+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-9624 | |||||||||
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タイトル | The Cryo-EM Structure of Human Pre-catalytic Spliceosome (B complex) at 3.8 angstrom resolution | |||||||||
マップデータ | The 3.8 Angstrom map of the human B complex | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 microfibril / 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 / RNA localization / U4atac snRNA binding ...microfibril / 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 / RNA localization / U4atac snRNA binding / mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / U6 snRNP / box C/D sno(s)RNA binding / U11/U12 snRNP / PH domain binding / dense fibrillar component / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / B-WICH 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 / proline-rich region 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 / positive regulation of protein targeting to mitochondrion / tRNA processing / Cajal body / U2-type prespliceosome / cyclosporin A binding / regulation of alternative mRNA splicing, via spliceosome / 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 / mRNA catabolic process / nuclear-transcribed mRNA catabolic process / mRNA 3'-splice site recognition / protein peptidyl-prolyl isomerization / MLL1 complex / spliceosomal tri-snRNP complex assembly / single fertilization / Major pathway of rRNA processing in the nucleolus and cytosol / U5 snRNA binding / U5 snRNP / positive regulation of viral genome replication / 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 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) / Human (ヒト) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.8 Å | |||||||||
データ登録者 | Zhan X / Yan C / Zhang X / Shi Y | |||||||||
資金援助 | 中国, 2件
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引用 | ジャーナル: Cell Res / 年: 2018 タイトル: Structures of the human pre-catalytic spliceosome and its precursor spliceosome. 著者: Xiechao Zhan / Chuangye Yan / Xiaofeng Zhang / Jianlin Lei / Yigong Shi / 要旨: The pre-catalytic spliceosome (B complex) is preceded by its precursor spliceosome (pre-B complex) and followed by the activated spliceosome (B complex). The pre-B-to-B and B-to-B transitions are ...The pre-catalytic spliceosome (B complex) is preceded by its precursor spliceosome (pre-B complex) and followed by the activated spliceosome (B complex). The pre-B-to-B and B-to-B transitions are driven by the ATPase/helicases Prp28 and Brr2, respectively. In this study, we report the cryo-electron microscopy structures of the human pre-B complex and the human B complex at an average resolution of 5.7 and 3.8 Å, respectively. In the pre-B complex, U1 and U2 small nuclear ribonucleoproteins (snRNPs) associate with two edges of the tetrahedron-shaped U4/U6.U5 tri-snRNP. The pre-mRNA is yet to be recognized by U5 or U6 small nuclear RNA (snRNA), and loop I of U5 snRNA remains unengaged. In the B complex, U1 snRNP and Prp28 are dissociated, the 5'-exon is anchored to loop I of U5 snRNA, and the 5'-splice site is recognized by U6 snRNA through duplex formation. In sharp contrast to S. cerevisiae, most components of U2 snRNP and tri-snRNP, exemplified by Brr2, undergo pronounced rearrangements in the human pre-B-to-B transition. Structural analysis reveals mechanistic insights into the assembly and activation of the human 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_9624.map.gz | 226.5 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-9624-v30.xml emd-9624.xml | 67.5 KB 67.5 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_9624.png | 98.5 KB | ||
その他 | emd_9624_additional.map.gz | 227.5 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-9624 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9624 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_9624_validation.pdf.gz | 555.6 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_9624_full_validation.pdf.gz | 555.2 KB | 表示 | |
XML形式データ | emd_9624_validation.xml.gz | 7 KB | 表示 | |
CIF形式データ | emd_9624_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-9624 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9624 | 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_9624.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 | The 3.8 Angstrom map of the human B complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.338 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: The 4.5 Angstrom map of the human B complex
ファイル | emd_9624_additional.map | ||||||||||||
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注釈 | The 4.5 Angstrom map of the human B complex | ||||||||||||
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 : Human Pre-catalytic spliceosome (B complex)
+超分子 #1: Human Pre-catalytic spliceosome (B complex)
+分子 #1: Pre-mRNA-processing-splicing factor 8
+分子 #6: Thioredoxin-like protein 4A
+分子 #7: 116 kDa U5 small nuclear ribonucleoprotein component
+分子 #8: Pre-mRNA-processing factor 6
+分子 #9: NHP2-like protein 1
+分子 #10: U4/U6 small nuclear ribonucleoprotein Prp31
+分子 #11: U4/U6.U5 tri-snRNP-associated protein 1
+分子 #12: U4/U6 small nuclear ribonucleoprotein Prp3
+分子 #13: SmB
+分子 #14: Small nuclear ribonucleoprotein Sm D1
+分子 #15: Small nuclear ribonucleoprotein Sm D2
+分子 #16: SmE
+分子 #17: SmF
+分子 #18: Small nuclear ribonucleoprotein G
+分子 #19: Small nuclear ribonucleoprotein Sm D3
+分子 #20: U5 small nuclear ribonucleoprotein 40 kDa protein
+分子 #21: WW domain-binding protein 4
+分子 #22: Peptidyl-prolyl cis-trans isomerase H
+分子 #23: Ubiquitin-like protein 5
+分子 #24: Microfibrillar-associated protein 1
+分子 #25: Pre-mRNA-splicing factor 38A
+分子 #26: Zinc finger matrin-type protein 2
+分子 #27: WD40 repeat-containing protein SMU1
+分子 #29: U2 small nuclear ribonucleoprotein A'
+分子 #30: U2 small nuclear ribonucleoprotein B''
+分子 #31: Splicing factor 3A subunit 1
+分子 #32: Splicing factor 3A subunit 2
+分子 #33: Splicing factor 3A subunit 3
+分子 #34: U6 snRNA-associated Sm-like protein LSm2
+分子 #35: U6 snRNA-associated Sm-like protein LSm3
+分子 #36: U6 snRNA-associated Sm-like protein LSm4
+分子 #37: U6 snRNA-associated Sm-like protein LSm5
+分子 #38: U6 snRNA-associated Sm-like protein LSm6
+分子 #39: U6 snRNA-associated Sm-like protein LSm7
+分子 #40: U6 snRNA-associated Sm-like protein LSm8
+分子 #41: U4/U6 small nuclear ribonucleoprotein Prp4
+分子 #42: Splicing factor 3B subunit 1
+分子 #43: Splicing factor 3B subunit 3
+分子 #44: SF3b14a, Splicing factor 3B subunit 6
+分子 #45: PHD finger-like domain-containing protein 5A
+分子 #46: SF3b5, Splicing factor 3B subunit 5
+分子 #47: SF3b145, Splicing factor 3B subunit 2
+分子 #48: SF3b49, Splicing factor 3B subunit 4
+分子 #49: Brr2, U5 small nuclear ribonucleoprotein 200 kDa helicase
+分子 #2: U4snRNA
+分子 #3: U5snRNA
+分子 #4: U6snRNA
+分子 #5: pre-mRNA
+分子 #28: U2snRNA
+分子 #50: INOSITOL HEXAKISPHOSPHATE
+分子 #51: GUANOSINE-5'-TRIPHOSPHATE
+分子 #52: MAGNESIUM 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) 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 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.8 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 137853 |
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初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |