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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 6gq1 | |||||||||||||||
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タイトル | Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP/sordarin) | |||||||||||||||
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![]() | RIBOSOME / Eukaryotic 80S riboosme / mRNA-tRNA translocation / diphthamide | |||||||||||||||
機能・相同性 | ![]() 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 / positive regulation of translational fidelity / Protein methylation / RMTs methylate histone arginines ...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 / 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 / translational elongation / 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 / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit export from nucleus / 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 / translation elongation factor 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) / DNA-(apurinic or apyrimidinic site) endonuclease activity / Neutrophil degranulation / cellular response to amino acid starvation / rescue of stalled ribosome / ribosome assembly / 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 / small-subunit processome / positive regulation of apoptotic signaling pathway / protein kinase C binding / macroautophagy / maintenance of translational fidelity / 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 / 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 / protein-folding chaperone 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 / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / negative regulation of gene expression / response to antibiotic / GTPase activity / mRNA binding / ubiquitin protein ligase binding / nucleolus / GTP binding / mitochondrion / RNA binding / zinc ion binding / nucleoplasm 類似検索 - 分子機能 | |||||||||||||||
生物種 | ![]() ![]() | |||||||||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.4 Å | |||||||||||||||
![]() | Pellegrino, S. / Demeshkina, N. / Mancera-Martinez, E. / Melnikov, S. / Simonetti, A. / Myasnikov, A. / Yusupov, M. / Yusupova, G. / Hashem, Y. | |||||||||||||||
資金援助 | ![]()
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![]() | ![]() 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
ムービー |
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構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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ダウンロード
PDBx/mmCIF形式 | ![]() | 4.5 MB | 表示 | ![]() |
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PDB形式 | ![]() | 表示 | ![]() | |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 1.5 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.7 MB | 表示 | |
XML形式データ | ![]() | 357.4 KB | 表示 | |
CIF形式データ | ![]() | 610.1 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
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リンク
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集合体
登録構造単位 | ![]()
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要素
-RNA鎖 , 6種, 6分子 1342AXAY
#1: RNA鎖 | 分子量: 1097493.875 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) ![]() ![]() 参照: REF: 831416132 |
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#2: RNA鎖 | 分子量: 38951.105 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) ![]() ![]() 参照: GenBank: 1329886537 |
#3: RNA鎖 | 分子量: 50682.922 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) ![]() ![]() 参照: GenBank: 1358044889 |
#47: RNA鎖 | 分子量: 578820.375 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) ![]() ![]() 参照: GenBank: 1329886537 |
#81: RNA鎖 | 分子量: 24518.570 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) ![]() ![]() 参照: GenBank: 176419 |
#82: RNA鎖 | 分子量: 2449.465 Da / 分子数: 1 / 由来タイプ: 合成 由来: (合成) ![]() ![]() |
-タンパク質 , 4種, 4分子 P0mAVAZ
#4: タンパク質 | 分子量: 20929.145 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) ![]() ![]() 参照: UniProt: P05317 |
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#43: タンパク質 | 分子量: 6032.321 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) ![]() ![]() 株: ATCC 204508 / S288c / 参照: UniProt: P0CH08 |
#79: タンパク質 | 分子量: 34710.023 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) ![]() ![]() 株: ATCC 204508 / S288c / 参照: UniProt: P38011 |
#83: タンパク質 | 分子量: 93318.992 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) ![]() ![]() 参照: UniProt: P32324 |
+60S ribosomal protein ... , 41種, 41分子 P2ABCDEFGHIJLMNOPQRSTUVWXYZabcd...
+40S ribosomal protein ... , 31種, 31分子 qrstuvwxyzAAABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAU
-タンパク質・ペプチド , 1種, 1分子 AW
#80: タンパク質・ペプチド | 分子量: 4148.841 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) ![]() ![]() 株: ATCC 204508 / S288c / 参照: UniProt: P05759 |
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-非ポリマー , 3種, 10分子 ![](data/chem/img/ZN.gif)
![](data/chem/img/SO1.gif)
![](data/chem/img/GCP.gif)
![](data/chem/img/SO1.gif)
![](data/chem/img/GCP.gif)
#84: 化合物 | ChemComp-ZN / #85: 化合物 | ChemComp-SO1 / [ | #86: 化合物 | ChemComp-GCP / | |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
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試料調製
構成要素 |
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分子量 | 値: 3.4 MDa / 実験値: NO | ||||||||||||||||||||||||
由来(天然) |
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由来(組換発現) | 生物種: synthetic construct (人工物) | ||||||||||||||||||||||||
緩衝液 | pH: 7.5 | ||||||||||||||||||||||||
緩衝液成分 |
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試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 277 K / 詳細: blot force 4, blot waiting time 30 s |
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電子顕微鏡撮影
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD |
撮影 | 平均露光時間: 1.5 sec. / 電子線照射量: 60 e/Å2 フィルム・検出器のモデル: FEI FALCON II (4k x 4k) |
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解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||
3次元再構成 | 解像度: 4.4 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 189700 / 対称性のタイプ: POINT | ||||||||||||
原子モデル構築 | プロトコル: OTHER / 空間: REAL |