+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-12926 | |||||||||
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タイトル | Cryo-EM structure of late human 39S mitoribosome assembly intermediates, state 5A | |||||||||
マップデータ | Local resolution filtered map | |||||||||
試料 |
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キーワード | 39S mitoribosome / ribosome biogenesis / RIBOSOME | |||||||||
機能・相同性 | 機能・相同性情報 negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / Complex I biogenesis / protein lipoylation / negative regulation of ribosome biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / rRNA import into mitochondrion / mitochondrial [2Fe-2S] assembly complex / Respiratory electron transport ...negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / Complex I biogenesis / protein lipoylation / negative regulation of ribosome biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / rRNA import into mitochondrion / mitochondrial [2Fe-2S] assembly complex / Respiratory electron transport / mitochondrial translational termination / mitochondrial translational elongation / 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 / mitochondrial large ribosomal subunit / mitochondrial fission / mitochondrial large ribosomal subunit binding / 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 ribosome / mitochondrial small ribosomal subunit / mitochondrial translation / aminoacyl-tRNA hydrolase activity / [2Fe-2S] cluster assembly / iron-sulfur cluster assembly / ribosomal large subunit binding / proton motive force-driven mitochondrial ATP synthesis / respiratory chain complex I / : / 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 / cellular response to leukemia inhibitory factor / fatty acid binding / mitochondrial membrane / fibrillar center / fatty acid biosynthetic process / double-stranded RNA binding / small ribosomal subunit rRNA binding / cell junction / 5S rRNA binding / large ribosomal subunit rRNA binding / endonuclease activity / 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 / mRNA binding / nucleotide binding / calcium ion binding / synapse / 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) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.7 Å | |||||||||
データ登録者 | Cheng J / Berninghausen O | |||||||||
引用 | ジャーナル: Nat Commun / 年: 2021 タイトル: A distinct assembly pathway of the human 39S late pre-mitoribosome. 著者: Jingdong Cheng / Otto Berninghausen / Roland Beckmann / 要旨: Assembly of the mitoribosome is largely enigmatic and involves numerous assembly factors. Little is known about their function and the architectural transitions of the pre-ribosomal intermediates. ...Assembly of the mitoribosome is largely enigmatic and involves numerous assembly factors. Little is known about their function and the architectural transitions of the pre-ribosomal intermediates. Here, we solve cryo-EM structures of the human 39S large subunit pre-ribosomes, representing five distinct late states. Besides the MALSU1 complex used as bait for affinity purification, we identify several assembly factors, including the DDX28 helicase, MRM3, GTPBP10 and the NSUN4-mTERF4 complex, all of which keep the 16S rRNA in immature conformations. The late transitions mainly involve rRNA domains IV and V, which form the central protuberance, the intersubunit side and the peptidyltransferase center of the 39S subunit. Unexpectedly, we find deacylated tRNA in the ribosomal E-site, suggesting a role in 39S assembly. Taken together, our study provides an architectural inventory of the distinct late assembly phase of the human 39S mitoribosome. | |||||||||
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_12926.map.gz | 105.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-12926-v30.xml emd-12926.xml | 71 KB 71 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_12926_fsc.xml | 12.8 KB | 表示 | FSCデータファイル |
画像 | emd_12926.png | 152.6 KB | ||
Filedesc metadata | emd-12926.cif.gz | 15.1 KB | ||
その他 | emd_12926_additional_1.map.gz | 140.7 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-12926 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12926 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_12926_validation.pdf.gz | 488.3 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_12926_full_validation.pdf.gz | 487.9 KB | 表示 | |
XML形式データ | emd_12926_validation.xml.gz | 13.2 KB | 表示 | |
CIF形式データ | emd_12926_validation.cif.gz | 17.8 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12926 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12926 | 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_12926.map.gz / 形式: CCP4 / 大きさ: 178 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Local resolution filtered 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: 1.084 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
-追加マップ: Unfiltered map
ファイル | emd_12926_additional_1.map | ||||||||||||
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注釈 | Unfiltered 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 39S mitoribosome assembly intermediates, state 5A
+超分子 #1: Human 39S mitoribosome assembly intermediates, state 5A
+分子 #1: 39S ribosomal protein L2, mitochondrial
+分子 #2: 39S ribosomal protein L3, mitochondrial
+分子 #3: 39S ribosomal protein L4, mitochondrial
+分子 #4: 39S ribosomal protein L9, mitochondrial
+分子 #5: 39S ribosomal protein L10, mitochondrial
+分子 #6: 39S ribosomal protein L11, mitochondrial
+分子 #7: 39S ribosomal protein L13, mitochondrial
+分子 #8: 39S ribosomal protein L14, mitochondrial
+分子 #9: 39S ribosomal protein L15, mitochondrial
+分子 #10: 39S ribosomal protein L16, mitochondrial
+分子 #11: 39S ribosomal protein L17, mitochondrial
+分子 #12: 39S ribosomal protein L18, mitochondrial
+分子 #13: 39S ribosomal protein L19, mitochondrial
+分子 #14: 39S ribosomal protein L20, mitochondrial
+分子 #15: 39S ribosomal protein L21, mitochondrial
+分子 #16: 39S ribosomal protein L22, mitochondrial
+分子 #17: 39S ribosomal protein L23, mitochondrial
+分子 #18: 39S ribosomal protein L24, mitochondrial
+分子 #19: 39S ribosomal protein L27, mitochondrial
+分子 #20: 39S ribosomal protein L28, mitochondrial
+分子 #21: 39S ribosomal protein L47, mitochondrial
+分子 #22: 39S ribosomal protein L30, mitochondrial
+分子 #23: 39S ribosomal protein L32, mitochondrial
+分子 #24: 39S ribosomal protein L33, mitochondrial
+分子 #25: 39S ribosomal protein L34, mitochondrial
+分子 #26: 39S ribosomal protein L35, mitochondrial
+分子 #27: 39S ribosomal protein L36, mitochondrial
+分子 #28: 39S ribosomal protein L37, mitochondrial
+分子 #29: 39S ribosomal protein L38, mitochondrial
+分子 #30: 39S ribosomal protein L39, mitochondrial
+分子 #31: 39S ribosomal protein L40, mitochondrial
+分子 #32: 39S ribosomal protein L41, mitochondrial
+分子 #33: 39S ribosomal protein L42, mitochondrial
+分子 #34: 39S ribosomal protein L43, mitochondrial
+分子 #35: 39S ribosomal protein L44, mitochondrial
+分子 #36: 39S ribosomal protein L45, mitochondrial
+分子 #37: 39S ribosomal protein L46, mitochondrial
+分子 #38: 39S ribosomal protein L48, mitochondrial
+分子 #39: 39S ribosomal protein L49, mitochondrial
+分子 #40: 39S ribosomal protein L50, mitochondrial
+分子 #41: 39S ribosomal protein L51, mitochondrial
+分子 #42: 39S ribosomal protein L52, mitochondrial
+分子 #43: 39S ribosomal protein L53, mitochondrial
+分子 #44: 39S ribosomal protein L54, mitochondrial
+分子 #45: 39S ribosomal protein L55, mitochondrial
+分子 #46: Ribosomal protein 63, mitochondrial
+分子 #47: Peptidyl-tRNA hydrolase ICT1, mitochondrial
+分子 #48: Growth arrest and DNA damage-inducible proteins-interacting protein 1
+分子 #49: 39S ribosomal protein S18a, mitochondrial
+分子 #50: 39S ribosomal protein S30, mitochondrial
+分子 #51: Mitochondrial assembly of ribosomal large subunit protein 1
+分子 #52: MIEF1 upstream open reading frame protein
+分子 #53: Acyl carrier protein, mitochondrial
+分子 #54: 16S rRNA
+分子 #55: mitochondrial Val tRNA
+分子 #56: mitochondrial tRNA
+分子 #57: ZINC ION
+分子 #58: MAGNESIUM ION
+分子 #59: 4'-PHOSPHOPANTETHEINE
-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 II (4k x 4k) 平均電子線量: 28.0 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: FLOOD BEAM / 撮影モード: BRIGHT FIELD |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |