+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-5977 | |||||||||
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タイトル | Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class I - 2 tRNA in non-rotated conformation) | |||||||||
マップデータ | Reconstruction of a yeast 80S ribosome in the classical state with 2 tRNA bound. (Class I) | |||||||||
試料 |
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キーワード | 80S ribosome / Kozak sequence / translation | |||||||||
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 / positive regulation of translational fidelity / Protein methylation / RMTs methylate histone arginines / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process ...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 / nonfunctional rRNA decay / pre-mRNA 5'-splice site binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 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) / 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 / regulation of cellular amino acid metabolic process / preribosome, large subunit precursor / translational elongation / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / positive regulation of protein kinase activity / protein-RNA complex assembly / regulation of translational fidelity / Ub-specific processing proteases / ribosomal subunit export from nucleus / translation regulator activity / ribosomal small 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 / maturation of LSU-rRNA / cellular response to amino acid starvation / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / translational initiation / macroautophagy / protein kinase C binding / maintenance of translational fidelity / modification-dependent protein catabolic process / cytoplasmic stress granule / 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 / 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 / translation / 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 / 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) / Escherichia coli (大腸菌) | |||||||||
手法 | 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 AF / Koh CS / Grigorieff N / Korostelev AA | |||||||||
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 | 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_5977.map.gz | 161.4 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-5977-v30.xml emd-5977.xml | 16.1 KB 16.1 KB | 表示 表示 | EMDBヘッダ |
画像 | 400_5977.gif 80_5977.gif | 60.3 KB 4.9 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-5977 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5977 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_5977_validation.pdf.gz | 375.5 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_5977_full_validation.pdf.gz | 375.1 KB | 表示 | |
XML形式データ | emd_5977_validation.xml.gz | 6.8 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5977 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5977 | HTTPS FTP |
-関連構造データ
関連構造データ | 3j78MC 5976C 3j77C C: 同じ文献を引用 (文献) M: このマップから作成された原子モデル |
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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
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_5977.map.gz / 形式: CCP4 / 大きさ: 173.8 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Reconstruction of a yeast 80S ribosome in the classical state with 2 tRNA bound. (Class I) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.05 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
-試料の構成要素
-全体 : 80S ribosome bound to mRNA containing Kozak sequence and to two tRNA
全体 | 名称: 80S ribosome bound to mRNA containing Kozak sequence and to two tRNA |
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要素 |
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-超分子 #1000: 80S ribosome bound to mRNA containing Kozak sequence and to two tRNA
超分子 | 名称: 80S ribosome bound to mRNA containing Kozak sequence and to two tRNA タイプ: sample / ID: 1000 / 詳細: Sample was monodisperse. / Number unique components: 3 |
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分子量 | 実験値: 3.5 MDa |
-超分子 #1: 80S ribosome
超分子 | 名称: 80S ribosome / タイプ: complex / ID: 1 / 組換発現: No / データベース: NCBI / Ribosome-details: ribosome-eukaryote: ALL |
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由来(天然) | 生物種: Saccharomyces cerevisiae (パン酵母) / 別称: Yeast |
分子量 | 実験値: 3.5 MDa |
-分子 #1: transfer RNA
分子 | 名称: transfer RNA / タイプ: rna / ID: 1 / Name.synonym: tRNA / 詳細: tRNA fmet / 分類: TRANSFER / Structure: OTHER / Synthetic?: No |
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由来(天然) | 生物種: Escherichia coli (大腸菌) |
分子量 | 理論値: 25 KDa |
-分子 #2: mRNA
分子 | 名称: mRNA / タイプ: rna / ID: 2 / 分類: OTHER / Structure: SINGLE STRANDED / Synthetic?: Yes |
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由来(天然) | 生物種: Saccharomyces cerevisiae (パン酵母) |
分子量 | 理論値: 5 KDa |
配列 | 文字列: AAAAAUGUAA AAAA |
-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
濃度 | 1.2 mg/mL |
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緩衝液 | pH: 7.5 詳細: 20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2, 0.3 U/uL RNasin |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 95 % / 装置: FEI VITROBOT MARK II |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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日付 | 2013年1月2日 |
撮影 | カテゴリ: CCD フィルム・検出器のモデル: FEI FALCON I (4k x 4k) デジタル化 - サンプリング間隔: 14 µm / 実像数: 4754 / 平均電子線量: 30 e/Å2 / ビット/ピクセル: 16 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 倍率(補正後): 133333 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 0.01 mm / 最大 デフォーカス(公称値): 4.844 µm / 最小 デフォーカス(公称値): 1.159 µm / 倍率(公称値): 133333 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
CTF補正 | 詳細: CTFFIND3, FREALIGN per micrograph |
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最終 再構成 | アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 6.3 Å / 解像度の算出法: OTHER ソフトウェア - 名称: EMAN2, IMAGIC, FREALIGN, RSAMPLE, CTFFIND3 使用した粒子像数: 23163 |
-原子モデル構築 1
初期モデル | PDB ID: 3u5b |
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ソフトウェア | 名称: Chimera, CNS |
詳細 | 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. |
精密化 | 空間: REAL / プロトコル: RIGID BODY FIT / 当てはまり具合の基準: cross-correlation |
得られたモデル | PDB-3j78: |
-原子モデル構築 2
初期モデル | PDB ID: 3u5c |
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ソフトウェア | 名称: Chimera, CNS |
詳細 | 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. |
精密化 | 空間: REAL / プロトコル: RIGID BODY FIT / 当てはまり具合の基準: cross-correlation |
得られたモデル | PDB-3j78: |
-原子モデル構築 3
初期モデル | PDB ID: 3u5d |
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ソフトウェア | 名称: Chimera, CNS |
詳細 | 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. |
精密化 | 空間: REAL / プロトコル: RIGID BODY FIT / 当てはまり具合の基準: cross-correlation |
得られたモデル | PDB-3j78: |
-原子モデル構築 4
初期モデル | PDB ID: 3u5e |
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ソフトウェア | 名称: Chimera, CNS |
詳細 | 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. |
精密化 | 空間: REAL / プロトコル: RIGID BODY FIT / 当てはまり具合の基準: cross-correlation |
得られたモデル | PDB-3j78: |
-原子モデル構築 5
初期モデル | PDB ID: 3i9b Chain - #0 - Chain ID: 1 / Chain - #1 - Chain ID: C / Chain - #2 - Chain ID: D |
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ソフトウェア | 名称: Chimera, CNS |
詳細 | 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. |
精密化 | 空間: REAL / プロトコル: RIGID BODY FIT / 当てはまり具合の基準: cross-correlation |
得られたモデル | PDB-3j78: |
-原子モデル構築 6
初期モデル | PDB ID: 3j3b |
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ソフトウェア | 名称: Chimera, CNS |
詳細 | 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. |
精密化 | 空間: REAL / プロトコル: RIGID BODY FIT / 当てはまり具合の基準: cross-correlation |
得られたモデル | PDB-3j78: |