+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-16525 | ||||||||||||||||||
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タイトル | Cryo-EM structure of native Otu2-bound ubiquitinated 43S pre-initiation complex | ||||||||||||||||||
マップデータ | Cryo-EM map of Otu2-bound ubiquitinated 43S pre-initiation complex | ||||||||||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / incipient cellular bud site / translation reinitiation / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / multi-eIF complex / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex ...eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / incipient cellular bud site / translation reinitiation / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / multi-eIF complex / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Negative regulators of DDX58/IFIH1 signaling / RMTs methylate histone arginines / positive regulation of translational fidelity / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / nonfunctional rRNA decay / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / preribosome, small subunit precursor / Ribosomal scanning and start codon recognition / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA destabilization / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / regulation of amino acid metabolic process / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal large subunit export from nucleus / protein deubiquitination / 90S preribosome / G-protein alpha-subunit binding / positive regulation of protein kinase activity / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of translational fidelity / Ub-specific processing proteases / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / translation regulator activity / 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) / DNA-(apurinic or apyrimidinic site) endonuclease activity / translation initiation factor binding / translation initiation factor activity / cellular response to amino acid starvation / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rescue of stalled ribosome / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / translational initiation / protein kinase C binding / maintenance of translational fidelity / modification-dependent protein catabolic process / cytoplasmic stress granule / protein tag activity / rRNA processing / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosome binding / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / cysteine-type deubiquitinase activity / negative regulation of translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / translation / negative regulation of gene expression / mRNA binding / ubiquitin protein ligase binding / nucleolus / ATP hydrolysis activity / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytosol / cytoplasm 類似検索 - 分子機能 | ||||||||||||||||||
生物種 | Saccharomyces cerevisiae (パン酵母) / Saccharomyces cerevisiae W303 (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: 3.0 Å | ||||||||||||||||||
データ登録者 | Ikeuchi K / Buschauer R / Cheng J / Berninghausen O / Becker T / Beckmann R | ||||||||||||||||||
資金援助 | ドイツ, 日本, 5件
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引用 | ジャーナル: Nat Commun / 年: 2023 タイトル: Molecular basis for recognition and deubiquitination of 40S ribosomes by Otu2. 著者: Ken Ikeuchi / Nives Ivic / Robert Buschauer / Jingdong Cheng / Thomas Fröhlich / Yoshitaka Matsuo / Otto Berninghausen / Toshifumi Inada / Thomas Becker / Roland Beckmann / 要旨: In actively translating 80S ribosomes the ribosomal protein eS7 of the 40S subunit is monoubiquitinated by the E3 ligase Not4 and deubiquitinated by Otu2 upon ribosomal subunit recycling. Despite its ...In actively translating 80S ribosomes the ribosomal protein eS7 of the 40S subunit is monoubiquitinated by the E3 ligase Not4 and deubiquitinated by Otu2 upon ribosomal subunit recycling. Despite its importance for translation efficiency the exact role and structural basis for this translational reset is poorly understood. Here, structural analysis by cryo-electron microscopy of native and reconstituted Otu2-bound ribosomal complexes reveals that Otu2 engages 40S subunits mainly between ribosome recycling and initiation stages. Otu2 binds to several sites on the intersubunit surface of the 40S that are not occupied by any other 40S-binding factors. This binding mode explains the discrimination against 80S ribosomes via the largely helical N-terminal domain of Otu2 as well as the specificity for mono-ubiquitinated eS7 on 40S. Collectively, this study reveals mechanistic insights into the Otu2-driven deubiquitination steps for translational reset during ribosome recycling/(re)initiation. | ||||||||||||||||||
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_16525.map.gz | 19.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-16525-v30.xml emd-16525.xml | 63.6 KB 63.6 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_16525_fsc.xml | 13.9 KB | 表示 | FSCデータファイル |
画像 | emd_16525.png | 179.6 KB | ||
その他 | emd_16525_half_map_1.map.gz emd_16525_half_map_2.map.gz | 261.9 MB 261.9 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-16525 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16525 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_16525_validation.pdf.gz | 977.3 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_16525_full_validation.pdf.gz | 976.8 KB | 表示 | |
XML形式データ | emd_16525_validation.xml.gz | 23.4 KB | 表示 | |
CIF形式データ | emd_16525_validation.cif.gz | 30.4 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16525 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16525 | 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_16525.map.gz / 形式: CCP4 / 大きさ: 282.6 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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注釈 | Cryo-EM map of Otu2-bound ubiquitinated 43S pre-initiation complex | ||||||||||||||||||||||||||||||||||||
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: 1.045 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
-ハーフマップ: Half map A
ファイル | emd_16525_half_map_1.map | ||||||||||||
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注釈 | Half map A | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half map B
ファイル | emd_16525_half_map_2.map | ||||||||||||
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注釈 | Half map B | ||||||||||||
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 : Yeast native 43S pre-initiation complex with deubiquitinating enz...
+超分子 #1: Yeast native 43S pre-initiation complex with deubiquitinating enz...
+分子 #1: Eukaryotic translation initiation factor 3 subunit I
+分子 #2: Eukaryotic translation initiation factor 3 subunit G
+分子 #3: Eukaryotic translation initiation factor 3 subunit A
+分子 #4: Eukaryotic translation initiation factor 3 subunit B
+分子 #5: Eukaryotic translation initiation factor 3 subunit C
+分子 #6: Eukaryotic translation initiation factor 4C
+分子 #7: SUI1 isoform 1
+分子 #8: RNA recognition motif (unknown)
+分子 #10: 40S ribosomal protein S0-A
+分子 #11: 40S ribosomal protein S1-A
+分子 #12: 40S ribosomal protein S2
+分子 #13: 40S ribosomal protein S4-B
+分子 #14: 40S ribosomal protein S6-B
+分子 #15: 40S ribosomal protein S8-A
+分子 #16: 40S ribosomal protein S9-A
+分子 #17: 40S ribosomal protein S11-A
+分子 #18: 40S ribosomal protein S13
+分子 #19: 40S ribosomal protein S14-A
+分子 #20: 40S ribosomal protein S21-A
+分子 #21: 40S ribosomal protein S22-A
+分子 #22: 40S ribosomal protein S23-A
+分子 #23: 40S ribosomal protein S24-A
+分子 #24: 40S ribosomal protein S26-A
+分子 #25: 40S ribosomal protein S27-A
+分子 #26: 40S ribosomal protein S30-A
+分子 #27: RPS15 isoform 1
+分子 #28: 40S ribosomal protein S3
+分子 #29: 40S ribosomal protein S5
+分子 #30: 40S ribosomal protein S10-A
+分子 #31: 40S ribosomal protein S12
+分子 #32: 40S ribosomal protein S16-A
+分子 #33: 40S ribosomal protein S17-A
+分子 #34: 40S ribosomal protein S18-A
+分子 #35: 40S ribosomal protein S19-A
+分子 #36: 40S ribosomal protein S20
+分子 #37: 40S ribosomal protein S25-A
+分子 #38: RPS29A isoform 1
+分子 #39: 40S ribosomal protein S31
+分子 #40: Guanine nucleotide-binding protein subunit beta-like protein
+分子 #41: 40S ribosomal protein S28-A
+分子 #42: Eukaryotic translation initiation factor 3 subunit J
+分子 #43: RLI1 isoform 1
+分子 #44: 60S ribosomal protein L40-A
+分子 #45: 60S ribosomal protein L41-A
+分子 #46: OTU domain-containing protein 2
+分子 #47: 40S ribosomal protein S7-A
+分子 #9: 18S ribosomal RNA
+分子 #48: MAGNESIUM ION
+分子 #49: ZINC ION
+分子 #50: IRON/SULFUR CLUSTER
+分子 #51: ADENOSINE-5'-DIPHOSPHATE
-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 |
-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: 46.4 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): 3.0 µm / 最小 デフォーカス(公称値): 0.5 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |