+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-13980 | ||||||||||||||||||
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タイトル | Human mitochondrial ribosome at 2.2 A resolution | ||||||||||||||||||
マップデータ | Local_masked_refined_composite_map | ||||||||||||||||||
試料 |
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キーワード | ribosome / mitochondrial translation / tRNA / mRNA / 2Fe-2S clusters / polyamines / rRNA modifications / post-translation modifications / cryo EM | ||||||||||||||||||
機能・相同性 | 機能・相同性情報 mitochondrial ribosome binding / rRNA import into mitochondrion / mitochondrial transcription / mitochondrial translational termination / mitochondrial translational elongation / mitochondrial ribosome assembly / translation release factor activity, codon nonspecific / positive regulation of mitochondrial translation / microprocessor complex / Mitochondrial translation elongation ...mitochondrial ribosome binding / rRNA import into mitochondrion / mitochondrial transcription / mitochondrial translational termination / mitochondrial translational elongation / mitochondrial ribosome assembly / translation release factor activity, codon nonspecific / positive regulation of mitochondrial translation / microprocessor complex / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / mitochondrial large ribosomal subunit / negative regulation of mitotic nuclear division / peptidyl-tRNA hydrolase / 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 ribosome / mitochondrial small ribosomal subunit / mitochondrial translation / aminoacyl-tRNA hydrolase activity / positive regulation of proteolysis / ribosomal small subunit binding / anatomical structure morphogenesis / RNA processing / Mitochondrial protein degradation / rescue of stalled ribosome / apoptotic signaling pathway / cellular response to leukemia inhibitory factor / fibrillar center / double-stranded RNA binding / small ribosomal subunit rRNA binding / cell junction / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / nuclear membrane / endonuclease activity / cell population proliferation / tRNA binding / mitochondrial inner membrane / negative regulation of translation / nuclear body / rRNA binding / ribosome / structural constituent of ribosome / mitochondrial matrix / ribonucleoprotein complex / translation / protein domain specific binding / intracellular membrane-bounded organelle / mRNA binding / nucleotide binding / synapse / GTP binding / nucleolus / apoptotic process / 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 | Homo sapiens (ヒト) | ||||||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.21 Å | ||||||||||||||||||
データ登録者 | Singh V / Itoh Y / Andrell J / Aibara S / Amunts A | ||||||||||||||||||
資金援助 | スウェーデン, European Union, 5件
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引用 | 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
添付画像 |
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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 | emd_13980.map.gz | 336.9 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-13980-v30.xml emd-13980.xml | 124.6 KB 124.6 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_13980_fsc.xml | 19 KB | 表示 | FSCデータファイル |
画像 | emd_13980.png | 152.7 KB | ||
マスクデータ | emd_13980_msk_1.map emd_13980_msk_2.map emd_13980_msk_3.map emd_13980_msk_4.map emd_13980_msk_5.map emd_13980_msk_6.map emd_13980_msk_7.map emd_13980_msk_8.map emd_13980_msk_9.map | 600.7 MB 600.7 MB 600.7 MB 600.7 MB 600.7 MB 600.7 MB 600.7 MB 600.7 MB 600.7 MB | マスクマップ | |
Filedesc metadata | emd-13980.cif.gz | 24.2 KB | ||
その他 | emd_13980_additional_1.map.gz emd_13980_additional_2.map.gz emd_13980_additional_3.map.gz emd_13980_half_map_1.map.gz emd_13980_half_map_2.map.gz | 2.2 GB 336.2 MB 483.2 MB 486 MB 486 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-13980 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13980 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_13980_validation.pdf.gz | 1.1 MB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_13980_full_validation.pdf.gz | 1.1 MB | 表示 | |
XML形式データ | emd_13980_validation.xml.gz | 27.6 KB | 表示 | |
CIF形式データ | emd_13980_validation.cif.gz | 36.4 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13980 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13980 | HTTPS FTP |
-関連構造データ
-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_13980.map.gz / 形式: CCP4 / 大きさ: 600.7 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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注釈 | Local_masked_refined_composite_map | ||||||||||||||||||||||||||||||||||||
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
+マスク #7
+マスク #8
+マスク #9
+追加マップ: super-sampled local masked refined composite map
+追加マップ: local resolution filtered sharpened map
+追加マップ: unsharpened map
+ハーフマップ: half map 2 unfiltered
+ハーフマップ: half map 1 unfiltered
-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: A/A-tRNA
+分子 #33: P/P-tRNA
+分子 #34: mRNA
+分子 #35: 16S mitochondrial rRNA
+分子 #36: mitochondrial tRNAVal
+分子 #89: E/E-tRNA
+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 L9, mitochondrial
+分子 #41: 39S ribosomal protein L10, mitochondrial
+分子 #42: 39S ribosomal protein L11, mitochondrial
+分子 #43: 39S ribosomal protein L13, mitochondrial
+分子 #44: 39S ribosomal protein L14, mitochondrial
+分子 #45: 39S ribosomal protein L15, mitochondrial
+分子 #46: 39S ribosomal protein L16, mitochondrial
+分子 #47: 39S ribosomal protein L17, mitochondrial
+分子 #48: 39S ribosomal protein L18, mitochondrial
+分子 #49: 39S ribosomal protein L19, mitochondrial
+分子 #50: 39S ribosomal protein L20, mitochondrial
+分子 #51: 39S ribosomal protein L21, mitochondrial
+分子 #52: 39S ribosomal protein L22, mitochondrial
+分子 #53: 39S ribosomal protein L23, mitochondrial
+分子 #54: 39S ribosomal protein L24, mitochondrial
+分子 #55: 39S ribosomal protein L27, mitochondrial
+分子 #56: 39S ribosomal protein L28, mitochondrial
+分子 #57: 39S ribosomal protein L47, mitochondrial
+分子 #58: 39S ribosomal protein L30, mitochondrial
+分子 #59: 39S ribosomal protein L32, mitochondrial
+分子 #60: 39S ribosomal protein L33, mitochondrial
+分子 #61: 39S ribosomal protein L34, mitochondrial
+分子 #62: 39S ribosomal protein L35, mitochondrial
+分子 #63: 39S ribosomal protein L36, mitochondrial
+分子 #64: 39S ribosomal protein L37, mitochondrial
+分子 #65: 39S ribosomal protein L38, mitochondrial
+分子 #66: 39S ribosomal protein L39, mitochondrial
+分子 #67: 39S ribosomal protein L40, mitochondrial
+分子 #68: 39S ribosomal protein L41, mitochondrial
+分子 #69: 39S ribosomal protein L42, mitochondrial
+分子 #70: 39S ribosomal protein L43, mitochondrial
+分子 #71: 39S ribosomal protein L44, mitochondrial
+分子 #72: 39S ribosomal protein L45, mitochondrial
+分子 #73: 39S ribosomal protein L46, mitochondrial
+分子 #74: 39S ribosomal protein L48, mitochondrial
+分子 #75: 39S ribosomal protein L49, mitochondrial
+分子 #76: 39S ribosomal protein L50, mitochondrial
+分子 #77: 39S ribosomal protein L51, mitochondrial
+分子 #78: 39S ribosomal protein L52, mitochondrial
+分子 #79: 39S ribosomal protein L53, mitochondrial
+分子 #80: 39S ribosomal protein L54, mitochondrial
+分子 #81: 39S ribosomal protein L55, mitochondrial
+分子 #82: Ribosomal protein 63, mitochondrial
+分子 #83: Peptidyl-tRNA hydrolase ICT1, mitochondrial
+分子 #84: Growth arrest and DNA damage-inducible proteins-interacting protein 1
+分子 #85: 39S ribosomal protein S18a, mitochondrial
+分子 #86: 39S ribosomal protein S30, mitochondrial
+分子 #87: 39S ribosomal protein L12, mitochondrial
+分子 #88: 39S ribosomal protein L1, mitochondrial
+分子 #90: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
+分子 #91: SPERMINE
+分子 #92: SPERMIDINE
+分子 #93: MAGNESIUM ION
+分子 #94: POTASSIUM ION
+分子 #95: ZINC ION
+分子 #96: FE2/S2 (INORGANIC) CLUSTER
+分子 #97: ADENOSINE-5'-TRIPHOSPHATE
+分子 #98: GUANOSINE-5'-DIPHOSPHATE
+分子 #99: 1,4-DIAMINOBUTANE
+分子 #100: VALINE
+分子 #101: 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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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
緩衝液 | pH: 7.5 |
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凍結 | 凍結剤: ETHANE |
-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 K2 SUMMIT (4k x 4k) 検出モード: COUNTING / 平均電子線量: 30.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
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): 2.8000000000000003 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 |