+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-11397 | |||||||||||||||
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タイトル | Human mitochondrial ribosome in complex with mRNA, A-site tRNA, P-site tRNA and E-site tRNA | |||||||||||||||
マップデータ | ||||||||||||||||
試料 |
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キーワード | Mitochondria / Ribosome / mRNA / tRNA / Translation | |||||||||||||||
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 / 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 / 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) / synthetic construct (人工物) | |||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.0 Å | |||||||||||||||
データ登録者 | Aibara S / Singh V | |||||||||||||||
資金援助 | スウェーデン, European Union, 4件
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引用 | ジャーナル: Elife / 年: 2020 タイトル: Structural basis of mitochondrial translation. 著者: Shintaro Aibara / Vivek Singh / Angelika Modelska / Alexey Amunts / 要旨: Translation of mitochondrial messenger RNA (mt-mRNA) is performed by distinct mitoribosomes comprising at least 36 mitochondria-specific proteins. How these mitoribosomal proteins assist in the ...Translation of mitochondrial messenger RNA (mt-mRNA) is performed by distinct mitoribosomes comprising at least 36 mitochondria-specific proteins. How these mitoribosomal proteins assist in the binding of mt-mRNA and to what extent they are involved in the translocation of transfer RNA (mt-tRNA) is unclear. To visualize the process of translation in human mitochondria, we report ~3.0 Å resolution structure of the human mitoribosome, including the L7/L12 stalk, and eight structures of its functional complexes with mt-mRNA, mt-tRNAs, recycling factor and additional trans factors. The study reveals a transacting protein module LRPPRC-SLIRP that delivers mt-mRNA to the mitoribosomal small subunit through a dedicated platform formed by the mitochondria-specific protein mS39. Mitoribosomal proteins of the large subunit mL40, mL48, and mL64 coordinate translocation of mt-tRNA. The comparison between those structures shows dynamic interactions between the mitoribosome and its ligands, suggesting a sequential mechanism of conformational changes. | |||||||||||||||
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_11397.map.gz | 301.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-11397-v30.xml emd-11397.xml | 105.2 KB 105.2 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_11397.png | 68.3 KB | ||
Filedesc metadata | emd-11397.cif.gz | 21.9 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-11397 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11397 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_11397_validation.pdf.gz | 438.1 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_11397_full_validation.pdf.gz | 437.7 KB | 表示 | |
XML形式データ | emd_11397_validation.xml.gz | 7.7 KB | 表示 | |
CIF形式データ | emd_11397_validation.cif.gz | 8.8 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11397 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11397 | 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_11397.map.gz / 形式: CCP4 / 大きさ: 536.4 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: 1.05 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
-試料の構成要素
+全体 : human mitochondrial ribosome
+超分子 #1: human mitochondrial ribosome
+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 #12: 28S ribosomal protein S34, mitochondrial
+分子 #13: 28S ribosomal protein S35, mitochondrial
+分子 #14: Coiled-coil-helix-coiled-coil-helix domain-containing protein 1
+分子 #15: Aurora kinase A-interacting protein
+分子 #16: Pentatricopeptide repeat domain-containing protein 3, mitochondrial
+分子 #18: 28S ribosomal protein S2, mitochondrial
+分子 #19: 28S ribosomal protein S24, mitochondrial
+分子 #20: 28S ribosomal protein S5, mitochondrial
+分子 #21: 28S ribosomal protein S6, mitochondrial
+分子 #22: 28S ribosomal protein S7, mitochondrial
+分子 #23: 28S ribosomal protein S9, mitochondrial
+分子 #24: 28S ribosomal protein S10, mitochondrial
+分子 #25: 28S ribosomal protein S11, mitochondrial
+分子 #26: 28S ribosomal protein S12, mitochondrial
+分子 #27: 28S ribosomal protein S14, mitochondrial
+分子 #28: 28S ribosomal protein S15, mitochondrial
+分子 #29: 28S ribosomal protein S16, mitochondrial
+分子 #30: 28S ribosomal protein S17, mitochondrial
+分子 #31: 28S ribosomal protein S18b, mitochondrial
+分子 #32: 28S ribosomal protein S18c, mitochondrial
+分子 #33: 28S ribosomal protein S21, mitochondrial
+分子 #34: 28S ribosomal protein S22, mitochondrial
+分子 #35: 28S ribosomal protein S23, mitochondrial
+分子 #36: 28S ribosomal protein S25, mitochondrial
+分子 #37: 28S ribosomal protein S26, mitochondrial
+分子 #38: 28S ribosomal protein S27, mitochondrial
+分子 #39: 28S ribosomal protein S28, mitochondrial
+分子 #40: 28S ribosomal protein S29, mitochondrial
+分子 #41: 28S ribosomal protein S31, mitochondrial
+分子 #42: 28S ribosomal protein S33, mitochondrial
+分子 #44: 39S ribosomal protein L2, mitochondrial
+分子 #45: 39S ribosomal protein L3, mitochondrial
+分子 #46: 39S ribosomal protein L4, mitochondrial
+分子 #47: 39S ribosomal protein L9, mitochondrial
+分子 #48: 39S ribosomal protein L10, mitochondrial
+分子 #49: 39S ribosomal protein L11, mitochondrial
+分子 #50: 39S ribosomal protein L13, mitochondrial
+分子 #51: 39S ribosomal protein L14, mitochondrial
+分子 #52: 39S ribosomal protein L15, mitochondrial
+分子 #53: 39S ribosomal protein L16, mitochondrial
+分子 #54: 39S ribosomal protein L17, mitochondrial
+分子 #55: 39S ribosomal protein L18, mitochondrial
+分子 #56: 39S ribosomal protein L19, mitochondrial
+分子 #57: 39S ribosomal protein L20, mitochondrial
+分子 #58: 39S ribosomal protein L21, mitochondrial
+分子 #59: 39S ribosomal protein L22, mitochondrial
+分子 #60: 39S ribosomal protein L23, mitochondrial
+分子 #61: 39S ribosomal protein L24, mitochondrial
+分子 #62: 39S ribosomal protein L27, mitochondrial
+分子 #63: 39S ribosomal protein L28, mitochondrial
+分子 #64: 39S ribosomal protein L47, mitochondrial
+分子 #65: 39S ribosomal protein L30, mitochondrial
+分子 #66: 39S ribosomal protein L42, mitochondrial
+分子 #67: 39S ribosomal protein L43, mitochondrial
+分子 #68: 39S ribosomal protein L44, mitochondrial
+分子 #69: 39S ribosomal protein L45, mitochondrial
+分子 #70: 39S ribosomal protein L46, mitochondrial
+分子 #71: 39S ribosomal protein L48, mitochondrial
+分子 #72: 39S ribosomal protein L49, mitochondrial
+分子 #73: 39S ribosomal protein L50, mitochondrial
+分子 #74: 39S ribosomal protein L51, mitochondrial
+分子 #75: 39S ribosomal protein L52, mitochondrial
+分子 #76: 39S ribosomal protein L53, mitochondrial
+分子 #77: 39S ribosomal protein L54, mitochondrial
+分子 #78: 39S ribosomal protein L55, mitochondrial
+分子 #79: Ribosomal protein 63, mitochondrial
+分子 #80: Peptidyl-tRNA hydrolase ICT1, mitochondrial
+分子 #81: Growth arrest and DNA damage-inducible proteins-interacting protein 1
+分子 #82: 39S ribosomal protein S18a, mitochondrial
+分子 #87: 39S ribosomal protein S30, mitochondrial
+分子 #88: 39S ribosomal protein L12, mitochondrial
+分子 #89: Quinupristin
+分子 #11: 16S mitochondrial rRNA
+分子 #17: 12S mitochondrial rRNA
+分子 #43: mitochondrial tRNAVal
+分子 #83: mRNA
+分子 #84: A-site tRNA
+分子 #85: P-site tRNA
+分子 #86: E-site tRNA
+分子 #90: ZINC ION
+分子 #91: MAGNESIUM ION
+分子 #92: 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-D...
+分子 #93: GUANOSINE-5'-TRIPHOSPHATE
-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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撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 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: OTHER / 撮影モード: BRIGHT FIELD |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期モデル | モデルのタイプ: PDB ENTRY |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 4.0 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 13350 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |