+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5juo | |||||||||||||||
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タイトル | Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure I (fully rotated 40S subunit) | |||||||||||||||
要素 |
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キーワード | RIBOSOME (リボソーム) / 80S-IRES / eEF2 / translocation / sordarin | |||||||||||||||
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 / Protein methylation / positive regulation of translational fidelity ...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 / Protein methylation / positive regulation of translational fidelity / RMTs methylate histone arginines / mTORC1-mediated signalling / ヒドロキシル化 / 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 / preribosome, small subunit precursor / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translational elongation / 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 / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / protein-RNA complex assembly / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / Ub-specific processing proteases / regulation of translational fidelity / positive regulation of protein kinase activity / ribosomal small 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) / ribosomal subunit export from nucleus / translation regulator activity / translation elongation factor activity / translational termination / 90S preribosome / DNA-(apurinic or apyrimidinic site) endonuclease activity / Neutrophil degranulation / rescue of stalled ribosome / cellular response to amino acid starvation / ribosome assembly / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 / positive regulation of apoptotic signaling pathway / small-subunit processome / protein kinase C binding / maintenance of translational fidelity / オートファジー / 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 / modification-dependent protein catabolic process / cytoplasmic stress granule / rRNA processing / protein tag activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / リボソーム生合成 / ribosome binding / 5S rRNA binding / large ribosomal subunit rRNA binding / small ribosomal subunit / protein-folding chaperone binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / リボソーム / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / 翻訳 (生物学) / 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 / 核小体 / GTP binding / ミトコンドリア / RNA binding / zinc ion binding 類似検索 - 分子機能 | |||||||||||||||
生物種 | Saccharomyces cerevisiae (パン酵母) Taura syndrome virus (ウイルス) | |||||||||||||||
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 Å | |||||||||||||||
データ登録者 | Abeyrathne, P. / Koh, C.S. / Grant, T. / Grigorieff, N. / Korostelev, A.A. | |||||||||||||||
資金援助 | 米国, 4件
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引用 | ジャーナル: Elife / 年: 2016 タイトル: Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome. 著者: Priyanka D Abeyrathne / Cha San Koh / Timothy Grant / Nikolaus Grigorieff / Andrei A Korostelev / 要旨: Internal ribosome entry sites (IRESs) mediate cap-independent translation of viral mRNAs. Using electron cryo-microscopy of a single specimen, we present five ribosome structures formed with the ...Internal ribosome entry sites (IRESs) mediate cap-independent translation of viral mRNAs. Using electron cryo-microscopy of a single specimen, we present five ribosome structures formed with the Taura syndrome virus IRES and translocase eEF2•GTP bound with sordarin. The structures suggest a trajectory of IRES translocation, required for translation initiation, and provide an unprecedented view of eEF2 dynamics. The IRES rearranges from extended to bent to extended conformations. This inchworm-like movement is coupled with ribosomal inter-subunit rotation and 40S head swivel. eEF2, attached to the 60S subunit, slides along the rotating 40S subunit to enter the A site. Its diphthamide-bearing tip at domain IV separates the tRNA-mRNA-like pseudoknot I (PKI) of the IRES from the decoding center. This unlocks 40S domains, facilitating head swivel and biasing IRES translocation via hitherto-elusive intermediates with PKI captured between the A and P sites. The structures suggest missing links in our understanding of tRNA translocation. | |||||||||||||||
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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 5juo.cif.gz | 5.1 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb5juo.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 5juo.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ju/5juo ftp://data.pdbj.org/pub/pdb/validation_reports/ju/5juo | HTTPS FTP |
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-関連構造データ
関連構造データ | 6643MC 6648MC 6644C 6645C 6646C 6647C 6649C 6650C 6651C 6652C 6653C 5jupC 5jusC 5jutC 5juuC M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 (文献) |
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類似構造データ |
-リンク
-集合体
登録構造単位 |
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-要素
-RNA鎖 , 5種, 5分子 ABCDEC
#1: RNA鎖 | 分子量: 579126.562 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: GenBank: 874346701 |
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#2: RNA鎖 | 分子量: 1097493.875 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: GenBank: 834774822 |
#3: RNA鎖 | 分子量: 50682.922 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: GenBank: 1043567390 |
#4: RNA鎖 | 分子量: 38951.105 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: GenBank: 1039022949 |
#83: RNA鎖 | 分子量: 64644.301 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Taura syndrome virus (ウイルス) / 参照: GenBank: 14701764 |
+タンパク質 , 77種, 77分子 EFGHIJKLMNOPQRSTUVWXYZAABACADAEAFAGAHA...
-タンパク質・ペプチド , 1種, 1分子 SA
#45: タンパク質・ペプチド | 分子量: 3354.243 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P0CX86 |
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-非ポリマー , 3種, 3分子
#84: 化合物 | ChemComp-GDP / |
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#85: 化合物 | ChemComp-MG / |
#86: 化合物 | ChemComp-SO1 / [ |
-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 |
-試料調製
構成要素 | 名称: Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2, GDP, sordarin and Taura Syndrome Virus IRES, Structure I (fully rotated 40S subunit) タイプ: RIBOSOME 詳細: ~10 degree rotated 40S body, ~12 degree swiveled 40S head, partially bent IRES. The following regions are modeled as RNA or protein backbone due to insufficient density: 25S nt 1967-2047, ...詳細: ~10 degree rotated 40S body, ~12 degree swiveled 40S head, partially bent IRES. The following regions are modeled as RNA or protein backbone due to insufficient density: 25S nt 1967-2047, 2063-2074, 18S nt 712-727, 1698-1705, IRES nt 6840-6846, proteins eS12 and eS31 Entity ID: #1-#83 / 由来: MULTIPLE SOURCES |
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緩衝液 | pH: 7.5 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | グリッドのサイズ: 200 divisions/in. |
急速凍結 | 凍結剤: ETHANE |
-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: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELDBright-field microscopy |
撮影 | 電子線照射量: 1.4 e/Å2 フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) |
-解析
CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3次元再構成 | 解像度: 4 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 38047 / 対称性のタイプ: POINT |