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万見- EMDB-21242: Structure of the human mitochondrial ribosome-EF-G1 complex (ClassIII) -
+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-21242 | |||||||||
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タイトル | Structure of the human mitochondrial ribosome-EF-G1 complex (ClassIII) | |||||||||
マップデータ | ClassIII 55S-EF-G1mt complex | |||||||||
試料 |
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キーワード | mitochondrial elongation factor-G1 / 55S ribosome / RIBOSOME | |||||||||
機能・相同性 | 機能・相同性情報 mitochondrial ribosome binding / 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 ribosome binding / 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 / 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 / mitochondrial translation / aminoacyl-tRNA hydrolase activity / positive regulation of proteolysis / ribosomal small subunit binding / anatomical structure morphogenesis / translation elongation factor activity / 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 / large ribosomal subunit / 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 / GTPase activity / mRNA binding / nucleotide binding / synapse / GTP binding / nucleolus / apoptotic process / positive regulation of DNA-templated transcription / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm 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: 2.96 Å | |||||||||
データ登録者 | Sharma MR / Koripella RK / Agrawal RK | |||||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Nat Commun / 年: 2020 タイトル: Structures of the human mitochondrial ribosome bound to EF-G1 reveal distinct features of mitochondrial translation elongation. 著者: Ravi Kiran Koripella / Manjuli R Sharma / Kalpana Bhargava / Partha P Datta / Prem S Kaushal / Pooja Keshavan / Linda L Spremulli / Nilesh K Banavali / Rajendra K Agrawal / 要旨: The mammalian mitochondrial ribosome (mitoribosome) and its associated translational factors have evolved to accommodate greater participation of proteins in mitochondrial translation. Here we ...The mammalian mitochondrial ribosome (mitoribosome) and its associated translational factors have evolved to accommodate greater participation of proteins in mitochondrial translation. Here we present the 2.68-3.96 Å cryo-EM structures of the human 55S mitoribosome in complex with the human mitochondrial elongation factor G1 (EF-G1) in three distinct conformational states, including an intermediate state and a post-translocational state. These structures reveal the role of several mitochondria-specific (mito-specific) mitoribosomal proteins (MRPs) and a mito-specific segment of EF-G1 in mitochondrial tRNA (tRNA) translocation. In particular, the mito-specific C-terminal extension in EF-G1 is directly involved in translocation of the acceptor arm of the A-site tRNA. In addition to the ratchet-like and independent head-swiveling motions exhibited by the small mitoribosomal subunit, we discover significant conformational changes in MRP mL45 at the nascent polypeptide-exit site within the large mitoribosomal subunit that could be critical for tethering of the elongating mitoribosome onto the inner-mitochondrial membrane. | |||||||||
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_21242.map.gz | 230 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-21242-v30.xml emd-21242.xml | 105.9 KB 105.9 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_21242.png | 249.7 KB | ||
Filedesc metadata | emd-21242.cif.gz | 22.2 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-21242 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21242 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_21242_validation.pdf.gz | 557.9 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_21242_full_validation.pdf.gz | 557.4 KB | 表示 | |
XML形式データ | emd_21242_validation.xml.gz | 7.3 KB | 表示 | |
CIF形式データ | emd_21242_validation.cif.gz | 8.5 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21242 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21242 | HTTPS FTP |
-関連構造データ
関連構造データ | 6vmiMC 6vlzC C: 同じ文献を引用 (文献) M: このマップから作成された原子モデル |
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類似構造データ | |
電子顕微鏡画像生データ | EMPIAR-10481 (タイトル: Structures of the human mitochondrial ribosome bound to EF-G1 reveal distinct features of mitochondrial translation elongation Data size: 753.5 Data #1: Aligned single-frame particles of human mitochondrial 55S-EF-Gmt complex [picked particles - single frame - processed]) |
-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_21242.map.gz / 形式: CCP4 / 大きさ: 244.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | ClassIII 55S-EF-G1mt complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.0961 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-EF-G1 complex
+超分子 #1: Human mitochondrial ribosome-EF-G1 complex
+分子 #1: 12s rRNA
+分子 #32: 16s rRNA
+分子 #33: tRNAval
+分子 #2: 28S ribosomal protein S2, mitochondrial
+分子 #3: 28S ribosomal protein S24, mitochondrial
+分子 #4: 28S ribosomal protein S6, mitochondrial
+分子 #5: 28S ribosomal protein S11, mitochondrial
+分子 #6: 28S ribosomal protein S12, mitochondrial
+分子 #7: 28S ribosomal protein S14, mitochondrial
+分子 #8: 28S ribosomal protein S16, mitochondrial
+分子 #9: 28S ribosomal protein S17, mitochondrial
+分子 #10: 28S ribosomal protein S18b, mitochondrial
+分子 #11: 28S ribosomal protein S18c, mitochondrial
+分子 #12: 28S ribosomal protein S21, mitochondrial
+分子 #13: 28S ribosomal protein S25, mitochondrial
+分子 #14: 28S ribosomal protein S28, mitochondrial
+分子 #15: 28S ribosomal protein S29, mitochondrial
+分子 #16: Coiled-coil-helix-coiled-coil-helix domain-containing protein 1
+分子 #17: 28S ribosomal protein S10, mitochondrial
+分子 #18: 28S ribosomal protein S15, mitochondrial
+分子 #19: 28S ribosomal protein S22, mitochondrial
+分子 #20: 28S ribosomal protein S23, mitochondrial
+分子 #21: 28S ribosomal protein S26, mitochondrial
+分子 #22: 28S ribosomal protein S27, mitochondrial
+分子 #23: 28S ribosomal protein S31, mitochondrial
+分子 #24: 28S ribosomal protein S33, mitochondrial
+分子 #25: 28S ribosomal protein S35, mitochondrial
+分子 #26: 28S ribosomal protein S34, mitochondrial
+分子 #27: Aurora kinase A-interacting protein
+分子 #28: Pentatricopeptide repeat domain-containing protein 3, mitochondrial
+分子 #29: 28S ribosomal protein S5, mitochondrial
+分子 #30: 28S ribosomal protein S7, mitochondrial
+分子 #31: 28S ribosomal protein S9, mitochondrial
+分子 #34: 39S ribosomal protein L2, mitochondrial
+分子 #35: 39S ribosomal protein L4, mitochondrial
+分子 #36: 39S ribosomal protein L9, mitochondrial
+分子 #37: 39S ribosomal protein L13, mitochondrial
+分子 #38: 39S ribosomal protein L14, mitochondrial
+分子 #39: 39S ribosomal protein L15, mitochondrial
+分子 #40: 39S ribosomal protein L17, mitochondrial
+分子 #41: 39S ribosomal protein L20, mitochondrial
+分子 #42: 39S ribosomal protein L21, mitochondrial
+分子 #43: 39S ribosomal protein L22, mitochondrial
+分子 #44: 39S ribosomal protein L27, mitochondrial
+分子 #45: 39S ribosomal protein L28, mitochondrial
+分子 #46: 39S ribosomal protein L47, mitochondrial
+分子 #47: 39S ribosomal protein L30, mitochondrial
+分子 #48: 39S ribosomal protein L32, mitochondrial
+分子 #49: 39S ribosomal protein L33, mitochondrial
+分子 #50: 39S ribosomal protein L34, mitochondrial
+分子 #51: 39S ribosomal protein L35, mitochondrial
+分子 #52: 39S ribosomal protein L36, mitochondrial
+分子 #53: 39S ribosomal protein L40, mitochondrial
+分子 #54: 39S ribosomal protein L43, mitochondrial
+分子 #55: 39S ribosomal protein L46, mitochondrial
+分子 #56: 39S ribosomal protein L49, mitochondrial
+分子 #57: 39S ribosomal protein L51, mitochondrial
+分子 #58: cDNA FLJ76418, highly similar to Homo sapiens mitochondrial ribos...
+分子 #59: 39S ribosomal protein L55, mitochondrial
+分子 #60: Ribosomal protein 63, mitochondrial
+分子 #61: Growth arrest and DNA damage-inducible proteins-interacting protein 1
+分子 #62: 39S ribosomal protein S18a, mitochondrial
+分子 #63: 39S ribosomal protein L11, mitochondrial
+分子 #64: 39S ribosomal protein L10, mitochondrial
+分子 #65: 39S ribosomal protein L16, mitochondrial
+分子 #66: Mitochondrial ribosomal protein L18, isoform CRA_b
+分子 #67: 39S ribosomal protein L23, mitochondrial
+分子 #68: 39S ribosomal protein L24, mitochondrial
+分子 #69: 39S ribosomal protein L3, mitochondrial
+分子 #70: 39S ribosomal protein L37, mitochondrial
+分子 #71: 39S ribosomal protein L38, mitochondrial
+分子 #72: 39S ribosomal protein L39, mitochondrial
+分子 #73: 39S ribosomal protein L41, mitochondrial
+分子 #74: 39S ribosomal protein L42, mitochondrial
+分子 #75: 39S ribosomal protein L44, mitochondrial
+分子 #76: 39S ribosomal protein L45, mitochondrial
+分子 #77: 39S ribosomal protein L48, mitochondrial
+分子 #78: 39S ribosomal protein L50, mitochondrial
+分子 #79: 39S ribosomal protein L53, mitochondrial
+分子 #80: 39S ribosomal protein L54, mitochondrial
+分子 #81: Peptidyl-tRNA hydrolase ICT1, mitochondrial
+分子 #82: 39S ribosomal protein S30, mitochondrial
+分子 #83: 39S ribosomal protein L19, mitochondrial
+分子 #84: 39S ribosomal protein L12, mitochondrial
+分子 #85: P-site finger
+分子 #86: Elongation factor G, mitochondrial
+分子 #87: mRNA
+分子 #88: P-site and E-site tRNA
+分子 #89: MAGNESIUM ION
+分子 #90: ZINC ION
+分子 #91: GUANOSINE-5'-DIPHOSPHATE
+分子 #92: 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: 7.5 |
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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) 検出モード: COUNTING / 平均電子線量: 69.2 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 |
-画像解析
初期モデル | モデルのタイプ: OTHER |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 2.96 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 150347 |
初期 角度割当 | タイプ: OTHER |
最終 角度割当 | タイプ: OTHER |