+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-7109 | ||||||||||||
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タイトル | S. cerevisiae spliceosomal post-catalytic P complex | ||||||||||||
マップデータ | Spliceosomal post-catalytic P complex | ||||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 U2-type post-spliceosomal complex / U2-type post-mRNA release spliceosomal complex / mRNA branch site recognition / spliceosomal complex disassembly / cellular bud site selection / pre-mRNA 3'-splice site binding / post-mRNA release spliceosomal complex / generation of catalytic spliceosome for first transesterification step / nuclear mRNA surveillance / cis assembly of pre-catalytic spliceosome ...U2-type post-spliceosomal complex / U2-type post-mRNA release spliceosomal complex / mRNA branch site recognition / spliceosomal complex disassembly / cellular bud site selection / pre-mRNA 3'-splice site binding / post-mRNA release spliceosomal complex / generation of catalytic spliceosome for first transesterification step / nuclear mRNA surveillance / cis assembly of pre-catalytic spliceosome / splicing factor binding / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U4/U6 snRNP / Prp19 complex / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / pre-mRNA binding / U2-type catalytic step 1 spliceosome / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / poly(U) RNA binding / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / commitment complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / Formation of TC-NER Pre-Incision Complex / generation of catalytic spliceosome for second transesterification step / spliceosomal complex assembly / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA replication origin binding / mRNA 5'-splice site recognition / protein K63-linked ubiquitination / regulation of RNA splicing / mRNA 3'-splice site recognition / Dual incision in TC-NER / spliceosomal tri-snRNP complex assembly / DNA replication initiation / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / positive regulation of cell cycle / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / nuclear periphery / positive regulation of RNA splicing / RNA polymerase II transcription regulatory region sequence-specific DNA binding / spliceosomal complex / RING-type E3 ubiquitin transferase / mRNA splicing, via spliceosome / ubiquitin-protein transferase activity / metallopeptidase activity / ubiquitin protein ligase activity / RNA helicase activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA helicase / cell cycle / DNA repair / GTPase activity / mRNA binding / chromatin binding / chromatin / GTP binding / ATP hydrolysis activity / mitochondrion / RNA binding / zinc ion binding / ATP binding / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||||||||
生物種 | Saccharomyces cerevisiae (パン酵母) / Baker's yeast (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: 3.3 Å | ||||||||||||
データ登録者 | Liu S / Li X / Zhou ZH / Zhao R | ||||||||||||
資金援助 | 米国, 3件
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引用 | ジャーナル: Science / 年: 2017 タイトル: Structure of the yeast spliceosomal postcatalytic P complex. 著者: Shiheng Liu / Xueni Li / Lingdi Zhang / Jiansen Jiang / Ryan C Hill / Yanxiang Cui / Kirk C Hansen / Z Hong Zhou / Rui Zhao / 要旨: The spliceosome undergoes dramatic changes in a splicing cycle. Structures of B, B, C, C*, and intron lariat spliceosome complexes revealed mechanisms of 5'-splice site (ss) recognition, branching, ...The spliceosome undergoes dramatic changes in a splicing cycle. Structures of B, B, C, C*, and intron lariat spliceosome complexes revealed mechanisms of 5'-splice site (ss) recognition, branching, and intron release, but lacked information on 3'-ss recognition, exon ligation, and exon release. Here we report a cryo-electron microscopy structure of the postcatalytic P complex at 3.3-angstrom resolution, revealing that the 3' ss is mainly recognized through non-Watson-Crick base pairing with the 5' ss and branch point. Furthermore, one or more unidentified proteins become stably associated with the P complex, securing the 3' exon and potentially regulating activity of the helicase Prp22. Prp22 binds nucleotides 15 to 21 in the 3' exon, enabling it to pull the intron-exon or ligated exons in a 3' to 5' direction to achieve 3'-ss proofreading or exon release, respectively. | ||||||||||||
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_7109.map.gz | 227.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-7109-v30.xml emd-7109.xml | 55.9 KB 55.9 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_7109.png | 68.3 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-7109 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7109 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_7109_validation.pdf.gz | 512.7 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_7109_full_validation.pdf.gz | 512.3 KB | 表示 | |
XML形式データ | emd_7109_validation.xml.gz | 6.8 KB | 表示 | |
CIF形式データ | emd_7109_validation.cif.gz | 7.8 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7109 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7109 | 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_7109.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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注釈 | Spliceosomal post-catalytic P complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.36 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 : Spliceosomal P complex
+超分子 #1: Spliceosomal P complex
+分子 #1: U2 snRNA
+分子 #2: U5 snRNA
+分子 #3: U6 snRNA
+分子 #4: RNA (34-MER)
+分子 #5: RNA (59-MER)
+分子 #6: Pre-mRNA-splicing factor Prp8
+分子 #7: Pre-mRNA-splicing factor SNU114
+分子 #8: Pre-mRNA-splicing factor PRP46
+分子 #9: Pre-mRNA-processing protein 45
+分子 #10: Pre-mRNA-splicing factor SLT11
+分子 #11: Pre-mRNA-splicing factor CWC2
+分子 #12: Pre-mRNA-splicing factor CWC15
+分子 #13: Pre-mRNA-splicing factor BUD31
+分子 #14: Pre-mRNA-splicing factor CWC21
+分子 #15: Pre-mRNA-splicing factor CWC22
+分子 #16: Pre-mRNA-processing factor Prp17
+分子 #17: Pre-mRNA-splicing factor Prp18
+分子 #18: Pre-mRNA-splicing factor SLU7
+分子 #19: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22
+分子 #20: Pre-mRNA-splicing factor SYF2
+分子 #21: Pre-mRNA-splicing factor CEF1
+分子 #22: Pre-mRNA-splicing factor CLF1
+分子 #23: Pre-mRNA-splicing factor SYF1
+分子 #24: Unknown protein fragment
+分子 #25: Unknown protein fragment
+分子 #26: Small nuclear ribonucleoprotein Sm D2
+分子 #27: Small nuclear ribonucleoprotein F
+分子 #28: Small nuclear ribonucleoprotein E
+分子 #29: Small nuclear ribonucleoprotein G
+分子 #30: Small nuclear ribonucleoprotein-associated protein B
+分子 #31: Small nuclear ribonucleoprotein Sm D3
+分子 #32: Small nuclear ribonucleoprotein Sm D1
+分子 #33: Lea1
+分子 #34: Msl1
+分子 #35: Pre-mRNA-processing factor Prp19
+分子 #36: Pre-mRNA-splicing factor SNT309
+分子 #37: MAGNESIUM ION
+分子 #38: INOSITOL HEXAKISPHOSPHATE
+分子 #39: GUANOSINE-5'-TRIPHOSPHATE
+分子 #40: 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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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) 検出モード: SUPER-RESOLUTION / 平均電子線量: 2.0 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
-原子モデル構築 1
詳細 | The author states the following for the pre-mRNA model building: For regions in the intron or exon where no clear sequence preferences were observed (Spingola et al., PMID 10024174), U, A, U, and A-U are used to represent a generic nucleotide, purine, pyrimidine, and standard Watson-Crick basepair, respectively, based on the EM density. Nucleotides -7 to +7 in the exon are modeled mostly as the preferred nucleotides in each position (Spingola et al. PMID 10024174) unless the density suggests otherwise. Some nucleotides in the intron seem to form basepairs with defined U2 or U6 snRNA sequence based on EM densities, and are modeled as complementary nucleotides to the corresponding U2 or U6 sequence unless the density suggests otherwise. |
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得られたモデル | PDB-6bk8: |