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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 | 55S human mitochondrial ribosome with mtRF1 and P-site tRNA | ||||||||||||
![]() | 55S human mitochondrial ribosome with mtRF1 and P-site tRNA | ||||||||||||
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![]() | human mitochondrial ribosome / release factor mtRF1 / non-canonical stop codon / RIBOSOME | ||||||||||||
機能・相同性 | ![]() translation release factor activity / 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 / translation release factor activity, codon specific ...translation release factor activity / 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 / translation release factor activity, codon specific / Mitochondrial translation elongation / Mitochondrial translation termination / positive regulation of mitochondrial translation / Mitochondrial translation initiation / negative regulation of mitotic nuclear division / 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 / mitochondrial large ribosomal subunit / 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: 3.1 Å | ||||||||||||
![]() | Saurer M / Leibundgut M / Scaiola A / Schoenhut T / Ban N | ||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Molecular basis of translation termination at noncanonical stop codons in human mitochondria. 著者: Martin Saurer / Marc Leibundgut / Hima Priyanka Nadimpalli / Alain Scaiola / Tanja Schönhut / Richard G Lee / Stefan J Siira / Oliver Rackham / René Dreos / Tea Lenarčič / Eva Kummer / ...著者: Martin Saurer / Marc Leibundgut / Hima Priyanka Nadimpalli / Alain Scaiola / Tanja Schönhut / Richard G Lee / Stefan J Siira / Oliver Rackham / René Dreos / Tea Lenarčič / Eva Kummer / David Gatfield / Aleksandra Filipovska / Nenad Ban / ![]() ![]() ![]() 要旨: The genetic code that specifies the identity of amino acids incorporated into proteins during protein synthesis is almost universally conserved. Mitochondrial genomes feature deviations from the ...The genetic code that specifies the identity of amino acids incorporated into proteins during protein synthesis is almost universally conserved. Mitochondrial genomes feature deviations from the standard genetic code, including the reassignment of two arginine codons to stop codons. The protein required for translation termination at these noncanonical stop codons to release the newly synthesized polypeptides is not currently known. In this study, we used gene editing and ribosomal profiling in combination with cryo-electron microscopy to establish that mitochondrial release factor 1 (mtRF1) detects noncanonical stop codons in human mitochondria by a previously unknown mechanism of codon recognition. We discovered that binding of mtRF1 to the decoding center of the ribosome stabilizes a highly unusual conformation in the messenger RNA in which the ribosomal RNA participates in specific recognition of the noncanonical stop codons. | ||||||||||||
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 | ![]() | 483.4 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 120.9 KB 120.9 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 17 KB | 表示 | ![]() |
画像 | ![]() | 200.6 KB | ||
Filedesc metadata | ![]() | 25.2 KB | ||
その他 | ![]() ![]() | 475.6 MB 475.6 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 1.3 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.3 MB | 表示 | |
XML形式データ | ![]() | 26.9 KB | 表示 | |
CIF形式データ | ![]() | 35.3 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 | 55S human mitochondrial ribosome with mtRF1 and P-site tRNA | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.06 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
-ハーフマップ: half map B
ファイル | emd_16897_half_map_1.map | ||||||||||||
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注釈 | half map B | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: half map A
ファイル | emd_16897_half_map_2.map | ||||||||||||
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注釈 | half map A | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
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試料の構成要素
+全体 : 55S human mitochondrial ribosome with mtRF1 and P-site tRNA
+超分子 #1: 55S human mitochondrial ribosome with mtRF1 and P-site tRNA
+分子 #1: 39S ribosomal protein L12, mitochondrial
+分子 #5: 39S ribosomal protein L22, mitochondrial
+分子 #6: 39S ribosomal protein L23, mitochondrial
+分子 #7: 39S ribosomal protein L24, mitochondrial
+分子 #8: 39S ribosomal protein L27, mitochondrial
+分子 #9: 39S ribosomal protein L28, mitochondrial
+分子 #10: 39S ribosomal protein L47, mitochondrial
+分子 #11: 39S ribosomal protein L30, mitochondrial
+分子 #12: 39S ribosomal protein L32, mitochondrial
+分子 #13: 39S ribosomal protein L33, mitochondrial
+分子 #14: 39S ribosomal protein L34, mitochondrial
+分子 #15: 39S ribosomal protein L35, mitochondrial
+分子 #16: 39S ribosomal protein L2, mitochondrial
+分子 #17: 39S ribosomal protein L3, mitochondrial
+分子 #18: 39S ribosomal protein L4, mitochondrial
+分子 #19: 39S ribosomal protein L9, mitochondrial
+分子 #20: 39S ribosomal protein L10, mitochondrial
+分子 #21: 39S ribosomal protein L11, mitochondrial
+分子 #22: 39S ribosomal protein L13, mitochondrial
+分子 #23: 39S ribosomal protein L14, mitochondrial
+分子 #24: 39S ribosomal protein L15, mitochondrial
+分子 #25: 39S ribosomal protein L16, mitochondrial
+分子 #26: 39S ribosomal protein L17, mitochondrial
+分子 #27: 39S ribosomal protein L18, mitochondrial
+分子 #28: 39S ribosomal protein L19, mitochondrial
+分子 #29: 39S ribosomal protein L20, mitochondrial
+分子 #30: 39S ribosomal protein L21, mitochondrial
+分子 #31: 39S ribosomal protein L52, mitochondrial
+分子 #32: 39S ribosomal protein L53, mitochondrial
+分子 #33: 39S ribosomal protein L54, mitochondrial
+分子 #34: 39S ribosomal protein L55, mitochondrial
+分子 #35: Ribosomal protein 63, mitochondrial
+分子 #36: Peptidyl-tRNA hydrolase ICT1, mitochondrial
+分子 #37: Growth arrest and DNA damage-inducible proteins-interacting protein 1
+分子 #38: 39S ribosomal protein S18a, mitochondrial
+分子 #39: 39S ribosomal protein S30, mitochondrial
+分子 #40: 39S ribosomal protein L1, mitochondrial
+分子 #41: 39S ribosomal protein L36, mitochondrial
+分子 #42: 39S ribosomal protein L37, mitochondrial
+分子 #43: 39S ribosomal protein L38, mitochondrial
+分子 #44: 39S ribosomal protein L39, mitochondrial
+分子 #45: 39S ribosomal protein L40, mitochondrial
+分子 #46: 39S ribosomal protein L41, mitochondrial
+分子 #47: 39S ribosomal protein L42, mitochondrial
+分子 #48: Large ribosomal subunit protein mL43
+分子 #49: 39S ribosomal protein L44, mitochondrial
+分子 #50: 39S ribosomal protein L45, mitochondrial
+分子 #51: 39S ribosomal protein L46, mitochondrial
+分子 #52: 39S ribosomal protein L48, mitochondrial
+分子 #53: 39S ribosomal protein L49, mitochondrial
+分子 #54: 39S ribosomal protein L50, mitochondrial
+分子 #55: 39S ribosomal protein L51, mitochondrial
+分子 #57: 28S ribosomal protein S35, mitochondrial
+分子 #58: 28S ribosomal protein S24, mitochondrial
+分子 #59: Aurora kinase A-interacting protein
+分子 #60: 28S ribosomal protein S6, mitochondrial
+分子 #61: 28S ribosomal protein S7, mitochondrial
+分子 #63: 28S ribosomal protein S10, mitochondrial
+分子 #65: 28S ribosomal protein S12, mitochondrial
+分子 #66: 28S ribosomal protein S14, mitochondrial
+分子 #67: 28S ribosomal protein S15, mitochondrial
+分子 #68: 28S ribosomal protein S16, mitochondrial
+分子 #69: 28S ribosomal protein S17, mitochondrial
+分子 #70: 28S ribosomal protein S18b, mitochondrial
+分子 #71: 28S ribosomal protein S18c, mitochondrial
+分子 #72: 28S ribosomal protein S21, mitochondrial
+分子 #73: 28S ribosomal protein S22, mitochondrial
+分子 #74: 28S ribosomal protein S23, mitochondrial
+分子 #75: 28S ribosomal protein S25, mitochondrial
+分子 #76: 28S ribosomal protein S26, mitochondrial
+分子 #77: 28S ribosomal protein S27, mitochondrial
+分子 #78: 28S ribosomal protein S28, mitochondrial
+分子 #79: 28S ribosomal protein S29, mitochondrial
+分子 #80: 28S ribosomal protein S31, mitochondrial
+分子 #81: 28S ribosomal protein S33, mitochondrial
+分子 #82: Peptide chain release factor 1, mitochondrial
+分子 #83: 28S ribosomal protein S2, mitochondrial
+分子 #84: Coiled-coil-helix-coiled-coil-helix domain-containing protein 1
+分子 #85: 28S ribosomal protein S5, mitochondrial
+分子 #86: Pentatricopeptide repeat domain-containing protein 3, mitochondrial
+分子 #87: 28S ribosomal protein S9, mitochondrial
+分子 #88: 28S ribosomal protein S11, mitochondrial
+分子 #89: 28S ribosomal protein S34, mitochondrial
+分子 #2: E-site tRNA
+分子 #3: 16S rRNA
+分子 #4: CP Val-tRNA(Val)
+分子 #56: 12S rRNA
+分子 #62: P-site Met-tRNA(Met)
+分子 #64: mRNA
+分子 #90: POTASSIUM ION
+分子 #91: MAGNESIUM ION
+分子 #92: VALINE
+分子 #93: ZINC ION
+分子 #94: FE-S-O HYBRID CLUSTER
+分子 #95: METHIONINE
+分子 #96: ADENOSINE-5'-TRIPHOSPHATE
+分子 #97: GUANOSINE-5'-DIPHOSPHATE
+分子 #98: 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 構成要素:
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グリッド | モデル: Quantifoil R2/2 / 材質: COPPER / 支持フィルム - #0 - Film type ID: 1 / 支持フィルム - #0 - 材質: CARBON / 支持フィルム - #0 - トポロジー: HOLEY / 支持フィルム - #1 - Film type ID: 2 / 支持フィルム - #1 - 材質: CARBON / 支持フィルム - #1 - トポロジー: CONTINUOUS / 前処理 - タイプ: GLOW DISCHARGE | |||||||||||||||
凍結 | 凍結剤: ETHANE-PROPANE / チャンバー内湿度: 100 % / チャンバー内温度: 277.15 K / 装置: FEI VITROBOT MARK IV | |||||||||||||||
詳細 | Affinity-purified 55S mitoribosome. |
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電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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特殊光学系 | エネルギーフィルター - スリット幅: 20 eV |
撮影 | フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 撮影したグリッド数: 2 / 実像数: 43882 / 平均電子線量: 60.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | C2レンズ絞り径: 100.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス(公称値): 3.0 µm / 最小 デフォーカス(公称値): 0.6 µm / 倍率(公称値): 81000 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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画像解析
-原子モデル構築 1
初期モデル |
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精密化 | 空間: REAL / プロトコル: FLEXIBLE FIT | |||||||||
得られたモデル | ![]() PDB-8oir: |