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基本情報
登録情報 | データベース: EMDB / ID: EMD-11096 | |||||||||
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タイトル | Cryo-EM structure of yeast Lso2 bound to 80S ribosomes under native condition | |||||||||
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![]() | Ribosome / hibernation | |||||||||
機能・相同性 | ![]() cytoplasmic translational elongation / ribosome hibernation / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Negative regulators of DDX58/IFIH1 signaling / positive regulation of translational fidelity / Protein methylation / RMTs methylate histone arginines / mTORC1-mediated signalling ...cytoplasmic translational elongation / ribosome hibernation / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Negative regulators of DDX58/IFIH1 signaling / positive regulation of translational fidelity / Protein methylation / RMTs methylate histone arginines / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / pre-mRNA 5'-splice site binding / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / response to cycloheximide / mRNA destabilization / 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) / negative regulation of mRNA splicing, via spliceosome / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / ribosomal large subunit export from nucleus / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / G-protein alpha-subunit binding / positive regulation of protein kinase activity / protein-RNA complex assembly / regulation of translational fidelity / Ub-specific processing proteases / ribosomal small subunit export from nucleus / translation regulator activity / ribosomal subunit export from nucleus / translational termination / 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) / translation repressor activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / cellular response to amino acid starvation / ribosome assembly / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / macroautophagy / small-subunit processome / positive regulation of apoptotic signaling pathway / protein kinase C binding / maintenance of translational fidelity / ribosomal large subunit assembly / cytoplasmic stress granule / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / intracellular iron ion homeostasis / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / translation / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / negative regulation of gene expression / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() ![]() ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.4 Å | |||||||||
![]() | Wells JN / Buschauer R | |||||||||
![]() | ![]() タイトル: Structure and function of yeast Lso2 and human CCDC124 bound to hibernating ribosomes. 著者: Jennifer N Wells / Robert Buschauer / Timur Mackens-Kiani / Katharina Best / Hanna Kratzat / Otto Berninghausen / Thomas Becker / Wendy Gilbert / Jingdong Cheng / Roland Beckmann / ![]() ![]() 要旨: Cells adjust to nutrient deprivation by reversible translational shutdown. This is accompanied by maintaining inactive ribosomes in a hibernation state, in which they are bound by proteins with ...Cells adjust to nutrient deprivation by reversible translational shutdown. This is accompanied by maintaining inactive ribosomes in a hibernation state, in which they are bound by proteins with inhibitory and protective functions. In eukaryotes, such a function was attributed to suppressor of target of Myb protein 1 (Stm1; SERPINE1 mRNA-binding protein 1 [SERBP1] in mammals), and recently, late-annotated short open reading frame 2 (Lso2; coiled-coil domain containing short open reading frame 124 [CCDC124] in mammals) was found to be involved in translational recovery after starvation from stationary phase. Here, we present cryo-electron microscopy (cryo-EM) structures of translationally inactive yeast and human ribosomes. We found Lso2/CCDC124 accumulating on idle ribosomes in the nonrotated state, in contrast to Stm1/SERBP1-bound ribosomes, which display a rotated state. Lso2/CCDC124 bridges the decoding sites of the small with the GTPase activating center (GAC) of the large subunit. This position allows accommodation of the duplication of multilocus region 34 protein (Dom34)-dependent ribosome recycling system, which splits Lso2-containing, but not Stm1-containing, ribosomes. We propose a model in which Lso2 facilitates rapid translation reactivation by stabilizing the recycling-competent state of inactive ribosomes. | |||||||||
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「今月の分子」の関連する項目 |
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ボクセルのサイズ | X=Y=Z: 1.084 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
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試料の構成要素
+全体 : Lso2-80S ribosome
+超分子 #1: Lso2-80S ribosome
+分子 #1: 18S rRNA
+分子 #3: 25S rRNA
+分子 #4: 5S rRNA
+分子 #5: 5.8S rRNA
+分子 #2: Protein LSO2
+分子 #6: 40S ribosomal protein S0-A
+分子 #7: 40S ribosomal protein S1-A
+分子 #8: 40S ribosomal protein S2
+分子 #9: 40S ribosomal protein S3
+分子 #10: 40S ribosomal protein S4-A
+分子 #11: 40S ribosomal protein S5
+分子 #12: 40S ribosomal protein S6-A
+分子 #13: 40S ribosomal protein S7-A
+分子 #14: 40S ribosomal protein S8-A
+分子 #15: 40S ribosomal protein S9-A
+分子 #16: 40S ribosomal protein S10-A
+分子 #17: 40S ribosomal protein S11-A
+分子 #18: 40S ribosomal protein S12
+分子 #19: 40S ribosomal protein S13
+分子 #20: 40S ribosomal protein S14-A
+分子 #21: 40S ribosomal protein S15
+分子 #22: 40S ribosomal protein S16-A
+分子 #23: 40S ribosomal protein S17-A
+分子 #24: 40S ribosomal protein S18-A
+分子 #25: 40S ribosomal protein S19-A
+分子 #26: 40S ribosomal protein S20
+分子 #27: 40S ribosomal protein S21-A
+分子 #28: 40S ribosomal protein S22-A
+分子 #29: 40S ribosomal protein S23-A
+分子 #30: 40S ribosomal protein S24-A
+分子 #31: 40S ribosomal protein S25-A
+分子 #32: 40S ribosomal protein S26-B
+分子 #33: 40S ribosomal protein S27-A
+分子 #34: 40S ribosomal protein S28-A
+分子 #35: 40S ribosomal protein S29-A
+分子 #36: 40S ribosomal protein S30-A
+分子 #37: Ubiquitin-40S ribosomal protein S31
+分子 #38: Guanine nucleotide-binding protein subunit beta-like protein
+分子 #39: 60S ribosomal protein L2-A
+分子 #40: 60S ribosomal protein L3
+分子 #41: 60S ribosomal protein L4-A
+分子 #42: 60S ribosomal protein L5
+分子 #43: 60S ribosomal protein L6-A
+分子 #44: 60S ribosomal protein L7-A
+分子 #45: 60S ribosomal protein L8-A
+分子 #46: 60S ribosomal protein L9-A
+分子 #47: 60S ribosomal protein L10
+分子 #48: 60S ribosomal protein L11-A
+分子 #49: 60S ribosomal protein L13-A
+分子 #50: 60S ribosomal protein L14-A
+分子 #51: 60S ribosomal protein L15-A
+分子 #52: 60S ribosomal protein L16-A
+分子 #53: 60S ribosomal protein L17-A
+分子 #54: 60S ribosomal protein L18-A
+分子 #55: 60S ribosomal protein L19-A
+分子 #56: 60S ribosomal protein L20-A
+分子 #57: 60S ribosomal protein L21-A
+分子 #58: 60S ribosomal protein L22-A
+分子 #59: 60S ribosomal protein L23-A
+分子 #60: 60S ribosomal protein L24-A
+分子 #61: 60S ribosomal protein L25
+分子 #62: 60S ribosomal protein L26-A
+分子 #63: 60S ribosomal protein L27-A
+分子 #64: 60S ribosomal protein L28
+分子 #65: 60S ribosomal protein L29
+分子 #66: 60S ribosomal protein L30
+分子 #67: 60S ribosomal protein L31-A
+分子 #68: 60S ribosomal protein L32
+分子 #69: 60S ribosomal protein L33-A
+分子 #70: 60S ribosomal protein L34-A
+分子 #71: 60S ribosomal protein L35-A
+分子 #72: 60S ribosomal protein L36-A
+分子 #73: 60S ribosomal protein L37-A
+分子 #74: 60S ribosomal protein L38
+分子 #75: 60S ribosomal protein L39
+分子 #76: Ubiquitin-60S ribosomal protein L40
+分子 #77: 60S ribosomal protein L41-B
+分子 #78: 60S ribosomal protein L42-A
+分子 #79: 60S ribosomal protein L43-A
+分子 #80: 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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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
緩衝液 | pH: 7.4 |
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凍結 | 凍結剤: ETHANE |
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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: FEI FALCON II (4k x 4k) 平均電子線量: 28.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
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 |
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画像解析
-原子モデル構築 1
精密化 | 空間: REAL / プロトコル: RIGID BODY FIT |
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得られたモデル | ![]() PDB-6z6j: |