+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-22198 | |||||||||
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タイトル | Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress | |||||||||
マップデータ | ||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / 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 ...negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / 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) / 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 / 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 / regulation of translational fidelity / protein-RNA complex assembly / translation regulator activity / ribosomal 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) / cellular response to amino acid starvation / rescue of stalled ribosome / 90S preribosome / 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 / 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 / rRNA processing / 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 / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / 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 / 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 | Saccharomyces cerevisiae (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: 3.2 Å | |||||||||
データ登録者 | Zhou Y / Bartesaghi A / Silva GM | |||||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Proc Natl Acad Sci U S A / 年: 2020 タイトル: Structural impact of K63 ubiquitin on yeast translocating ribosomes under oxidative stress. 著者: Ye Zhou / Panagiotis L Kastritis / Shannon E Dougherty / Jonathan Bouvette / Allen L Hsu / Laura Burbaum / Shyamal Mosalaganti / Stefan Pfeffer / Wim J H Hagen / Friedrich Förster / Mario J ...著者: Ye Zhou / Panagiotis L Kastritis / Shannon E Dougherty / Jonathan Bouvette / Allen L Hsu / Laura Burbaum / Shyamal Mosalaganti / Stefan Pfeffer / Wim J H Hagen / Friedrich Förster / Mario J Borgnia / Christine Vogel / Martin Beck / Alberto Bartesaghi / Gustavo M Silva / 要旨: Subpopulations of ribosomes are responsible for fine tuning the control of protein synthesis in dynamic environments. K63 ubiquitination of ribosomes has emerged as a new posttranslational ...Subpopulations of ribosomes are responsible for fine tuning the control of protein synthesis in dynamic environments. K63 ubiquitination of ribosomes has emerged as a new posttranslational modification that regulates protein synthesis during cellular response to oxidative stress. K63 ubiquitin, a type of ubiquitin chain that functions independently of the proteasome, modifies several sites at the surface of the ribosome, however, we lack a molecular understanding on how this modification affects ribosome structure and function. Using cryoelectron microscopy (cryo-EM), we resolved the first three-dimensional (3D) structures of K63 ubiquitinated ribosomes from oxidatively stressed yeast cells at 3.5-3.2 Å resolution. We found that K63 ubiquitinated ribosomes are also present in a polysome arrangement, similar to that observed in yeast polysomes, which we determined using cryoelectron tomography (cryo-ET). We further showed that K63 ubiquitinated ribosomes are captured uniquely at the rotated pretranslocation stage of translation elongation. In contrast, cryo-EM structures of ribosomes from mutant cells lacking K63 ubiquitin resolved at 4.4-2.7 Å showed 80S ribosomes represented in multiple states of translation, suggesting that K63 ubiquitin regulates protein synthesis at a selective stage of elongation. Among the observed structural changes, ubiquitin mediates the destabilization of proteins in the 60S P-stalk and in the 40S beak, two binding regions of the eukaryotic elongation factor eEF2. These changes would impact eEF2 function, thus, inhibiting translocation. Our findings help uncover the molecular effects of K63 ubiquitination on ribosomes, providing a model of translation control during oxidative stress, which supports elongation halt at pretranslocation. | |||||||||
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_22198.map.gz | 202.5 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-22198-v30.xml emd-22198.xml | 91.4 KB 91.4 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_22198_fsc.xml | 16.9 KB | 表示 | FSCデータファイル |
画像 | emd_22198.png | 141.8 KB | ||
マスクデータ | emd_22198_msk_1.map | 421.9 MB | マスクマップ | |
その他 | emd_22198_half_map_1.map.gz emd_22198_half_map_2.map.gz | 337.9 MB 338 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-22198 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22198 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_22198_validation.pdf.gz | 691.5 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_22198_full_validation.pdf.gz | 691.1 KB | 表示 | |
XML形式データ | emd_22198_validation.xml.gz | 25.3 KB | 表示 | |
CIF形式データ | emd_22198_validation.cif.gz | 33.7 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22198 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22198 | 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_22198.map.gz / 形式: CCP4 / 大きさ: 421.9 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 1.36 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
-マスク #1
ファイル | emd_22198_msk_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_22198_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #2
ファイル | emd_22198_half_map_2.map | ||||||||||||
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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 : K63 ubiquitinated Ribosome
+超分子 #1: K63 ubiquitinated Ribosome
+分子 #1: 60S ribosomal protein L2-A
+分子 #2: RPL3 isoform 1
+分子 #3: RPL4A isoform 1
+分子 #4: RPL5 isoform 1
+分子 #5: 60S ribosomal protein L6-A
+分子 #6: 60S ribosomal protein L7-A
+分子 #7: RPL8A isoform 1
+分子 #8: RPL9A isoform 1
+分子 #9: RPL10 isoform 1
+分子 #10: RPL11B isoform 1
+分子 #11: 60S ribosomal protein L13-A
+分子 #12: 60S ribosomal protein L14-A
+分子 #13: 60S ribosomal protein L15-A
+分子 #14: 60S ribosomal protein L16-A
+分子 #15: 60S ribosomal protein L17-A
+分子 #16: 60S ribosomal protein L18-A
+分子 #17: 60S ribosomal protein L19-A
+分子 #18: 60S ribosomal protein L20-A
+分子 #19: 60S ribosomal protein L21-A
+分子 #20: 60S ribosomal protein L22-A
+分子 #21: 60S ribosomal protein L23-A
+分子 #22: RPL24A isoform 1
+分子 #23: 60S ribosomal protein L25
+分子 #24: 60S ribosomal protein L26-A
+分子 #25: 60S ribosomal protein L27-A
+分子 #26: 40S ribosomal protein S10-A
+分子 #27: 40S ribosomal protein S11-A
+分子 #31: 60S ribosomal protein L28
+分子 #32: RPL29 isoform 1
+分子 #33: 60S ribosomal protein L30
+分子 #34: 60S ribosomal protein L31-A
+分子 #35: RPL32 isoform 1
+分子 #36: 60S ribosomal protein L33-A
+分子 #37: 60S ribosomal protein L34-A
+分子 #38: 60S ribosomal protein L35-A
+分子 #39: 60S ribosomal protein L36-A
+分子 #40: 60S ribosomal protein L37-A
+分子 #41: RPL38 isoform 1
+分子 #42: 60S ribosomal protein L39
+分子 #43: RPL41A isoform 1
+分子 #44: 60S ribosomal protein L42-A
+分子 #45: 60S ribosomal protein L43-A
+分子 #47: 40S ribosomal protein S0-A
+分子 #48: RPS1A isoform 1
+分子 #49: RPS2 isoform 1
+分子 #50: RPS3 isoform 1
+分子 #51: 40S ribosomal protein S4-A
+分子 #52: Rps5p
+分子 #53: 40S ribosomal protein S6-A
+分子 #54: 40S ribosomal protein S7-A
+分子 #55: RPS8A isoform 1
+分子 #56: 40S ribosomal protein S9-A
+分子 #57: 40S ribosomal protein S13
+分子 #58: 40S ribosomal protein S14-B
+分子 #59: RPS15 isoform 1
+分子 #60: 40S ribosomal protein S16-A
+分子 #61: 40S ribosomal protein S17-B
+分子 #62: 40S ribosomal protein S18-A
+分子 #63: 40S ribosomal protein S19-A
+分子 #64: RPS20 isoform 1
+分子 #65: 40S ribosomal protein S21-A
+分子 #66: RPS22A isoform 1
+分子 #67: 40S ribosomal protein S23-A
+分子 #68: 40S ribosomal protein S24-A
+分子 #69: RPS25A isoform 1
+分子 #70: RPS26B isoform 1
+分子 #71: 40S ribosomal protein S27-A
+分子 #72: RPS28A isoform 1
+分子 #73: RPS29A isoform 1
+分子 #74: Guanine nucleotide-binding protein subunit beta-like protein
+分子 #28: 35S ribosomal RNA
+分子 #29: 5S ribosomal RNA
+分子 #30: 5.8S ribosomal RNA
+分子 #46: 18S ribosomal RNA
+分子 #75: Transfer RNA
+分子 #76: 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: 7.5 |
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グリッド | モデル: Quantifoil R2/1 / 材質: COPPER / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY |
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: FEI FALCON II (4k x 4k) 検出モード: INTEGRATING / デジタル化 - 画像ごとのフレーム数: 1-7 / 実像数: 5243 / 平均電子線量: 25.0 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 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |