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データを開く
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基本情報
登録情報 | ![]() | ||||||||||||||||||
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タイトル | Human mitochondrial ribosome in complex with mRNA, A/P- and P/E-tRNAs at 2.98 A resolution | ||||||||||||||||||
![]() | Local_mask_refined_composite_map_APPE_locres_filtered | ||||||||||||||||||
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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 ribosome assembly / mitochondrial translational elongation / mitochondrial translational termination / microprocessor complex / translation release factor activity, codon nonspecific / Mitochondrial translation elongation / Mitochondrial translation termination ...mitochondrial ribosome binding / rRNA import into mitochondrion / mitochondrial transcription / mitochondrial ribosome assembly / mitochondrial translational elongation / mitochondrial translational termination / 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 / cytoplasmic translation / nuclear body / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / mitochondrial matrix / ribonucleoprotein complex / translation / cell cycle / protein domain specific binding / intracellular membrane-bounded organelle / nucleotide binding / mRNA binding / apoptotic process / synapse / nucleolus / GTP binding / positive regulation of DNA-templated transcription / mitochondrion / RNA binding / extracellular space / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||||||||||||||
生物種 | ![]() | ||||||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.98 Å | ||||||||||||||||||
![]() | Singh V / Itoh Y / Amunts A / Aibara S | ||||||||||||||||||
資金援助 | European Union, 5件
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![]() | ![]() 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
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ダウンロードとリンク
-EMDBアーカイブ
マップデータ | ![]() | 338.1 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 119.7 KB 119.7 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 19.1 KB | 表示 | ![]() |
画像 | ![]() | 124.4 KB | ||
マスクデータ | ![]() ![]() ![]() ![]() ![]() ![]() | 600.7 MB 600.7 MB 600.7 MB 600.7 MB 600.7 MB 600.7 MB | ![]() | |
Filedesc metadata | ![]() | 23.7 KB | ||
その他 | ![]() ![]() ![]() ![]() ![]() | 337.9 MB 1 GB 337.9 MB 487.3 MB 487.3 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 1.2 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.2 MB | 表示 | |
XML形式データ | ![]() | 27.5 KB | 表示 | |
CIF形式データ | ![]() | 36.3 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
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||
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注釈 | Local_mask_refined_composite_map_APPE_locres_filtered | ||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
+マスク #1
+マスク #2
+マスク #3
+マスク #4
+マスク #5
+マスク #6
+追加マップ: Local resolution filtered map APPE
+追加マップ: Supersampled local mask refined composite map APPE locres filtered
+追加マップ: Unsharpened map APPE
+ハーフマップ: half map unfiltered 1
+ハーフマップ: half map unfiltered 2
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試料の構成要素
+全体 : Human mitochondrial ribosome
+超分子 #1: Human mitochondrial ribosome
+分子 #1: 12S mitochondrial rRNA
+分子 #32: mRNA
+分子 #33: A/P-tRNA
+分子 #34: P/E-tRNA
+分子 #35: 16S mitochondrial rRNA
+分子 #36: mitochondrial tRNAVal
+分子 #2: 28S ribosomal protein S2, mitochondrial
+分子 #3: 28S ribosomal protein S24, mitochondrial
+分子 #4: 28S ribosomal protein S5, mitochondrial
+分子 #5: 28S ribosomal protein S6, mitochondrial
+分子 #6: 28S ribosomal protein S7, mitochondrial
+分子 #7: 28S ribosomal protein S9, mitochondrial
+分子 #8: 28S ribosomal protein S10, mitochondrial
+分子 #9: 28S ribosomal protein S11, mitochondrial
+分子 #10: 28S ribosomal protein S12, mitochondrial
+分子 #11: 28S ribosomal protein S14, mitochondrial
+分子 #12: 28S ribosomal protein S15, mitochondrial
+分子 #13: 28S ribosomal protein S16, mitochondrial
+分子 #14: 28S ribosomal protein S17, mitochondrial
+分子 #15: 28S ribosomal protein S18b, mitochondrial
+分子 #16: 28S ribosomal protein S18c, mitochondrial
+分子 #17: MRPS21 isoform 1
+分子 #18: 28S ribosomal protein S22, mitochondrial
+分子 #19: 28S ribosomal protein S23, mitochondrial
+分子 #20: 28S ribosomal protein S25, mitochondrial
+分子 #21: 28S ribosomal protein S26, mitochondrial
+分子 #22: 28S ribosomal protein S27, mitochondrial
+分子 #23: 28S ribosomal protein S28, mitochondrial
+分子 #24: 28S ribosomal protein S29, mitochondrial
+分子 #25: 28S ribosomal protein S31, mitochondrial
+分子 #26: 28S ribosomal protein S33, mitochondrial
+分子 #27: 28S ribosomal protein S34, mitochondrial
+分子 #28: 28S ribosomal protein S35, mitochondrial
+分子 #29: Coiled-coil-helix-coiled-coil-helix domain-containing protein 1
+分子 #30: Aurora kinase A-interacting protein
+分子 #31: Pentatricopeptide repeat domain-containing protein 3, mitochondrial
+分子 #37: 39S ribosomal protein L2, mitochondrial
+分子 #38: 39S ribosomal protein L3, mitochondrial
+分子 #39: 39S ribosomal protein L4, mitochondrial
+分子 #40: 39S ribosomal protein L10, mitochondrial
+分子 #41: 39S ribosomal protein L11, mitochondrial
+分子 #42: 39S ribosomal protein L13, mitochondrial
+分子 #43: 39S ribosomal protein L14, mitochondrial
+分子 #44: 39S ribosomal protein L15, mitochondrial
+分子 #45: 39S ribosomal protein L16, mitochondrial
+分子 #46: 39S ribosomal protein L17, mitochondrial
+分子 #47: 39S ribosomal protein L18, mitochondrial
+分子 #48: 39S ribosomal protein L20, mitochondrial
+分子 #49: 39S ribosomal protein L21, mitochondrial
+分子 #50: 39S ribosomal protein L22, mitochondrial
+分子 #51: 39S ribosomal protein L23, mitochondrial
+分子 #52: 39S ribosomal protein L24, mitochondrial
+分子 #53: 39S ribosomal protein L27, mitochondrial
+分子 #54: 39S ribosomal protein L28, mitochondrial
+分子 #55: 39S ribosomal protein L47, mitochondrial
+分子 #56: 39S ribosomal protein L30, mitochondrial
+分子 #57: 39S ribosomal protein L32, mitochondrial
+分子 #58: 39S ribosomal protein L33, mitochondrial
+分子 #59: 39S ribosomal protein L34, mitochondrial
+分子 #60: 39S ribosomal protein L35, mitochondrial
+分子 #61: 39S ribosomal protein L36, mitochondrial
+分子 #62: 39S ribosomal protein L37, mitochondrial
+分子 #63: 39S ribosomal protein L38, mitochondrial
+分子 #64: 39S ribosomal protein L39, mitochondrial
+分子 #65: 39S ribosomal protein L40, mitochondrial
+分子 #66: 39S ribosomal protein L41, mitochondrial
+分子 #67: 39S ribosomal protein L42, mitochondrial
+分子 #68: Large ribosomal subunit protein mL43
+分子 #69: 39S ribosomal protein L44, mitochondrial
+分子 #70: 39S ribosomal protein L45, mitochondrial
+分子 #71: 39S ribosomal protein L46, mitochondrial
+分子 #72: 39S ribosomal protein L48, mitochondrial
+分子 #73: 39S ribosomal protein L49, mitochondrial
+分子 #74: 39S ribosomal protein L50, mitochondrial
+分子 #75: 39S ribosomal protein L51, mitochondrial
+分子 #76: 39S ribosomal protein L52, mitochondrial
+分子 #77: 39S ribosomal protein L53, mitochondrial
+分子 #78: 39S ribosomal protein L54, mitochondrial
+分子 #79: 39S ribosomal protein L55, mitochondrial
+分子 #80: Ribosomal protein 63, mitochondrial
+分子 #81: Peptidyl-tRNA hydrolase ICT1, mitochondrial
+分子 #82: Growth arrest and DNA damage-inducible proteins-interacting protein 1
+分子 #83: 39S ribosomal protein S18a, mitochondrial
+分子 #84: 39S ribosomal protein S30, mitochondrial
+分子 #85: 39S ribosomal protein L12, mitochondrial
+分子 #86: 39S ribosomal protein L19, mitochondrial
+分子 #87: 39S ribosomal protein L9, mitochondrial
+分子 #88: 39S ribosomal protein L1, mitochondrial
+分子 #89: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
+分子 #90: SPERMINE
+分子 #91: SPERMIDINE
+分子 #92: POTASSIUM ION
+分子 #93: MAGNESIUM ION
+分子 #94: ZINC ION
+分子 #95: FE2/S2 (INORGANIC) CLUSTER
+分子 #96: ADENOSINE-5'-TRIPHOSPHATE
+分子 #97: GUANOSINE-5'-DIPHOSPHATE
+分子 #98: 1,4-DIAMINOBUTANE
+分子 #99: VALINE
+分子 #100: water
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
緩衝液 | pH: 7.5 |
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凍結 | 凍結剤: ETHANE |
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電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 平均電子線量: 30.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 照射モード: SPOT SCAN / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2.6 µm / 最小 デフォーカス(公称値): 0.6 µm |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |