+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3j78 | |||||||||
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タイトル | Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class I - non-rotated ribosome with 2 tRNAs) | |||||||||
要素 |
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キーワード | RIBOSOME (リボソーム) / 80S ribosome / Kozak sequence (コザック配列) / translation (翻訳 (生物学)) / tRNA (転移RNA) / hybrid-state / classical-state | |||||||||
機能・相同性 | 機能・相同性情報 : / 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 ...: / 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) / 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 / 90S preribosome / translational termination / DNA-(apurinic or apyrimidinic site) endonuclease activity / 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 / 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 / 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 / 翻訳 (生物学) / 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 / 核小体 / ミトコンドリア / RNA binding / zinc ion binding / 核質 / metal ion binding / 細胞核 / 細胞質基質 / 細胞質 類似検索 - 分子機能 | |||||||||
生物種 | Saccharomyces cerevisiae (パン酵母) Escherichia coli (大腸菌) | |||||||||
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: 6.3 Å | |||||||||
データ登録者 | Svidritskiy, E. / Brilot, A.F. / Koh, C.S. / Grigorieff, N. / Korostelev, A.A. | |||||||||
引用 | ジャーナル: Structure / 年: 2014 タイトル: Structures of yeast 80S ribosome-tRNA complexes in the rotated and nonrotated conformations. 著者: Egor Svidritskiy / Axel F Brilot / Cha San Koh / Nikolaus Grigorieff / Andrei A Korostelev / 要旨: The structural understanding of eukaryotic translation lags behind that of translation on bacterial ribosomes. Here, we present two subnanometer resolution structures of S. cerevisiae 80S ribosome ...The structural understanding of eukaryotic translation lags behind that of translation on bacterial ribosomes. Here, we present two subnanometer resolution structures of S. cerevisiae 80S ribosome complexes formed with either one or two tRNAs and bound in response to an mRNA fragment containing the Kozak consensus sequence. The ribosomes adopt two globally different conformations that are related to each other by the rotation of the small subunit. Comparison with bacterial ribosome complexes reveals that the global structures and modes of intersubunit rotation of the yeast ribosome differ significantly from those in the bacterial counterpart, most notably in the regions involving the tRNA, small ribosomal subunit, and conserved helix 69 of the large ribosomal subunit. The structures provide insight into ribosome dynamics implicated in tRNA translocation and help elucidate the role of the Kozak fragment in positioning an open reading frame during translation initiation in eukaryotes. | |||||||||
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 | 3j78.cif.gz | 4.8 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3j78.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 3j78.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/j7/3j78 ftp://data.pdbj.org/pub/pdb/validation_reports/j7/3j78 | HTTPS FTP |
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-関連構造データ
関連構造データ | 5977MC 5976C 3j77C 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 | |
電子顕微鏡画像生データ | EMPIAR-10016 (タイトル: Yeast 80S Ribosome - tRNA- Kozak mRNA complexes, Frealign Input Particle Stack Data size: 42.0 Data #1: Frealign input particle stack [picked particles - multiframe - processed]) |
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
+60S ribosomal protein ... , 43種, 43分子 L1L2L3L4L5L6L7L8L9606162636465666768697071727374757677787980...
-タンパク質 , 2種, 2分子 P0RC
#44: タンパク質 | 分子量: 33749.121 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: P05317 |
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#45: タンパク質 | 分子量: 34841.219 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: P38011 |
+40S ribosomal protein ... , 32種, 32分子 S0S1S2S3S4S5S6S7S8S910111213141516171819202122232425262728293031
-RNA鎖 , 6種, 7分子 1S2S8S5SETPTMR
#78: 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) | ||
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#79: RNA鎖 | 分子量: 1097148.625 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) | ||
#80: 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) | ||
#81: 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) | ||
#82: RNA鎖 | 分子量: 24802.785 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (大腸菌) #83: RNA鎖 | | 分子量: 4533.844 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Saccharomyces cerevisiae (パン酵母) |
-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 |
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分子量 | 値: 3.5 MDa / 実験値: YES | ||||||||||||||||||||
緩衝液 | 名称: 20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2 / pH: 7.5 / 詳細: 20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2 | ||||||||||||||||||||
試料 | 濃度: 1.2 mg/ml / 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 II / 凍結剤: ETHANE / 湿度: 95 % / 詳細: Plunged into liquid ethane (FEI VITROBOT MARK II) |
-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 / 日付: 2013年1月2日 |
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 / 倍率(公称値): 133333 X / 倍率(補正後): 133333 X / 最大 デフォーカス(公称値): 4844 nm / 最小 デフォーカス(公称値): 1159 nm / Cs: 0.01 mm / カメラ長: 0 mm |
試料ホルダ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER 傾斜角・最大: 0 ° / 傾斜角・最小: 0 ° |
撮影 | 電子線照射量: 30 e/Å2 フィルム・検出器のモデル: FEI FALCON I (4k x 4k) |
画像スキャン | デジタル画像の数: 4754 |
放射 | プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 相対比: 1 |
-解析
EMソフトウェア |
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CTF補正 | 詳細: CTFFIND3, FREALIGN per micrograph | |||||||||||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | |||||||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 手法: Projection Matching / 解像度: 6.3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 23163 / ピクセルサイズ(公称値): 1.05 Å / ピクセルサイズ(実測値): 1.05 Å / 詳細: (Single particle--Applied symmetry: C1) / 対称性のタイプ: POINT | |||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT / 空間: REAL / Target criteria: cross-correlation 詳細: REFINEMENT PROTOCOL--rigid body DETAILS--3U5B, 3U5C, 3U5D, and 3U5E were combined prior to fitting. tRNAs and mRNA were modeled using individual tRNAs and mRNA from the crystal structure ...詳細: REFINEMENT PROTOCOL--rigid body DETAILS--3U5B, 3U5C, 3U5D, and 3U5E were combined prior to fitting. tRNAs and mRNA were modeled using individual tRNAs and mRNA from the crystal structure (3I9B) of the classical-state 70S ribosome. The structure of rpL1 was obtained by homology modeling from PDB ID 3J3B. | |||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | 3D fitting-ID: 1 / Source name: PDB / タイプ: experimental model
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