+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-6890 | ||||||||||||
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タイトル | Cryo-EM structure of the human activated spliceosome (late Bact) at 6.5 angstrom | ||||||||||||
マップデータ | Cryo-EM structure of the human activated spliceosome (late Bact) at 6.5 angstrom | ||||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 RES complex / U11/U12 snRNP / post-mRNA release spliceosomal complex / 3'-5' RNA helicase activity / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / generation of catalytic spliceosome for first transesterification step / U7 snRNP / B-WICH complex ...RES complex / U11/U12 snRNP / post-mRNA release spliceosomal complex / 3'-5' RNA helicase activity / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / generation of catalytic spliceosome for first transesterification step / 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 / embryonic brain development / splicing factor binding / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / protein methylation / U12-type spliceosomal complex / miRNA processing / methylosome / Prp19 complex / 7-methylguanosine cap hypermethylation / positive regulation of androgen receptor activity / poly(A) binding / U1 snRNP binding / mRNA 3'-end processing / blastocyst formation / pICln-Sm protein complex / pre-mRNA binding / U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / sno(s)RNA-containing ribonucleoprotein complex / SMN-Sm protein complex / C2H2 zinc finger domain binding / regulation of mRNA splicing, via spliceosome / spliceosomal tri-snRNP complex / P granule / telomerase holoenzyme complex / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / U2-type precatalytic spliceosome / commitment complex / Transport of Mature mRNA derived from an Intron-Containing Transcript / telomerase RNA binding / transcription regulator inhibitor activity / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / SAGA complex / positive regulation of mRNA splicing, via spliceosome / RNA Polymerase II Transcription Termination / positive regulation of transcription by RNA polymerase III / U1 snRNP / ubiquitin-ubiquitin ligase activity / WD40-repeat domain binding / pattern recognition receptor activity / lipid biosynthetic process / U2-type prespliceosome / K63-linked polyubiquitin modification-dependent protein binding / cyclosporin A binding / positive regulation of transcription by RNA polymerase I / precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / regulation of alternative mRNA splicing, via spliceosome / protein K63-linked ubiquitination / regulation of RNA splicing / antiviral innate immune response / blastocyst development / mRNA 3'-splice site recognition / protein localization to nucleus / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / proteasomal protein catabolic process / positive regulation of G1/S transition of mitotic cell cycle / U5 snRNP / transcription-coupled nucleotide-excision repair / positive regulation of viral genome replication / RNA processing / U2 snRNA binding / U6 snRNA binding / regulation of DNA repair / spliceosomal snRNP assembly / protein peptidyl-prolyl isomerization / Cajal body / pre-mRNA intronic binding / negative regulation of canonical NF-kappaB signal transduction / 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 / lipid droplet / mRNA Splicing - Major Pathway / RNA splicing / helicase activity / positive regulation of RNA splicing / positive regulation of protein export from nucleus 類似検索 - 分子機能 | ||||||||||||
生物種 | Homo sapiens (ヒト) / Human (ヒト) / unidentified adenovirus (ウイルス) | ||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 6.5 Å | ||||||||||||
データ登録者 | Zhang X / Yan C / Zhan X / Li L / Lei J / Shi Y | ||||||||||||
資金援助 | 中国, 3件
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引用 | ジャーナル: Cell Res / 年: 2018 タイトル: Structure of the human activated spliceosome in three conformational states. 著者: Xiaofeng Zhang / Chuangye Yan / Xiechao Zhan / Lijia Li / Jianlin Lei / Yigong Shi / 要旨: During each cycle of pre-mRNA splicing, the pre-catalytic spliceosome (B complex) is converted into the activated spliceosome (B complex), which has a well-formed active site but cannot proceed to ...During each cycle of pre-mRNA splicing, the pre-catalytic spliceosome (B complex) is converted into the activated spliceosome (B complex), which has a well-formed active site but cannot proceed to the branching reaction. Here, we present the cryo-EM structure of the human B complex in three distinct conformational states. The EM map allows atomic modeling of nearly all protein components of the U2 small nuclear ribonucleoprotein (snRNP), including three of the SF3a complex and seven of the SF3b complex. The structure of the human B complex contains 52 proteins, U2, U5, and U6 small nuclear RNA (snRNA), and a pre-mRNA. Three distinct conformations have been captured, representing the early, mature, and late states of the human B complex. These complexes differ in the orientation of the Switch loop of Prp8, the splicing factors RNF113A and NY-CO-10, and most components of the NineTeen complex (NTC) and the NTC-related complex. Analysis of these three complexes and comparison with the B and C complexes reveal an ordered flux of components in the B-to-B and the B-to-B transitions, which ultimately prime the active site for the branching 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_6890.map.gz | 228.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-6890-v30.xml emd-6890.xml | 75.2 KB 75.2 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_6890.png | 171.8 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-6890 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6890 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_6890_validation.pdf.gz | 498.6 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_6890_full_validation.pdf.gz | 498.2 KB | 表示 | |
XML形式データ | emd_6890_validation.xml.gz | 7.1 KB | 表示 | |
CIF形式データ | emd_6890_validation.cif.gz | 8.1 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6890 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6890 | 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_6890.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 structure of the human activated spliceosome (late Bact) at 6.5 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: 1.338 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
-試料の構成要素
+全体 : late Bact splieosome
+超分子 #1: late Bact splieosome
+分子 #1: Pre-mRNA-processing-splicing factor 8
+分子 #3: 116 kDa U5 small nuclear ribonucleoprotein component
+分子 #4: U5 small nuclear ribonucleoprotein 200 kDa helicase
+分子 #5: U5 small nuclear ribonucleoprotein 40 kDa protein
+分子 #6: Small nuclear ribonucleoprotein Sm D3
+分子 #7: Small nuclear ribonucleoprotein-associated proteins B and B'
+分子 #8: Small nuclear ribonucleoprotein Sm D1
+分子 #9: Small nuclear ribonucleoprotein Sm D2
+分子 #10: Small nuclear ribonucleoprotein F
+分子 #11: Small nuclear ribonucleoprotein E
+分子 #12: Small nuclear ribonucleoprotein G
+分子 #16: U2 small nuclear ribonucleoprotein A'
+分子 #17: U2 small nuclear ribonucleoprotein B''
+分子 #18: Splicing factor 3A subunit 3
+分子 #19: Splicing factor 3A subunit 1
+分子 #20: Splicing factor 3A subunit 2
+分子 #21: Splicing factor 3B subunit 1
+分子 #22: Splicing factor 3B subunit 2
+分子 #23: Splicing factor 3B subunit 3
+分子 #24: Splicing factor 3B subunit 4
+分子 #25: Splicing factor 3B subunit 6
+分子 #26: PHD finger-like domain-containing protein 5A
+分子 #27: Splicing factor 3B subunit 5
+分子 #28: Crooked neck-like protein 1
+分子 #29: Cell division cycle 5-like protein
+分子 #30: Pre-mRNA-processing factor 19
+分子 #31: Pre-mRNA-splicing factor SPF27
+分子 #32: Pre-mRNA-splicing factor SYF1
+分子 #33: Intron-binding protein aquarius
+分子 #34: Protein BUD31 homolog
+分子 #35: Pre-mRNA-splicing factor RBM22
+分子 #36: Spliceosome-associated protein CWC15 homolog
+分子 #37: Skip
+分子 #38: Peptidyl-prolyl cis-trans isomerase-like 1
+分子 #39: Pleiotropic regulator 1
+分子 #40: Serine/arginine repetitive matrix protein 2
+分子 #41: Pre-mRNA-splicing factor CWC22 homolog
+分子 #42: Pre-mRNA-processing factor 17
+分子 #43: Smad nuclear-interacting protein 1
+分子 #44: RNA-binding motif protein, X-linked 2
+分子 #45: BUD13 homolog
+分子 #46: Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16
+分子 #47: Peptidyl-prolyl cis-trans isomerase E
+分子 #2: U5 snRNA
+分子 #13: U6 snRNA
+分子 #14: pre-mRNA
+分子 #15: U2 snRNA
+分子 #48: INOSITOL HEXAKISPHOSPHATE
+分子 #49: ALANINE
+分子 #50: GUANOSINE-5'-TRIPHOSPHATE
+分子 #51: MAGNESIUM ION
+分子 #52: 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 / 詳細: 20 mM HEPES-KOH, pH 7.9, 150 mM NaCl, 1.5 mM MgCl2 |
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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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特殊光学系 | エネルギーフィルター - 名称: GIF Quantum LS |
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: 48.0 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 / Cs: 2.7 mm |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |