+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-0047 | |||||||||
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タイトル | Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP/sordarin) | |||||||||
マップデータ | ||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / 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 / RMTs methylate histone arginines / positive regulation of translational fidelity / Protein methylation ...Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / 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 / 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 / hexon binding / 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 / 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 / Ribosomal scanning and start codon recognition / response to cycloheximide / 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 / negative regulation of mRNA splicing, via spliceosome / preribosome, large subunit precursor / regulation of amino acid metabolic process / L13a-mediated translational silencing of Ceruloplasmin expression / translational elongation / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / 90S preribosome / positive regulation of protein kinase activity / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Ub-specific processing proteases / regulation of translational fidelity / protein-RNA complex assembly / translation elongation factor activity / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / translation regulator activity / 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) / Neutrophil degranulation / maturation of LSU-rRNA / DNA-(apurinic or apyrimidinic site) endonuclease 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 / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / translational initiation / macroautophagy / protein kinase C binding / maintenance of translational fidelity / cytoplasmic stress granule / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / 加水分解酵素; 酸無水物に作用; GTPに作用・細胞または細胞小器官の運動に関与 / ribosome biogenesis / viral capsid / ribosome binding / protein-folding chaperone binding / ribosomal small subunit assembly / ribosomal large subunit assembly / small ribosomal subunit / large ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / translation / negative regulation of gene expression / response to antibiotic / GTPase activity / mRNA binding / ubiquitin protein ligase binding / GTP binding / host cell nucleus 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: 4.4 Å | |||||||||
データ登録者 | Pellegrino S / Demeshkina N / Mancera-Martinez E / Melnikov S / Simonetti A / Myasnikov A / Yusupov M / Yusupova G / Hashem Y | |||||||||
引用 | ジャーナル: J Mol Biol / 年: 2018 タイトル: Structural Insights into the Role of Diphthamide on Elongation Factor 2 in mRNA Reading-Frame Maintenance. 著者: Simone Pellegrino / Natalia Demeshkina / Eder Mancera-Martinez / Sergey Melnikov / Angelita Simonetti / Alexander Myasnikov / Marat Yusupov / Gulnara Yusupova / Yaser Hashem / 要旨: One of the most critical steps of protein biosynthesis is the coupled movement of mRNA, which encodes genetic information, with tRNAs on the ribosome. In eukaryotes, this process is catalyzed by a ...One of the most critical steps of protein biosynthesis is the coupled movement of mRNA, which encodes genetic information, with tRNAs on the ribosome. In eukaryotes, this process is catalyzed by a conserved G-protein, the elongation factor 2 (eEF2), which carries a unique post-translational modification, called diphthamide, found in all eukaryotic species. Here we present near-atomic resolution cryo-electron microscopy structures of yeast 80S ribosome complexes containing mRNA, tRNA and eEF2 trapped in different GTP-hydrolysis states which provide further structural insights into the role of diphthamide in the mechanism of translation fidelity in eukaryotes. | |||||||||
履歴 |
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-構造の表示
構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
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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_0047.map.gz | 25.1 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-0047-v30.xml emd-0047.xml | 107.2 KB 107.2 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_0047.png | 275.2 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-0047 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0047 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_0047_validation.pdf.gz | 266.6 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_0047_full_validation.pdf.gz | 265.7 KB | 表示 | |
XML形式データ | emd_0047_validation.xml.gz | 6.6 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0047 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0047 | 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_0047.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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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: 1.1 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 : 80S ribosome in complex with mRNA, tRNA and eEF2 in presence of n...
+超分子 #1: 80S ribosome in complex with mRNA, tRNA and eEF2 in presence of n...
+超分子 #2: 80S ribosome
+超分子 #3: RNA
+分子 #1: Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), m...
+分子 #2: 5.8S ribosomal RNA
+分子 #3: 5S ribosomal RNA
+分子 #47: 18S ribosomal RNA
+分子 #81: Transfer RNA - Phe
+分子 #82: Messenger RNA
+分子 #4: 60S acidic ribosomal protein P0
+分子 #5: 60S ribosomal protein L12-A
+分子 #6: 60S ribosomal protein L2-A
+分子 #7: 60S ribosomal protein L3
+分子 #8: 60S ribosomal protein L4-A
+分子 #9: 60S ribosomal protein L5
+分子 #10: 60S ribosomal protein L6-A
+分子 #11: 60S ribosomal protein L7-A
+分子 #12: 60S ribosomal protein L8-A
+分子 #13: 60S ribosomal protein L9-A
+分子 #14: 60S ribosomal protein L10
+分子 #15: 60S ribosomal protein L11-B
+分子 #16: 60S ribosomal protein L13-A
+分子 #17: 60S ribosomal protein L14-A
+分子 #18: 60S ribosomal protein L15-A
+分子 #19: 60S ribosomal protein L16-A
+分子 #20: 60S ribosomal protein L17-A
+分子 #21: 60S ribosomal protein L18-A
+分子 #22: 60S ribosomal protein L19-A
+分子 #23: 60S ribosomal protein L20-A
+分子 #24: 60S ribosomal protein L21-A
+分子 #25: 60S ribosomal protein L22-A
+分子 #26: 60S ribosomal protein L23-A
+分子 #27: 60S ribosomal protein L24-A
+分子 #28: 60S ribosomal protein L25
+分子 #29: 60S ribosomal protein L26-A
+分子 #30: 60S ribosomal protein L27-A
+分子 #31: 60S ribosomal protein L28
+分子 #32: 60S ribosomal protein L29
+分子 #33: 60S ribosomal protein L30
+分子 #34: 60S ribosomal protein L31-A
+分子 #35: 60S ribosomal protein L32
+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: 60S ribosomal protein L38
+分子 #42: 60S ribosomal protein L39
+分子 #43: Ubiquitin-60S ribosomal protein L40
+分子 #44: 60S ribosomal protein L41-B
+分子 #45: 60S ribosomal protein L42-A
+分子 #46: 60S ribosomal protein L43-A
+分子 #48: 40S ribosomal protein S0-A
+分子 #49: 40S ribosomal protein S1-A
+分子 #50: 40S ribosomal protein S2
+分子 #51: 40S ribosomal protein S3
+分子 #52: 40S ribosomal protein S4-A
+分子 #53: 40S ribosomal protein S5
+分子 #54: 40S ribosomal protein S6-A
+分子 #55: 40S ribosomal protein S7-A
+分子 #56: 40S ribosomal protein S8-A
+分子 #57: 40S ribosomal protein S9-A
+分子 #58: 40S ribosomal protein S10-A
+分子 #59: 40S ribosomal protein S11-A
+分子 #60: 40S ribosomal protein S12
+分子 #61: 40S ribosomal protein S13
+分子 #62: 40S ribosomal protein S14-B
+分子 #63: 40S ribosomal protein S15
+分子 #64: 40S ribosomal protein S16-A
+分子 #65: 40S ribosomal protein S17-B
+分子 #66: 40S ribosomal protein S18-A
+分子 #67: 40S ribosomal protein S19-A
+分子 #68: 40S ribosomal protein S20
+分子 #69: 40S ribosomal protein S21-A
+分子 #70: 40S ribosomal protein S22-A
+分子 #71: 40S ribosomal protein S23-A
+分子 #72: 40S ribosomal protein S24-A
+分子 #73: 40S ribosomal protein S25-A
+分子 #74: 40S ribosomal protein S26-B
+分子 #75: 40S ribosomal protein S27-A
+分子 #76: 40S ribosomal protein S28-A
+分子 #77: 40S ribosomal protein S29-A
+分子 #78: 40S ribosomal protein S30-A
+分子 #79: Guanine nucleotide-binding protein subunit beta-like protein
+分子 #80: Ubiquitin-40S ribosomal protein S31
+分子 #83: Elongation factor 2
+分子 #84: ZINC ION
+分子 #85: [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA...
+分子 #86: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
-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 構成要素:
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凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK IV / 詳細: blot force 4, blot waiting time 30 s. |
-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) 平均露光時間: 1.5 sec. / 平均電子線量: 60.0 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 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期モデル | モデルのタイプ: PDB ENTRY PDBモデル - PDB ID: |
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最終 再構成 | 想定した対称性 - 点群: C1 (非対称) / 解像度のタイプ: BY AUTHOR / 解像度: 4.4 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: RELION / 使用した粒子像数: 189700 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
-原子モデル構築 1
精密化 | 空間: REAL / プロトコル: OTHER |
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得られたモデル | PDB-6gq1: |