+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-13329 | |||||||||
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タイトル | Structure of the human mitoribosomal large subunit in complex with NSUN4.MTERF4.GTPBP7 and MALSU1.L0R8F8.mt-ACP | |||||||||
マップデータ | Postprocessed map | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 regulation of respiratory system process / rRNA modification in the mitochondrion / regulation of mitochondrial translation / tRNA (cytidine-5-)-methyltransferase activity / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / rRNA (cytosine-C5-)-methyltransferase activity / Complex I biogenesis / protein lipoylation / negative regulation of ribosome biogenesis ...regulation of respiratory system process / rRNA modification in the mitochondrion / regulation of mitochondrial translation / tRNA (cytidine-5-)-methyltransferase activity / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / rRNA (cytosine-C5-)-methyltransferase activity / Complex I biogenesis / protein lipoylation / negative regulation of ribosome biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / rRNA import into mitochondrion / rRNA methyltransferase activity / mitochondrial [2Fe-2S] assembly complex / Respiratory electron transport / 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 / iron-sulfur cluster assembly complex / protein targeting to mitochondrion / mitochondrial large ribosomal subunit binding / mitochondrial fission / camera-type eye development / 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 / rRNA methylation / [2Fe-2S] cluster assembly / aminoacyl-tRNA hydrolase activity / respiratory chain complex I / mitochondrial ribosome / iron-sulfur cluster assembly / mitochondrial translation / ribosomal large subunit binding / proton motive force-driven mitochondrial ATP synthesis / : / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / acyl binding / anatomical structure morphogenesis / acyl carrier activity / RNA processing / Mitochondrial protein degradation / aerobic respiration / rescue of stalled ribosome / ribosomal large subunit biogenesis / 転移酵素; 一炭素原子の基を移すもの; メチル基を移すもの / cellular response to leukemia inhibitory factor / methyltransferase activity / fatty acid binding / mitochondrial membrane / fibrillar center / fatty acid biosynthetic process / rRNA processing / double-stranded RNA binding / small ribosomal subunit rRNA binding / cell junction / heart development / large ribosomal subunit rRNA binding / double-stranded DNA binding / 5S rRNA binding / endonuclease activity / mitochondrial inner membrane / negative regulation of translation / nuclear body / rRNA binding / ribosome / mitochondrial matrix / structural constituent of ribosome / ribonucleoprotein complex / translation / protein domain specific binding / GTPase activity / mRNA binding / nucleotide binding / calcium ion binding / synapse / GTP binding / regulation of DNA-templated transcription / nucleolus / apoptotic process / mitochondrion / RNA binding / extracellular space / nucleoplasm / nucleus / plasma membrane / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) / Human (ヒト) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.4 Å | |||||||||
データ登録者 | Chandrasekaran V / Desai N / Burton NO / Yang H / Price J / Miska EA / Ramakrishnan V | |||||||||
資金援助 | 英国, 2件
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引用 | ジャーナル: Elife / 年: 2021 タイトル: Visualizing formation of the active site in the mitochondrial ribosome. 著者: Viswanathan Chandrasekaran / Nirupa Desai / Nicholas O Burton / Hanting Yang / Jon Price / Eric A Miska / V Ramakrishnan / 要旨: Ribosome assembly is an essential and conserved process that is regulated at each step by specific factors. Using cryo-electron microscopy (cryo-EM), we visualize the formation of the conserved ...Ribosome assembly is an essential and conserved process that is regulated at each step by specific factors. Using cryo-electron microscopy (cryo-EM), we visualize the formation of the conserved peptidyl transferase center (PTC) of the human mitochondrial ribosome. The conserved GTPase GTPBP7 regulates the correct folding of 16S ribosomal RNA (rRNA) helices and ensures 2'-O-methylation of the PTC base U3039. GTPBP7 binds the RNA methyltransferase NSUN4 and MTERF4, which sequester H68-71 of the 16S rRNA and allow biogenesis factors to access the maturing PTC. Mutations that disrupt binding of their orthologs to the large subunit potently activate mitochondrial stress and cause viability, development, and sterility defects. Next-generation RNA sequencing reveals widespread gene expression changes in these mutant animals that are indicative of mitochondrial stress response activation. We also answer the long-standing question of why NSUN4, but not its enzymatic activity, is indispensable for mitochondrial protein synthesis. | |||||||||
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_13329.map.gz | 54.9 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-13329-v30.xml emd-13329.xml | 79.2 KB 79.2 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_13329_fsc.xml | 18.1 KB | 表示 | FSCデータファイル |
画像 | emd_13329.png | 207.3 KB | ||
マスクデータ | emd_13329_msk_1.map | 512 MB | マスクマップ | |
その他 | emd_13329_additional_1.map.gz emd_13329_additional_2.map.gz emd_13329_half_map_1.map.gz emd_13329_half_map_2.map.gz | 407.9 MB 454.5 MB 412.5 MB 412.7 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-13329 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13329 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_13329_validation.pdf.gz | 477.3 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_13329_full_validation.pdf.gz | 476.9 KB | 表示 | |
XML形式データ | emd_13329_validation.xml.gz | 26.5 KB | 表示 | |
CIF形式データ | emd_13329_validation.cif.gz | 35.1 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13329 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13329 | 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_13329.map.gz / 形式: CCP4 / 大きさ: 512 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Postprocessed 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: 1.04 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
-マスク #1
ファイル | emd_13329_msk_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Refined map
ファイル | emd_13329_additional_1.map | ||||||||||||
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注釈 | Refined map | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: deepEMhancer map for interpretation
ファイル | emd_13329_additional_2.map | ||||||||||||
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注釈 | deepEMhancer map for interpretation | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half2 map
ファイル | emd_13329_half_map_1.map | ||||||||||||
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注釈 | Half2 map | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half1 map
ファイル | emd_13329_half_map_2.map | ||||||||||||
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注釈 | Half1 map | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
+全体 : human mitoribosomal large subunit assembly intermediate
+超分子 #1: human mitoribosomal large subunit assembly intermediate
+分子 #1: 39S ribosomal protein L32, mitochondrial
+分子 #2: 39S ribosomal protein L33, mitochondrial
+分子 #3: 39S ribosomal protein L34, mitochondrial
+分子 #4: 39S ribosomal protein L35, mitochondrial
+分子 #5: 39S ribosomal protein L36, mitochondrial
+分子 #6: 39S ribosomal protein L37, mitochondrial
+分子 #7: 39S ribosomal protein L38, mitochondrial
+分子 #8: 39S ribosomal protein L39, mitochondrial
+分子 #9: 39S ribosomal protein L40, mitochondrial
+分子 #10: 39S ribosomal protein L41, mitochondrial
+分子 #13: 39S ribosomal protein L9, mitochondrial
+分子 #14: 39S ribosomal protein L2, mitochondrial
+分子 #15: 39S ribosomal protein L3, mitochondrial
+分子 #16: 39S ribosomal protein L4, mitochondrial
+分子 #17: 39S ribosomal protein L10, mitochondrial
+分子 #18: 39S ribosomal protein L11, mitochondrial
+分子 #19: 39S ribosomal protein L13, mitochondrial
+分子 #20: 39S ribosomal protein L14, mitochondrial
+分子 #21: 39S ribosomal protein L15, mitochondrial
+分子 #22: 39S ribosomal protein L16, mitochondrial
+分子 #23: 39S ribosomal protein L17, mitochondrial
+分子 #24: 39S ribosomal protein L18, mitochondrial
+分子 #25: 39S ribosomal protein L19, mitochondrial
+分子 #26: 39S ribosomal protein L20, mitochondrial
+分子 #27: 39S ribosomal protein L21, mitochondrial
+分子 #28: 39S ribosomal protein L22, mitochondrial
+分子 #29: 39S ribosomal protein L23, mitochondrial
+分子 #30: 39S ribosomal protein L24, mitochondrial
+分子 #31: 39S ribosomal protein L27, mitochondrial
+分子 #32: 39S ribosomal protein L28, mitochondrial
+分子 #33: 39S ribosomal protein L47, mitochondrial
+分子 #34: 39S ribosomal protein L30, mitochondrial
+分子 #35: 39S ribosomal protein L42, mitochondrial
+分子 #36: 39S ribosomal protein L43, mitochondrial
+分子 #37: 39S ribosomal protein L44, mitochondrial
+分子 #38: 39S ribosomal protein L45, mitochondrial
+分子 #39: 39S ribosomal protein L46, mitochondrial
+分子 #40: 39S ribosomal protein L48, mitochondrial
+分子 #41: 39S ribosomal protein L49, mitochondrial
+分子 #42: 39S ribosomal protein L50, mitochondrial
+分子 #43: 39S ribosomal protein L51, mitochondrial
+分子 #44: 39S ribosomal protein L52, mitochondrial
+分子 #45: 39S ribosomal protein L53, mitochondrial
+分子 #46: 39S ribosomal protein L54, mitochondrial
+分子 #47: 39S ribosomal protein L55, mitochondrial
+分子 #48: Ribosomal protein 63, mitochondrial
+分子 #49: Peptidyl-tRNA hydrolase ICT1, mitochondrial
+分子 #50: Growth arrest and DNA damage-inducible proteins-interacting protein 1
+分子 #51: 39S ribosomal protein S18a, mitochondrial
+分子 #52: 39S ribosomal protein S30, mitochondrial
+分子 #53: mL65
+分子 #54: Mitochondrial assembly of ribosomal large subunit protein 1
+分子 #55: MIEF1 upstream open reading frame protein
+分子 #56: Acyl carrier protein, mitochondrial
+分子 #57: Transcription termination factor 4, mitochondrial
+分子 #58: 5-methylcytosine rRNA methyltransferase NSUN4
+分子 #59: Mitochondrial ribosome-associated GTPase 1
+分子 #11: 16S rRNA
+分子 #12: mt-tRNAVal
+分子 #60: ZINC ION
+分子 #61: ADENOSINE-5'-MONOPHOSPHATE
+分子 #62: URIDINE-5'-MONOPHOSPHATE
+分子 #63: CYTIDINE-5'-MONOPHOSPHATE
+分子 #64: O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
+分子 #65: GUANOSINE-5'-MONOPHOSPHATE
+分子 #66: PSEUDOURIDINE-5'-MONOPHOSPHATE
+分子 #67: MAGNESIUM ION
+分子 #68: 4'-PHOSPHOPANTETHEINE
+分子 #69: S-ADENOSYLMETHIONINE
+分子 #70: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
-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: 7.4 |
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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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撮影 | フィルム・検出器のモデル: FEI FALCON III (4k x 4k) 検出モード: INTEGRATING / 平均電子線量: 1.1 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: FLOOD BEAM / 撮影モード: BRIGHT FIELD |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |