+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-0514 | |||||||||
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タイトル | Structural insights into unique features of the human mitochondrial ribosome recycling | |||||||||
マップデータ | Cryo-EM structure of mammalian mitochondrial 55S ribosome with mtRRF-Class1 | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 mitochondrial ribosome binding / rRNA import into mitochondrion / ribosome disassembly / mitochondrial translational termination / mitochondrial ribosome assembly / mitochondrial translational elongation / translation release factor activity, codon nonspecific / microprocessor complex / Mitochondrial translation elongation / positive regulation of mitochondrial translation ...mitochondrial ribosome binding / rRNA import into mitochondrion / ribosome disassembly / mitochondrial translational termination / mitochondrial ribosome assembly / mitochondrial translational elongation / translation release factor activity, codon nonspecific / microprocessor complex / Mitochondrial translation elongation / positive regulation of mitochondrial translation / Mitochondrial translation termination / Mitochondrial translation initiation / negative regulation of mitotic nuclear division / 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 / aminoacyl-tRNA hydrolase activity / mitochondrial ribosome / mitochondrial translation / ribosomal large subunit binding / positive regulation of proteolysis / ribosomal small subunit binding / anatomical structure morphogenesis / 転写後修飾 / rescue of stalled ribosome / cellular response to leukemia inhibitory factor / apoptotic signaling pathway / small ribosomal subunit rRNA binding / 核小体 / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / double-stranded RNA binding / regulation of translation / 細胞結合 / small ribosomal subunit / 5S rRNA binding / endonuclease activity / 核膜 / ミトコンドリア内膜 / cell population proliferation / tRNA binding / negative regulation of translation / rRNA binding / nuclear body / リボソーム / ミトコンドリアマトリックス / structural constituent of ribosome / 細胞周期 / ribonucleoprotein complex / 翻訳 (生物学) / protein domain specific binding / nucleotide binding / mRNA binding / intracellular membrane-bounded organelle / シナプス / apoptotic process / GTP binding / 核小体 / ミトコンドリア / extracellular space / RNA binding / 核質 / 細胞核 / 細胞膜 / 細胞質基質 / 細胞質 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: 3.9 Å | |||||||||
データ登録者 | Sharma MR / Koripella RK / Agrawal RK | |||||||||
資金援助 | 米国, 2件
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引用 | ジャーナル: Proc Natl Acad Sci U S A / 年: 2019 タイトル: Structural insights into unique features of the human mitochondrial ribosome recycling. 著者: Ravi K Koripella / Manjuli R Sharma / Paul Risteff / Pooja Keshavan / Rajendra K Agrawal / 要旨: Mammalian mitochondrial ribosomes (mitoribosomes) are responsible for synthesizing proteins that are essential for oxidative phosphorylation (ATP generation). Despite their common ancestry with ...Mammalian mitochondrial ribosomes (mitoribosomes) are responsible for synthesizing proteins that are essential for oxidative phosphorylation (ATP generation). Despite their common ancestry with bacteria, the composition and structure of the human mitoribosome and its translational factors are significantly different from those of their bacterial counterparts. The mammalian mitoribosome recycling factor (RRF) carries a mito-specific N terminus extension (NTE), which is necessary for the function of RRF Here we present a 3.9-Å resolution cryo-electron microscopic (cryo-EM) structure of the human 55S mitoribosome-RRF complex, which reveals α-helix and loop structures for the NTE that makes multiple mito-specific interactions with functionally critical regions of the mitoribosome. These include ribosomal RNA segments that constitute the peptidyl transferase center (PTC) and those that connect PTC with the GTPase-associated center and with mitoribosomal proteins L16 and L27. Our structure reveals the presence of a tRNA in the pe/E position and a rotation of the small mitoribosomal subunit on RRF binding. In addition, we observe an interaction between the pe/E tRNA and a mito-specific protein, mL64. These findings help understand the unique features of mitoribosome recycling. | |||||||||
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_0514.map.gz | 197.1 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-0514-v30.xml emd-0514.xml | 92.7 KB 92.7 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_0514.png | 178.7 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-0514 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0514 | 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_0514.map.gz / 形式: CCP4 / 大きさ: 209.3 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Cryo-EM structure of mammalian mitochondrial 55S ribosome with mtRRF-Class1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.09 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 : Structural insights into unique features of the human mitochondri...
+超分子 #1: Structural insights into unique features of the human mitochondri...
+分子 #1: 16S rRNA
+分子 #2: mt-tRNAVal
+分子 #54: E-site tRNA
+分子 #56: 12S rRNA
+分子 #3: 39S ribosomal protein L2, mitochondrial
+分子 #4: 39S ribosomal protein L3, mitochondrial
+分子 #5: 39S ribosomal protein L4, mitochondrial
+分子 #6: 39S ribosomal protein L9, mitochondrial
+分子 #7: 39S ribosomal protein L10, mitochondrial
+分子 #8: 39S ribosomal protein L11, mitochondrial
+分子 #9: 39S ribosomal protein L13, mitochondrial
+分子 #10: 39S ribosomal protein L14, mitochondrial
+分子 #11: 39S ribosomal protein L15, mitochondrial
+分子 #12: 39S ribosomal protein L16, mitochondrial
+分子 #13: 39S ribosomal protein L17, mitochondrial
+分子 #14: 39S ribosomal protein L18, mitochondrial
+分子 #15: 39S ribosomal protein L19, mitochondrial
+分子 #16: 39S ribosomal protein L20, mitochondrial
+分子 #17: 39S ribosomal protein L21, mitochondrial
+分子 #18: 39S ribosomal protein L22, mitochondrial
+分子 #19: 39S ribosomal protein L23, mitochondrial
+分子 #20: 39S ribosomal protein L24, mitochondrial
+分子 #21: 39S ribosomal protein L27, mitochondrial
+分子 #22: 39S ribosomal protein L28, mitochondrial
+分子 #23: 39S ribosomal protein L47, mitochondrial
+分子 #24: 39S ribosomal protein L30, mitochondrial
+分子 #25: 39S ribosomal protein L32, mitochondrial
+分子 #26: 39S ribosomal protein L33, mitochondrial
+分子 #27: 39S ribosomal protein L34, mitochondrial
+分子 #28: 39S ribosomal protein L35, mitochondrial
+分子 #29: 39S ribosomal protein L36, mitochondrial
+分子 #30: 39S ribosomal protein L37, mitochondrial
+分子 #31: 39S ribosomal protein L38, mitochondrial
+分子 #32: 39S ribosomal protein L39, mitochondrial
+分子 #33: 39S ribosomal protein L40, mitochondrial
+分子 #34: 39S ribosomal protein L41, 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: Unknown protein/protein extension
+分子 #55: Ribosome-recycling factor, mitochondrial
+分子 #57: 28S ribosomal protein S2, mitochondrial
+分子 #58: 28S ribosomal protein S24, mitochondrial
+分子 #59: 28S ribosomal protein S5, mitochondrial
+分子 #60: 28S ribosomal protein S6, mitochondrial
+分子 #61: 28S ribosomal protein S7, mitochondrial
+分子 #62: 28S ribosomal protein S9, mitochondrial
+分子 #63: 28S ribosomal protein S10, mitochondrial
+分子 #64: 28S ribosomal protein S11, mitochondrial
+分子 #65: 28S ribosomal protein S12, mitochondrial
+分子 #66: 28S ribosomal protein S14, mitochondrial
+分子 #67: 28S ribosomal protein S15, mitochondrial
+分子 #68: 28S ribosomal protein S16, mitochondrial
+分子 #69: 28S ribosomal protein S17, mitochondrial
+分子 #70: 28S ribosomal protein S18b, mitochondrial
+分子 #71: 28S ribosomal protein S18c, mitochondrial
+分子 #72: 28S ribosomal protein S21, mitochondrial
+分子 #73: 28S ribosomal protein S22, mitochondrial
+分子 #74: 28S ribosomal protein S23, mitochondrial
+分子 #75: 28S ribosomal protein S25, mitochondrial
+分子 #76: 28S ribosomal protein S26, mitochondrial
+分子 #77: 28S ribosomal protein S27, mitochondrial
+分子 #78: 28S ribosomal protein S28, mitochondrial
+分子 #79: 28S ribosomal protein S29, mitochondrial
+分子 #80: 28S ribosomal protein S31, mitochondrial
+分子 #81: 28S ribosomal protein S33, mitochondrial
+分子 #82: 28S ribosomal protein S34, mitochondrial
+分子 #83: 28S ribosomal protein S35, mitochondrial
+分子 #84: Coiled-coil-helix-coiled-coil-helix domain-containing protein 1
+分子 #85: Aurora kinase A-interacting protein
+分子 #86: Pentatricopeptide repeat domain-containing protein 3, mitochondrial
+分子 #87: MAGNESIUM ION
+分子 #88: ZINC ION
-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: 7.6 |
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グリッド | 詳細: unspecified |
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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電子線 | 加速電圧: 300 kV / 電子線源: OTHER |
電子光学系 | 照射モード: OTHER / 撮影モード: OTHER |
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: 70.0 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
CTF補正 | ソフトウェア - 名称: RELION (ver. 2.0) |
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初期モデル | モデルのタイプ: PDB ENTRY PDBモデル - PDB ID: |
初期 角度割当 | タイプ: PROJECTION MATCHING / ソフトウェア - 名称: RELION (ver. 2.0) |
最終 3次元分類 | クラス数: 2 / ソフトウェア - 名称: cryoSPARC |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD / ソフトウェア - 名称: cryoSPARC |
最終 再構成 | 想定した対称性 - 点群: C1 (非対称) / 解像度のタイプ: BY AUTHOR / 解像度: 3.9 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: cryoSPARC / 使用した粒子像数: 67116 |