+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-12764 | |||||||||
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タイトル | Human mitochondrial ribosome large subunit assembly intermediate with MTERF4-NSUN4, MRM2, MTG1 and the MALSU module | |||||||||
マップデータ | Locally filtered map from CryoSPARC non-uniform refinement | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 regulation of respiratory system process / tRNA (cytidine-5-)-methyltransferase activity / rRNA modification in the mitochondrion / regulation of mitochondrial translation / rRNA 2'-O-methylation / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (cytosine-C5-)-methyltransferase activity / Complex I biogenesis ...regulation of respiratory system process / tRNA (cytidine-5-)-methyltransferase activity / rRNA modification in the mitochondrion / regulation of mitochondrial translation / rRNA 2'-O-methylation / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (cytosine-C5-)-methyltransferase activity / Complex I biogenesis / protein lipoylation / negative regulation of ribosome biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / mitochondrial [2Fe-2S] assembly complex / Respiratory electron transport / rRNA methyltransferase activity / RNA methylation / 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 / protein targeting to mitochondrion / camera-type eye development / iron-sulfur cluster assembly complex / mitochondrial large ribosomal subunit / mitochondrial fission / mitochondrial large ribosomal subunit binding / 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 / rRNA methylation / 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 respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / 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 / large ribosomal subunit / cell junction / heart development / 5S rRNA binding / large ribosomal subunit rRNA binding / double-stranded DNA 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 / GTPase activity / mRNA binding / nucleotide binding / calcium ion binding / synapse / regulation of DNA-templated transcription / GTP binding / nucleolus / apoptotic process / positive regulation of DNA-templated transcription / mitochondrion / RNA binding / 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: 2.6 Å | |||||||||
データ登録者 | Valentin Gese G / Hallberg BM | |||||||||
引用 | ジャーナル: Nat Commun / 年: 2021 タイトル: Structural basis for late maturation steps of the human mitoribosomal large subunit. 著者: Miriam Cipullo / Genís Valentín Gesé / Anas Khawaja / B Martin Hällberg / Joanna Rorbach / 要旨: Mitochondrial ribosomes (mitoribosomes) synthesize a critical set of proteins essential for oxidative phosphorylation. Therefore, mitoribosomal function is vital to the cellular energy supply. ...Mitochondrial ribosomes (mitoribosomes) synthesize a critical set of proteins essential for oxidative phosphorylation. Therefore, mitoribosomal function is vital to the cellular energy supply. Mitoribosome biogenesis follows distinct molecular pathways that remain poorly understood. Here, we determine the cryo-EM structures of mitoribosomes isolated from human cell lines with either depleted or overexpressed mitoribosome assembly factor GTPBP5, allowing us to capture consecutive steps during mitoribosomal large subunit (mt-LSU) biogenesis. Our structures provide essential insights into the last steps of 16S rRNA folding, methylation and peptidyl transferase centre (PTC) completion, which require the coordinated action of nine assembly factors. We show that mammalian-specific MTERF4 contributes to the folding of 16S rRNA, allowing 16 S rRNA methylation by MRM2, while GTPBP5 and NSUN4 promote fine-tuning rRNA rearrangements leading to PTC formation. Moreover, our data reveal an unexpected involvement of the elongation factor mtEF-Tu in mt-LSU assembly, where mtEF-Tu interacts with GTPBP5, similar to its interaction with tRNA during translational elongation. | |||||||||
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_12764.map.gz | 50.4 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-12764-v30.xml emd-12764.xml | 77.8 KB 77.8 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_12764_fsc.xml | 20.8 KB | 表示 | FSCデータファイル |
画像 | emd_12764.png | 60 KB | ||
その他 | emd_12764_additional_1.map.gz emd_12764_half_map_1.map.gz emd_12764_half_map_2.map.gz | 47.1 MB 50.4 MB 50.4 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-12764 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12764 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_12764_validation.pdf.gz | 524.3 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_12764_full_validation.pdf.gz | 523.4 KB | 表示 | |
XML形式データ | emd_12764_validation.xml.gz | 18.5 KB | 表示 | |
CIF形式データ | emd_12764_validation.cif.gz | 27.1 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12764 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12764 | 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_12764.map.gz / 形式: CCP4 / 大きさ: 54.3 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Locally filtered map from CryoSPARC non-uniform refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 これらの図は立方格子座標系で作成されたものです | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.02 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: Map post-processed with DeepEMhancer
ファイル | emd_12764_additional_1.map | ||||||||||||
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注釈 | Map post-processed with DeepEMhancer | ||||||||||||
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_12764_half_map_1.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 |
-ハーフマップ: Half map B
ファイル | emd_12764_half_map_2.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 |
-試料の構成要素
+全体 : 55S subunit assembly intermediate
+超分子 #1: 55S subunit assembly intermediate
+分子 #1: 16S rRNA
+分子 #2: MT-TRNAVAL
+分子 #3: Mitochondrial ribosome-associated GTPase 1
+分子 #4: 39S ribosomal protein L2, mitochondrial
+分子 #5: 39S ribosomal protein L3, mitochondrial
+分子 #6: 39S ribosomal protein L4, mitochondrial
+分子 #7: 39S ribosomal protein L9, mitochondrial
+分子 #8: 39S ribosomal protein L10, mitochondrial
+分子 #9: 39S ribosomal protein L11, mitochondrial
+分子 #10: 39S ribosomal protein L13, mitochondrial
+分子 #11: 39S ribosomal protein L14, mitochondrial
+分子 #12: 39S ribosomal protein L15, mitochondrial
+分子 #13: 39S ribosomal protein L16, mitochondrial
+分子 #14: 39S ribosomal protein L17, mitochondrial
+分子 #15: Mitochondrial ribosomal protein L18, isoform CRA_b
+分子 #16: 39S ribosomal protein L19, mitochondrial
+分子 #17: 39S ribosomal protein L20, mitochondrial
+分子 #18: 39S ribosomal protein L21, mitochondrial
+分子 #19: 39S ribosomal protein L22, mitochondrial
+分子 #20: 39S ribosomal protein L23, mitochondrial
+分子 #21: 39S ribosomal protein L24, mitochondrial
+分子 #22: 39S ribosomal protein L27, mitochondrial
+分子 #23: 39S ribosomal protein L28, mitochondrial
+分子 #24: 39S ribosomal protein L47, mitochondrial
+分子 #25: 39S ribosomal protein L30, mitochondrial
+分子 #26: 39S ribosomal protein L42, mitochondrial
+分子 #27: 39S ribosomal protein L32, mitochondrial
+分子 #28: 39S ribosomal protein L33, mitochondrial
+分子 #29: 39S ribosomal protein L34, mitochondrial
+分子 #30: 39S ribosomal protein L35, mitochondrial
+分子 #31: 39S ribosomal protein L36, mitochondrial
+分子 #32: 39S ribosomal protein L37, mitochondrial
+分子 #33: 39S ribosomal protein L38, mitochondrial
+分子 #34: 39S ribosomal protein L39, mitochondrial
+分子 #35: 39S ribosomal protein L40, mitochondrial
+分子 #36: 39S ribosomal protein L41, mitochondrial
+分子 #37: 39S ribosomal protein L43, mitochondrial
+分子 #38: 39S ribosomal protein L44, mitochondrial
+分子 #39: 39S ribosomal protein L45, mitochondrial
+分子 #40: 39S ribosomal protein L46, mitochondrial
+分子 #41: 39S ribosomal protein L48, mitochondrial
+分子 #42: 39S ribosomal protein L49, mitochondrial
+分子 #43: 39S ribosomal protein L50, mitochondrial
+分子 #44: 39S ribosomal protein L51, mitochondrial
+分子 #45: 39S ribosomal protein L52, mitochondrial
+分子 #46: 39S ribosomal protein L53, mitochondrial
+分子 #47: 39S ribosomal protein L54, mitochondrial
+分子 #48: 39S ribosomal protein L55, mitochondrial
+分子 #49: Ribosomal protein 63, mitochondrial
+分子 #50: Peptidyl-tRNA hydrolase ICT1, mitochondrial
+分子 #51: Growth arrest and DNA damage-inducible proteins-interacting protein 1
+分子 #52: 39S ribosomal protein S18a, mitochondrial
+分子 #53: 39S ribosomal protein S30, mitochondrial
+分子 #54: rRNA methyltransferase 2, mitochondrial
+分子 #55: 5-methylcytosine rRNA methyltransferase NSUN4
+分子 #56: Transcription termination factor 4, mitochondrial
+分子 #57: MIEF1 upstream open reading frame protein
+分子 #58: Mitochondrial assembly of ribosomal large subunit protein 1
+分子 #59: 39S ribosomal protein L12, mitochondrial
+分子 #60: Acyl carrier protein, mitochondrial
+分子 #61: Unknown residues
+分子 #62: MAGNESIUM ION
+分子 #63: GUANOSINE-5'-DIPHOSPHATE
+分子 #64: ZINC ION
+分子 #65: S-ADENOSYLMETHIONINE
+分子 #66: 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 | TFS KRIOS |
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特殊光学系 | エネルギーフィルター - 名称: GIF Bioquantum / エネルギーフィルター - スリット幅: 10 eV |
撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 平均電子線量: 48.2 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 20.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |