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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: 7qi4 | ||||||||||||||||||
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タイトル | Human mitochondrial ribosome at 2.2 A resolution (bound to partly built tRNAs and mRNA) | ||||||||||||||||||
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![]() | RIBOSOME / mitochondrial translation / tRNA / mRNA / 2Fe-2S clusters / polyamines / rRNA modifications / post-translation modifications / cryo EM | ||||||||||||||||||
機能・相同性 | ![]() mitochondrial ribosome binding / rRNA import into mitochondrion / mitochondrial transcription / mitochondrial translational elongation / mitochondrial translational termination / mitochondrial ribosome assembly / microprocessor complex / translation release factor activity, codon nonspecific / Mitochondrial translation elongation / Mitochondrial translation termination ...mitochondrial ribosome binding / rRNA import into mitochondrion / mitochondrial transcription / mitochondrial translational elongation / mitochondrial translational termination / mitochondrial ribosome assembly / microprocessor complex / translation release factor activity, codon nonspecific / Mitochondrial translation elongation / Mitochondrial translation termination / positive regulation of mitochondrial translation / Mitochondrial translation initiation / negative regulation of mitotic nuclear division / mitochondrial large ribosomal subunit / 加水分解酵素; エステル加水分解酵素; 5'-リン酸モノエステル産生エンドリボヌクレアーゼ / peptidyl-tRNA hydrolase / mitochondrial small ribosomal subunit / aminoacyl-tRNA hydrolase activity / mitochondrial ribosome / mitochondrial translation / positive regulation of proteolysis / ribosomal small subunit binding / anatomical structure morphogenesis / RNA processing / Mitochondrial protein degradation / rescue of stalled ribosome / cellular response to leukemia inhibitory factor / apoptotic signaling pathway / fibrillar center / double-stranded RNA binding / cell junction / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / nuclear membrane / cytosolic small ribosomal subunit / endonuclease activity / cell population proliferation / cytosolic large ribosomal subunit / mitochondrial inner membrane / tRNA binding / nuclear body / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / mitochondrial matrix / ribonucleoprotein complex / translation / protein domain specific binding / intracellular membrane-bounded organelle / nucleotide binding / mRNA binding / synapse / apoptotic process / nucleolus / GTP binding / positive regulation of DNA-templated transcription / mitochondrion / RNA binding / extracellular space / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm 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: 2.21 Å | ||||||||||||||||||
![]() | Singh, V. / Itoh, Y. / Amunts, A. | ||||||||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Mitoribosome structure with cofactors and modifications reveals mechanism of ligand binding and interactions with L1 stalk. 著者: Vivek Singh / Yuzuru Itoh / Samuel Del'Olio / Asem Hassan / Andreas Naschberger / Rasmus Kock Flygaard / Yuko Nobe / Keiichi Izumikawa / Shintaro Aibara / Juni Andréll / Paul C Whitford / ...著者: Vivek Singh / Yuzuru Itoh / Samuel Del'Olio / Asem Hassan / Andreas Naschberger / Rasmus Kock Flygaard / Yuko Nobe / Keiichi Izumikawa / Shintaro Aibara / Juni Andréll / Paul C Whitford / Antoni Barrientos / Masato Taoka / Alexey Amunts / ![]() ![]() ![]() ![]() ![]() ![]() 要旨: The mitoribosome translates mitochondrial mRNAs and regulates energy conversion that is a signature of aerobic life forms. We present a 2.2 Å resolution structure of human mitoribosome together ...The mitoribosome translates mitochondrial mRNAs and regulates energy conversion that is a signature of aerobic life forms. We present a 2.2 Å resolution structure of human mitoribosome together with validated mitoribosomal RNA (rRNA) modifications, including aminoacylated CP-tRNA. The structure shows how mitoribosomal proteins stabilise binding of mRNA and tRNA helping to align it in the decoding center, whereas the GDP-bound mS29 stabilizes intersubunit communication. Comparison between different states, with respect to tRNA position, allowed us to characterize a non-canonical L1 stalk, and molecular dynamics simulations revealed how it facilitates tRNA transitions in a way that does not require interactions with rRNA. We also report functionally important polyamines that are depleted when cells are subjected to an antibiotic treatment. The structural, biochemical, and computational data illuminate the principal functional components of the translation mechanism in mitochondria and provide a description of the structure and function of the human mitoribosome. #1: ![]() タイトル: Mitoribosome structure with cofactors and modifications reveals mechanism of ligand binding and interactions with L1 stalk. 著者: Vivek Singh / Yuzuru Itoh / Samuel Del'Olio / Asem Hassan / Andreas Naschberger / Rasmus Kock Flygaard / Yuko Nobe / Keiichi Izumikawa / Shintaro Aibara / Juni Andréll / Paul C Whitford / ...著者: Vivek Singh / Yuzuru Itoh / Samuel Del'Olio / Asem Hassan / Andreas Naschberger / Rasmus Kock Flygaard / Yuko Nobe / Keiichi Izumikawa / Shintaro Aibara / Juni Andréll / Paul C Whitford / Antoni Barrientos / Masato Taoka / Alexey Amunts / ![]() ![]() ![]() ![]() ![]() ![]() 要旨: The mitoribosome translates mitochondrial mRNAs and regulates energy conversion that is a signature of aerobic life forms. We present a 2.2 Å resolution structure of human mitoribosome together ...The mitoribosome translates mitochondrial mRNAs and regulates energy conversion that is a signature of aerobic life forms. We present a 2.2 Å resolution structure of human mitoribosome together with validated mitoribosomal RNA (rRNA) modifications, including aminoacylated CP-tRNA. The structure shows how mitoribosomal proteins stabilise binding of mRNA and tRNA helping to align it in the decoding center, whereas the GDP-bound mS29 stabilizes intersubunit communication. Comparison between different states, with respect to tRNA position, allowed us to characterize a non-canonical L1 stalk, and molecular dynamics simulations revealed how it facilitates tRNA transitions in a way that does not require interactions with rRNA. We also report functionally important polyamines that are depleted when cells are subjected to an antibiotic treatment. The structural, biochemical, and computational data illuminate the principal functional components of the translation mechanism in mitochondria and provide a description of the structure and function of the human mitoribosome. #2: ジャーナル: bioRxiv / 年: 2023 タイトル: Structure of mitoribosome reveals mechanism of mRNA binding, tRNA interactions with L1 stalk, roles of cofactors and rRNA modifications. 著者: Vivek Singh / Yuzuru Itoh / Samuel Del'Olio / Asem Hassan / Andreas Naschberger / Rasmus Kock Flygaard / Yuko Nobe / Keiichi Izumikawa / Shintaro Aibara / Juni Andréll / Paul C Whitford / ...著者: Vivek Singh / Yuzuru Itoh / Samuel Del'Olio / Asem Hassan / Andreas Naschberger / Rasmus Kock Flygaard / Yuko Nobe / Keiichi Izumikawa / Shintaro Aibara / Juni Andréll / Paul C Whitford / Antoni Barrientos / Masato Taoka / Alexey Amunts 要旨: The mitoribosome translates mitochondrial mRNAs and regulates energy conversion that is a signature of aerobic life forms. We present a 2.2 Å resolution structure of human mitoribosome together with ...The mitoribosome translates mitochondrial mRNAs and regulates energy conversion that is a signature of aerobic life forms. We present a 2.2 Å resolution structure of human mitoribosome together with validated mitoribosomal RNA (rRNA) modifications, including aminoacylated CP-tRNA . The structure shows how mitoribosomal proteins stabilise binding of mRNA and tRNA helping to align it in the decoding center, whereas the GDP-bound mS29 stabilizes intersubunit communication. Comparison between different states, with respect to tRNA position, allowed to characterize a non-canonical L1 stalk, and molecular dynamics simulations revealed how it facilitates tRNA transition in a way that does not require interactions with rRNA. We also report functionally important polyamines that are depleted when cells are subjected to an antibiotic treatment. The structural, biochemical, and computational data illuminate the principal functional components of the translation mechanism in mitochondria and provide the most complete description so far of the structure and function of the human mitoribosome. | ||||||||||||||||||
履歴 |
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構造の表示
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 | ![]() | 7.1 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
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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-関連構造データ
関連構造データ | ![]() 13980MC ![]() 7qi5C ![]() 7qi6C 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 ( |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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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 , 7種, 7分子 AAAwAxAzABAy
#1: RNA鎖 | 分子量: 306218.312 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: cell / 由来: (天然) ![]() |
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#32: RNA鎖 | 分子量: 6971.210 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: cell / 由来: (天然) ![]() |
#33: RNA鎖 | 分子量: 22354.291 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: cell / 由来: (天然) ![]() |
#34: RNA鎖 | 分子量: 10826.415 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: cell / 由来: (天然) ![]() |
#35: RNA鎖 | 分子量: 499786.438 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: cell / 由来: (天然) ![]() |
#36: RNA鎖 | 分子量: 22989.752 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: cell / 由来: (天然) ![]() |
#89: RNA鎖 | 分子量: 16669.957 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: cell / 由来: (天然) ![]() |
+28S ribosomal protein ... , 26種, 26分子 ABACADAEAFAGAHAIAJAKALAMANAOAPARASATAUAVAWAXAYAZA0A1
-タンパク質 , 7種, 7分子 AQA2A3A4opq
#17: タンパク質 | 分子量: 10806.689 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: cell / 由来: (天然) ![]() |
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#29: タンパク質 | 分子量: 13540.856 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: cell / 由来: (天然) ![]() |
#30: タンパク質 | 分子量: 22395.326 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: cell / 由来: (天然) ![]() |
#31: タンパク質 | 分子量: 78648.547 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: cell / 由来: (天然) ![]() |
#82: タンパク質 | 分子量: 12292.333 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: cell / 由来: (天然) ![]() |
#83: タンパク質 | 分子量: 23674.203 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: cell / 由来: (天然) ![]() |
#84: タンパク質 | 分子量: 25426.895 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: cell / 由来: (天然) ![]() |
+39S ribosomal protein ... , 49種, 54分子 DEFHIJKLMNOPQRSTUVWXYZ01234567...
-非ポリマー , 12種, 8277分子 ![](data/chem/img/NAD.gif)
![](data/chem/img/SPM.gif)
![](data/chem/img/SPD.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/PUT.gif)
![](data/chem/img/VAL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SPM.gif)
![](data/chem/img/SPD.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/PUT.gif)
![](data/chem/img/VAL.gif)
![](data/chem/img/HOH.gif)
#90: 化合物 | ChemComp-NAD / | ||||||||||||||||||
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#91: 化合物 | ChemComp-SPM / | ||||||||||||||||||
#92: 化合物 | ChemComp-SPD / #93: 化合物 | ChemComp-MG / #94: 化合物 | ChemComp-K / #95: 化合物 | #96: 化合物 | #97: 化合物 | ChemComp-ATP / | #98: 化合物 | ChemComp-GDP / | #99: 化合物 | ChemComp-PUT / | #100: 化合物 | ChemComp-VAL / | #101: 水 | ChemComp-HOH / | |
-詳細
研究の焦点であるリガンドがあるか | Y |
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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 | 名称: Human mitochondrial ribosome / タイプ: RIBOSOME / Entity ID: #1-#33, #89, #34-#35, #37-#88 / 由来: NATURAL |
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由来(天然) | 生物種: ![]() |
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 |
急速凍結 | 凍結剤: ETHANE |
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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 / 最大 デフォーカス(公称値): 2800 nm / 最小 デフォーカス(公称値): 600 nm |
撮影 | 電子線照射量: 30 e/Å2 / 検出モード: COUNTING フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) |
電子光学装置 | エネルギーフィルタースリット幅: 20 eV |
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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: 2.21 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 509691 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
拘束条件 |
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