing factor SLU7
+分子 #31: Small nuclear ribonucleoprotein Sm D3
+分子 #32: Small nuclear ribonucleoprotein E
+分子 #33: Small nuclear ribonucleoprotein F
+分子 #34: Small nuclear ribonucleoprotein G
+分子 #35: Small nuclear ribonucleoprotein Sm D1
+分子 #36: Small nuclear ribonucleoprotein Sm D2
+分子 #37: CDC40 isoform 1
+分子 #38: SNT309 isoform 1
+分子 #39: Pre-mRNA-processing factor 19
+分子 #40: Pre-mRNA-splicing factor SYF2
+分子 #41: MAGNESIUM ION
+分子 #42: POTASSIUM ION
+分子 #43: D-chiro inositol hexakisphosphate
+分子 #44: GUANOSINE-5'-TRIPHOSPHATE
+分子 #45: 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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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 R2/2 / 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 |
-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 K2 SUMMIT (4k x 4k) 撮影したグリッド数: 9 / 実像数: 24115 / 平均電子線量: 40.0 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 |
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: EMDB MAP |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 2.8 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: RELION (ver. 3.1) / 使用した粒子像数: 403474 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |