+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-4302 | |||||||||
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タイトル | Structure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors | |||||||||
マップデータ | Structure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 nuclear mRNA surveillance of mRNA 3'-end processing / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / TRAMP complex / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent CUT catabolic process / protein-RNA complex remodeling / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing ...nuclear mRNA surveillance of mRNA 3'-end processing / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / TRAMP complex / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent CUT catabolic process / protein-RNA complex remodeling / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / regulation of ribosomal subunit export from nucleus / TRAMP-dependent tRNA surveillance pathway / RNA fragment catabolic process / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / exosome (RNase complex) / nuclear exosome (RNase complex) / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 加水分解酵素 / 3'-5' RNA helicase activity / rRNA catabolic process / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / histone mRNA catabolic process / nuclear mRNA surveillance / PeBoW complex / Antigen processing: Ubiquitination & Proteasome degradation / 7S RNA binding / rRNA primary transcript binding / poly(A) binding / positive regulation of ATP-dependent activity / RNA catabolic process / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear-transcribed mRNA catabolic process / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of 5.8S rRNA / ribosomal subunit export from nucleus / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / ATPase activator activity / Formation of a pool of free 40S subunits / ribosomal large subunit binding / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of mRNA splicing, via spliceosome / protein-RNA complex assembly / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal large subunit export from nucleus / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of translational fidelity / ribonucleoprotein complex binding / 転写後修飾 / enzyme regulator activity / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / Neutrophil degranulation / translation initiation factor activity / nuclear periphery / small-subunit processome / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / maintenance of translational fidelity / オートファジー / 転写後修飾 / rRNA processing / ribosomal large subunit assembly / metallopeptidase activity / large ribosomal subunit rRNA binding / protein transport / double-stranded RNA binding / リボソーム生合成 / 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 / 5S rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / 3'-5'-RNA exonuclease activity / ATPase binding / double-stranded DNA binding / 遺伝子発現の調節 / negative regulation of translation / RNA helicase activity / single-stranded RNA binding / nucleic acid binding / rRNA binding / oxidoreductase activity / ヘリカーゼ / リボソーム / structural constituent of ribosome / 翻訳 (生物学) / nucleotide binding / mRNA binding / GTPase activity / protein-containing complex binding / GTP binding 類似検索 - 分子機能 | |||||||||
生物種 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (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: 3.9 Å | |||||||||
データ登録者 | Schuller JM / Falk S / Conti E | |||||||||
資金援助 | ベルギー, 1件
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引用 | ジャーナル: Science / 年: 2018 タイトル: Structure of the nuclear exosome captured on a maturing preribosome. 著者: Jan Michael Schuller / Sebastian Falk / Lisa Fromm / Ed Hurt / Elena Conti / 要旨: The RNA exosome complex processes and degrades a wide range of transcripts, including ribosomal RNAs (rRNAs). We used cryo-electron microscopy to visualize the yeast nuclear exosome holocomplex ...The RNA exosome complex processes and degrades a wide range of transcripts, including ribosomal RNAs (rRNAs). We used cryo-electron microscopy to visualize the yeast nuclear exosome holocomplex captured on a precursor large ribosomal subunit (pre-60) during 7-to-5.8 rRNA processing. The cofactors of the nuclear exosome are sandwiched between the ribonuclease core complex (Exo-10) and the remodeled "foot" structure of the pre-60 particle, which harbors the 5.8 rRNA precursor. The exosome-associated helicase Mtr4 recognizes the preribosomal substrate by docking to specific sites on the 25 rRNA, captures the 3' extension of the 5.8 rRNA, and channels it toward Exo-10. The structure elucidates how the exosome forms a structural and functional unit together with its massive pre-60 substrate to process rRNA during ribosome maturation. | |||||||||
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_4302.map.gz | 260.4 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-4302-v30.xml emd-4302.xml | 78.2 KB 78.2 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_4302.png | 569 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-4302 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4302 | 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_4302.map.gz / 形式: CCP4 / 大きさ: 325 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Structure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.35 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 : Structure of the Nop53 pre-60S particle bound to the exosome nucl...
+超分子 #1: Structure of the Nop53 pre-60S particle bound to the exosome nucl...
+超分子 #2: pre-60S particle
+超分子 #3: exosome nuclear cofactors
+分子 #1: 7S ribosomal RNA
+分子 #50: 25S ribosomal RNA
+分子 #51: 5S ribosomal RNA
+分子 #2: 60S ribosomal protein L2-A
+分子 #3: 60S ribosomal protein L3
+分子 #4: 60S ribosomal protein L4-A
+分子 #5: 60S ribosomal protein L5
+分子 #6: 60S ribosomal protein L6-A
+分子 #7: 60S ribosomal protein L7-A
+分子 #8: 60S ribosomal protein L8-A
+分子 #9: 60S ribosomal protein L9-A
+分子 #10: Bud site selection protein 20
+分子 #11: 60S ribosomal protein L11-A
+分子 #12: 60S ribosomal protein L13-A
+分子 #13: 60S ribosomal protein L14-A
+分子 #14: 60S ribosomal protein L15-A
+分子 #15: 60S ribosomal protein L16-A
+分子 #16: 60S ribosomal protein L17-A
+分子 #17: 60S ribosomal protein L18-A
+分子 #18: 60S ribosomal protein L19-A
+分子 #19: 60S ribosomal protein L20-A
+分子 #20: 60S ribosomal protein L21-A
+分子 #21: 60S ribosomal protein L22-A
+分子 #22: 60S ribosomal protein L23-A
+分子 #23: Ribosome assembly factor MRT4
+分子 #24: 60S ribosomal protein L25
+分子 #25: 60S ribosomal protein L26-A
+分子 #26: 60S ribosomal protein L27-A
+分子 #27: 60S ribosomal protein L28
+分子 #28: Nucleolar GTP-binding protein 1
+分子 #29: 60S ribosomal protein L30
+分子 #30: 60S ribosomal protein L31-A
+分子 #31: 60S ribosomal protein L32
+分子 #32: 60S ribosomal protein L33-A
+分子 #33: 60S ribosomal protein L34-A
+分子 #34: 60S ribosomal protein L35-A
+分子 #35: 60S ribosomal protein L36-A
+分子 #36: 60S ribosomal protein L37-A
+分子 #37: 60S ribosomal protein L38
+分子 #38: 60S ribosomal protein L39
+分子 #39: Nucleolar GTP-binding protein 2
+分子 #40: Pescadillo homolog
+分子 #41: 60S ribosomal protein L43-A
+分子 #42: Ribosome biogenesis protein NSA2
+分子 #43: Nuclear GTP-binding protein NUG1
+分子 #44: Ribosome biogenesis protein RLP24
+分子 #45: Ribosome biogenesis protein RPF2
+分子 #46: Regulator of ribosome biosynthesis
+分子 #47: Ribosome assembly protein 4
+分子 #48: Eukaryotic translation initiation factor 6
+分子 #49: UPF0642 protein YBL028C
+分子 #52: Probable metalloprotease ARX1
+分子 #53: rRNA-processing protein CGR1
+分子 #54: Exosome complex exonuclease RRP6
+分子 #55: Exosome complex protein LRP1
+分子 #56: ATP-dependent RNA helicase DOB1
+分子 #57: MPP6
+分子 #58: ZINC ION
+分子 #59: GUANOSINE-5'-TRIPHOSPHATE
+分子 #60: 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: 7.5 |
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凍結 | 凍結剤: ETHANE-PROPANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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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 FIELDBright-field microscopy |
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: 38.4 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期 角度割当 | タイプ: PROJECTION MATCHING |
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最終 角度割当 | タイプ: PROJECTION MATCHING |
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.9 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 22439 |