+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-32794 | |||||||||
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タイトル | Cryo-EM structure of a yeast pre-40S ribosomal subunit - State Tsr1-2 (with Rps2) | |||||||||
マップデータ | local resolution filtered | |||||||||
試料 |
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キーワード | ribosome biogenesis / 40S ribosome / RIBOSOME | |||||||||
機能・相同性 | 機能・相同性情報 18S rRNA (guanine1575-N7)-methyltransferase / rRNA (guanine-N7)-methylation / tRNA methyltransferase complex / rRNA (guanine) methyltransferase activity / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA primary transcript binding / positive regulation of translational fidelity / Protein methylation / RMTs methylate histone arginines ...18S rRNA (guanine1575-N7)-methyltransferase / rRNA (guanine-N7)-methylation / tRNA methyltransferase complex / rRNA (guanine) methyltransferase activity / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA primary transcript binding / positive regulation of translational fidelity / Protein methylation / RMTs methylate histone arginines / mTORC1-mediated signalling / Protein hydroxylation / U3 snoRNA binding / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / 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 / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / proteasome assembly / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / regulation of translational fidelity / ribosomal subunit export from nucleus / ribonucleoprotein complex binding / ribosomal small 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) / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / maintenance of translational fidelity / cytoplasmic stress granule / rRNA processing / unfolded protein binding / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / translation / GTPase activity / mRNA binding / nucleolus / GTP binding / mitochondrion / RNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | Saccharomyces cerevisiae (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: 3.8 Å | |||||||||
データ登録者 | Cheng J / Lau B / Thoms M / Ameismeier M / Berninghausen O / Hurt E / Beckmann R | |||||||||
資金援助 | 1件
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引用 | ジャーナル: Nucleic Acids Res / 年: 2022 タイトル: The nucleoplasmic phase of pre-40S formation prior to nuclear export. 著者: Jingdong Cheng / Benjamin Lau / Matthias Thoms / Michael Ameismeier / Otto Berninghausen / Ed Hurt / Roland Beckmann / 要旨: Biogenesis of the small ribosomal subunit in eukaryotes starts in the nucleolus with the formation of a 90S precursor and ends in the cytoplasm. Here, we elucidate the enigmatic structural ...Biogenesis of the small ribosomal subunit in eukaryotes starts in the nucleolus with the formation of a 90S precursor and ends in the cytoplasm. Here, we elucidate the enigmatic structural transitions of assembly intermediates from human and yeast cells during the nucleoplasmic maturation phase. After dissociation of all 90S factors, the 40S body adopts a close-to-mature conformation, whereas the 3' major domain, later forming the 40S head, remains entirely immature. A first coordination is facilitated by the assembly factors TSR1 and BUD23-TRMT112, followed by re-positioning of RRP12 that is already recruited early to the 90S for further head rearrangements. Eventually, the uS2 cluster, CK1 (Hrr25 in yeast) and the export factor SLX9 associate with the pre-40S to provide export competence. These exemplary findings reveal the evolutionary conserved mechanism of how yeast and humans assemble the 40S ribosomal subunit, but reveal also a few minor differences. | |||||||||
履歴 |
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-構造の表示
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_32794.map.gz | 105.9 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-32794-v30.xml emd-32794.xml | 31 KB 31 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_32794_fsc.xml | 12.8 KB | 表示 | FSCデータファイル |
画像 | emd_32794.png | 135.1 KB | ||
Filedesc metadata | emd-32794.cif.gz | 9 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-32794 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32794 | HTTPS FTP |
-関連構造データ
関連構造データ | 7wtpMC 7wtnC 7wtoC 7wtqC 7wtrC 7wtsC 7wttC 7wtuC 7wtvC 7wtwC 7wtxC 7wtzC 7wu0C M: このマップから作成された原子モデル C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-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_32794.map.gz / 形式: CCP4 / 大きさ: 178 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | local resolution filtered | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.059 Å | ||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-試料の構成要素
+全体 : Yeast pre-40S ribosomal subunit
+超分子 #1: Yeast pre-40S ribosomal subunit
+分子 #1: 18S rRNA
+分子 #2: 40S ribosomal protein S1-A
+分子 #3: 40S ribosomal protein S2
+分子 #4: 40S ribosomal protein S4-A
+分子 #5: 40S ribosomal protein S6-A
+分子 #6: 40S ribosomal protein S7-A
+分子 #7: 40S ribosomal protein S8-A
+分子 #8: 40S ribosomal protein S9-A
+分子 #9: 40S ribosomal protein S11-A
+分子 #10: 40S ribosomal protein S13
+分子 #11: 40S ribosomal protein S14-A
+分子 #12: 40S ribosomal protein S22-A
+分子 #13: 40S ribosomal protein S23-A
+分子 #14: 40S ribosomal protein S24-A
+分子 #15: 40S ribosomal protein S27-A
+分子 #16: 40S ribosomal protein S30-A
+分子 #17: Pre-rRNA-processing protein PNO1
+分子 #18: 18S rRNA (guanine(1575)-N(7))-methyltransferase
+分子 #19: Ribosome biogenesis protein TSR1
+分子 #20: 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: 7.4 |
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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) 検出モード: COUNTING / 平均電子線量: 44.0 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 / 最大 デフォーカス(公称値): 2.5 µm / 最小 デフォーカス(公称値): 0.8 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |