+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-7809 | |||||||||
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タイトル | Human nuclear exosome-MTR4 RNA complex - composite map after focused reconstruction | |||||||||
マップデータ | Composite map after focused reconstructions for a human nuclear exosome-RNA helicase complex | |||||||||
試料 |
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キーワード | RNA exosome / RNA degradation / ribonuclease / helicase / SF2 / RNA-protein complex / translocase / nuclear / HYDROLASE | |||||||||
機能・相同性 | 機能・相同性情報 DNA deamination / nucleolar exosome (RNase complex) / snRNA catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / TRAMP complex / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent CUT catabolic process / nuclear mRNA surveillance of mRNA 3'-end processing / positive regulation of mRNA cis splicing, via spliceosome ...DNA deamination / nucleolar exosome (RNase complex) / snRNA catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / TRAMP complex / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent CUT catabolic process / nuclear mRNA surveillance of mRNA 3'-end processing / positive regulation of mRNA cis splicing, via spliceosome / mRNA decay by 3' to 5' exoribonuclease / regulation of telomerase RNA localization to Cajal body / U1 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / U5 snRNA 3'-end processing / CUT catabolic process / RNA exonuclease activity / cytoplasmic exosome (RNase complex) / exosome (RNase complex) / nuclear polyadenylation-dependent rRNA catabolic process / U4 snRNA 3'-end processing / nuclear exosome (RNase complex) / poly(A)-dependent snoRNA 3'-end processing / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / ATF4 activates genes in response to endoplasmic reticulum stress / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / histone mRNA catabolic process / nuclear mRNA surveillance / positive regulation of isotype switching / rRNA catabolic process / 7S RNA binding / mRNA 3'-UTR AU-rich region binding / isotype switching / 加水分解酵素; エステル加水分解酵素; 5'-リン酸モノエステル産生エンドリボヌクレアーゼ / RNA catabolic process / telomerase RNA binding / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / KSRP (KHSRP) binds and destabilizes mRNA / nuclear chromosome / maturation of 5.8S rRNA / mRNA catabolic process / nuclear-transcribed mRNA catabolic process / negative regulation of telomere maintenance via telomerase / Major pathway of rRNA processing in the nucleolus and cytosol / RNA processing / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / guanyl-nucleotide exchange factor activity / small-subunit processome / euchromatin / fibrillar center / mRNA splicing, via spliceosome / rRNA processing / chromosome / ribosomal small subunit biogenesis / positive regulation of cell growth / 加水分解酵素; エステル加水分解酵素; 5'-リン酸モノエステル産生エキソリボヌクレアーゼ / 3'-5'-RNA exonuclease activity / endonuclease activity / defense response to virus / RNA polymerase II-specific DNA-binding transcription factor binding / RNA helicase activity / single-stranded RNA binding / RNA helicase / nuclear speck / immune response / intracellular membrane-bounded organelle / DNA repair / nucleotide binding / DNA damage response / nucleolus / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / RNA binding / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / metal ion binding / cytoplasm / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) / synthetic construct (人工物) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.45 Å | |||||||||
データ登録者 | Weick E-M / Lima CD | |||||||||
資金援助 | 米国, 2件
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引用 | ジャーナル: Cell / 年: 2018 タイトル: Helicase-Dependent RNA Decay Illuminated by a Cryo-EM Structure of a Human Nuclear RNA Exosome-MTR4 Complex. 著者: Eva-Maria Weick / M Rhyan Puno / Kurt Januszyk / John C Zinder / Michael A DiMattia / Christopher D Lima / 要旨: The ribonucleolytic RNA exosome interacts with RNA helicases to degrade RNA. To understand how the 3' to 5' Mtr4 helicase engages RNA and the nuclear exosome, we reconstituted 14-subunit Mtr4- ...The ribonucleolytic RNA exosome interacts with RNA helicases to degrade RNA. To understand how the 3' to 5' Mtr4 helicase engages RNA and the nuclear exosome, we reconstituted 14-subunit Mtr4-containing RNA exosomes from Saccharomyces cerevisiae, Schizosaccharomyces pombe, and human and show that they unwind structured substrates to promote degradation. We loaded a human exosome with an optimized DNA-RNA chimera that stalls MTR4 during unwinding and determined its structure to an overall resolution of 3.45 Å by cryoelectron microscopy (cryo-EM). The structure reveals an RNA-engaged helicase atop the non-catalytic core, with RNA captured within the central channel and DIS3 exoribonuclease active site. MPP6 tethers MTR4 to the exosome through contacts to the RecA domains of MTR4. EXOSC10 remains bound to the core, but its catalytic module and cofactor C1D are displaced by RNA-engaged MTR4. Competition for the exosome core may ensure that RNA is committed to degradation by DIS3 when engaged by MTR4. | |||||||||
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_7809.map.gz | 5.5 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-7809-v30.xml emd-7809.xml | 36.4 KB 36.4 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_7809.png | 52.6 KB | ||
Filedesc metadata | emd-7809.cif.gz | 11.1 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-7809 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7809 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_7809_validation.pdf.gz | 360.7 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_7809_full_validation.pdf.gz | 360.2 KB | 表示 | |
XML形式データ | emd_7809_validation.xml.gz | 6.9 KB | 表示 | |
CIF形式データ | emd_7809_validation.cif.gz | 7.9 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7809 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7809 | HTTPS FTP |
-関連構造データ
関連構造データ | 6d6rMC 7808C 7810C 7812C 7813C 7814C 7815C 7818C 7819C 6d6qC C: 同じ文献を引用 (文献) M: このマップから作成された原子モデル |
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類似構造データ |
-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_7809.map.gz / 形式: CCP4 / 大きさ: 216 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Composite map after focused reconstructions for a human nuclear exosome-RNA helicase complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.07 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 : Human nuclear exosome-MTR4 helicase captured after unwinding a DN...
+超分子 #1: Human nuclear exosome-MTR4 helicase captured after unwinding a DN...
+分子 #1: Exosome complex component RRP45
+分子 #2: Exosome complex component RRP41
+分子 #3: Exosome complex component RRP43
+分子 #4: Exosome complex component RRP46
+分子 #5: Exosome complex component RRP42
+分子 #6: Exosome complex component MTR3
+分子 #7: Exosome complex component RRP40
+分子 #8: Exosome complex component RRP4
+分子 #9: Exosome complex component CSL4
+分子 #10: Exosome component 10
+分子 #11: Exosome complex exonuclease RRP44
+分子 #12: M-phase phosphoprotein 6
+分子 #13: Exosome RNA helicase MTR4
+分子 #14: RNA (5'-R(*AP*GP*CP*AP*CP*CP*GP*UP*AP*AP*AP*GP*AP*CP*GP*C)-3')
+分子 #15: DNA/RNA (62-MER)
+分子 #16: ZINC ION
+分子 #17: MAGNESIUM ION
+分子 #18: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
-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
濃度 | 1.0 mg/mL | |||||||||||||||||||||
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緩衝液 | pH: 8 構成要素:
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グリッド | モデル: Quantifoil R2/2 / 材質: GOLD / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 60 sec. / 前処理 - 雰囲気: AIR / 前処理 - 気圧: 0.037 kPa | |||||||||||||||||||||
凍結 | 凍結剤: ETHANE / チャンバー内温度: 298 K / 装置: FEI VITROBOT MARK IV / 詳細: 30 sec wait time, 2.5 sec blot time. | |||||||||||||||||||||
詳細 | Sample was monodisperse upon elution from gel filtration prior to vitrification. |
-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 / 実像数: 1439 / 平均電子線量: 85.23 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 | Models were rebuilt manually using Coot, with real space refinement with local scaling followed by Phenix real space refinement with suboptimal global scaling. |
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精密化 | 空間: REAL / プロトコル: BACKBONE TRACE / 温度因子: 73.6 / 当てはまり具合の基準: Correlation coefficient |
得られたモデル | PDB-6d6r: |