+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-9525 | |||||||||
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タイトル | Cryo-EM structure of the Catalytic Step I spliceosome (C complex) at 3.4 angstrom resolution | |||||||||
マップデータ | Cryo-EM map of Catalytic Step I spliceosome (C complex) at 3.4 angstrom | |||||||||
試料 |
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キーワード | RNA splicing / Spliceosome / Catalytic Step I / Intron lariat / RNA BINDING PROTEIN-RNA complex | |||||||||
機能・相同性 | 機能・相同性情報 post-spliceosomal complex / mRNA branch site recognition / U2-type post-mRNA release spliceosomal complex / cellular bud site selection / post-mRNA release spliceosomal complex / generation of catalytic spliceosome for first transesterification step / cis assembly of pre-catalytic spliceosome / splicing factor binding / U4/U6 snRNP / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) ...post-spliceosomal complex / mRNA branch site recognition / U2-type post-mRNA release spliceosomal complex / cellular bud site selection / post-mRNA release spliceosomal complex / generation of catalytic spliceosome for first transesterification step / cis assembly of pre-catalytic spliceosome / 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 / 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 / DNA replication origin binding / Gap-filling DNA repair synthesis and ligation in TC-NER / mRNA 5'-splice site recognition / protein K63-linked ubiquitination / mRNA 3'-splice site recognition / Dual incision in TC-NER / spliceosomal tri-snRNP complex assembly / DNA replication initiation / U5 snRNA binding / positive regulation of cell cycle / 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 / nuclear periphery / positive regulation of RNA splicing / spliceosomal complex / RING-type E3 ubiquitin transferase / mRNA splicing, via spliceosome / ubiquitin-protein transferase activity / metallopeptidase activity / ubiquitin protein ligase activity / DNA repair / GTPase activity / mRNA binding / chromatin binding / GTP binding / chromatin / mitochondrion / DNA binding / RNA binding / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm 類似検索 - 分子機能 | |||||||||
生物種 | Saccharomyces cerevisiae S288c (パン酵母) / Saccharomyces cerevisiae S288C (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: 3.4 Å | |||||||||
データ登録者 | Wan R / Yan C | |||||||||
引用 | ジャーナル: Science / 年: 2016 タイトル: Structure of a yeast catalytic step I spliceosome at 3.4 Å resolution. 著者: Ruixue Wan / Chuangye Yan / Rui Bai / Gaoxingyu Huang / Yigong Shi / 要旨: Each cycle of pre-messenger RNA splicing, carried out by the spliceosome, comprises two sequential transesterification reactions, which result in the removal of an intron and the joining of two exons. ...Each cycle of pre-messenger RNA splicing, carried out by the spliceosome, comprises two sequential transesterification reactions, which result in the removal of an intron and the joining of two exons. Here we report an atomic structure of a catalytic step I spliceosome (known as the C complex) from Saccharomyces cerevisiae, as determined by cryo-electron microscopy at an average resolution of 3.4 angstroms. In the structure, the 2'-OH of the invariant adenine nucleotide in the branch point sequence (BPS) is covalently joined to the phosphate at the 5' end of the 5' splice site (5'SS), forming an intron lariat. The freed 5' exon remains anchored to loop I of U5 small nuclear RNA (snRNA), and the 5'SS and BPS of the intron form duplexes with conserved U6 and U2 snRNA sequences, respectively. Specific placement of these RNA elements at the catalytic cavity of Prp8 is stabilized by 15 protein components, including Snu114 and the splicing factors Cwc21, Cwc22, Cwc25, and Yju2. These features, representing the conformation of the spliceosome after the first-step reaction, predict structural changes that are needed for the execution of the second-step transesterification reaction. | |||||||||
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_9525.map.gz | 229 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-9525-v30.xml emd-9525.xml | 62 KB 62 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_9525.png | 184.4 KB | ||
Filedesc metadata | emd-9525.cif.gz | 14 KB | ||
その他 | emd_9525_additional_1.map.gz emd_9525_additional_2.map.gz | 228.9 MB 228.8 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-9525 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9525 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_9525_validation.pdf.gz | 639.1 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_9525_full_validation.pdf.gz | 638.7 KB | 表示 | |
XML形式データ | emd_9525_validation.xml.gz | 7 KB | 表示 | |
CIF形式データ | emd_9525_validation.cif.gz | 8 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9525 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9525 | 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_9525.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 | Cryo-EM map of Catalytic Step I spliceosome (C complex) at 3.4 angstrom | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.306 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
-追加マップ: Cryo-EM map of Catalytic Step I spliceosome (C...
ファイル | emd_9525_additional_1.map | ||||||||||||
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注釈 | Cryo-EM map of Catalytic Step I spliceosome (C complex) at 3.65 angstrom | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Cryo-EM map of Catalytic Step I spliceosome (C...
ファイル | emd_9525_additional_2.map | ||||||||||||
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注釈 | Cryo-EM map of Catalytic Step I spliceosome (C complex) at 4.6 angstrom | ||||||||||||
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 : Spliceosomal C Complex
+超分子 #1: Spliceosomal C Complex
+分子 #1: Pre-mRNA-splicing factor 8
+分子 #2: Pre-mRNA-splicing factor SNU114
+分子 #9: Pre-mRNA-splicing factor CWC21
+分子 #10: Pre-mRNA-splicing factor PRP46
+分子 #11: Pre-mRNA-processing protein 45
+分子 #12: Pre-mRNA-splicing factor SLT11
+分子 #13: Pre-mRNA-splicing factor CWC2
+分子 #14: Pre-mRNA-splicing factor CWC15
+分子 #15: Pre-mRNA-splicing factor BUD31
+分子 #16: Pre-mRNA-splicing factor CWC22
+分子 #17: Pre-mRNA-splicing factor CEF1
+分子 #18: Pre-mRNA-splicing factor CLF1
+分子 #19: Protein CWC16
+分子 #20: Pre-mRNA-splicing factor CWC25
+分子 #21: Pre-mRNA-splicing factor ISY1
+分子 #22: Pre-mRNA-splicing factor SYF2
+分子 #23: Pre-mRNA-splicing factor SYF1
+分子 #24: Pre-mRNA-processing factor 17
+分子 #25: Pre-mRNA-processing factor 19
+分子 #26: Pre-mRNA-splicing factor SNT309
+分子 #27: Small nuclear ribonucleoprotein-associated protein B
+分子 #28: Small nuclear ribonucleoprotein E
+分子 #29: Small nuclear ribonucleoprotein F
+分子 #30: Small nuclear ribonucleoprotein G
+分子 #31: Small nuclear ribonucleoprotein Sm D3
+分子 #32: Small nuclear ribonucleoprotein Sm D1
+分子 #33: Small nuclear ribonucleoprotein Sm D2
+分子 #34: U2 small nuclear ribonucleoprotein B''
+分子 #35: U2 small nuclear ribonucleoprotein A'
+分子 #3: U5 snRNA
+分子 #4: U6 snRNA
+分子 #5: U2 snRNA
+分子 #6: Intron_BPS
+分子 #7: 5'-Exon
+分子 #8: 5'-Splicing Site
+分子 #36: GUANOSINE-5'-TRIPHOSPHATE
+分子 #37: MAGNESIUM ION
+分子 #38: 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: 8 詳細: The CEB buffer (10 mM Tris-HCl, pH 8.0, 75 mM NaCl, 1 mM Mg(OAc)2, 1 mM imidazole, 0.01% NP40, 1 mM TCEP, 0.5 mM EGTA) |
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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) デジタル化 - スキャナー: OTHER / 平均電子線量: 4.7 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 EMDB ID: |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.4 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 161066 |
初期 角度割当 | タイプ: ANGULAR RECONSTITUTION |
最終 角度割当 | タイプ: ANGULAR RECONSTITUTION |