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基本情報
登録情報 | ![]() | ||||||||||||||||||
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タイトル | Human mitochondrial ribosome in complex with LRPPRC, SLIRP, A-site, P-site, E-site tRNAs and mRNA | ||||||||||||||||||
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![]() | mitochondrial translation / mRNA delivery / RIBOSOME | ||||||||||||||||||
機能・相同性 | ![]() negative regulation of mitochondrial RNA catabolic process / Mitochondrial RNA degradation / mitochondrial RNA catabolic process / regulation of mitochondrial translation / rRNA import into mitochondrion / mitochondrial transcription / flagellated sperm motility / mitochondrial translational termination / mitochondrial ribosome assembly / mitochondrial translational elongation ...negative regulation of mitochondrial RNA catabolic process / Mitochondrial RNA degradation / mitochondrial RNA catabolic process / regulation of mitochondrial translation / rRNA import into mitochondrion / mitochondrial transcription / flagellated sperm motility / mitochondrial translational termination / mitochondrial ribosome assembly / mitochondrial translational elongation / Mitochondrial translation elongation / Mitochondrial translation termination / translation release factor activity, codon nonspecific / Mitochondrial translation initiation / translation release factor activity / negative regulation of mitotic nuclear division / mitochondrial large ribosomal subunit / nuclear outer membrane / peptidyl-tRNA hydrolase / mitochondrial ribosome / 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 / nuclear inner membrane / mitochondrial small ribosomal subunit / peptidyl-tRNA hydrolase activity / mitochondrial translation / mitochondrion transport along microtubule / beta-tubulin binding / spermatid development / positive regulation of proteolysis / mitochondrial nucleoid / sperm flagellum / ribosomal small subunit binding / single fertilization / anatomical structure morphogenesis / mRNA transport / RNA processing / rescue of stalled ribosome / Mitochondrial protein degradation / cellular response to leukemia inhibitory factor / acrosomal vesicle / condensed nuclear chromosome / mRNA 3'-UTR binding / mitochondrion organization / apoptotic signaling pathway / autophagy / fibrillar center / cell junction / regulation of translation / single-stranded DNA binding / double-stranded RNA binding / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / microtubule binding / large ribosomal subunit rRNA binding / small ribosomal subunit rRNA binding / endonuclease activity / nuclear membrane / microtubule / cytoskeleton / tRNA binding / cell population proliferation / mitochondrial inner membrane / negative regulation of translation / rRNA binding / nuclear body / ribosome / structural constituent of ribosome / mitochondrial matrix / protein domain specific binding / translation / ribonucleoprotein complex / nucleotide binding / intracellular membrane-bounded organelle / mRNA binding / apoptotic process / ubiquitin protein ligase binding / GTP binding / positive regulation of DNA-templated transcription / nucleolus / perinuclear region of cytoplasm / mitochondrion / extracellular space / RNA binding / nucleoplasm / nucleus / membrane / plasma membrane / cytosol / cytoplasm 類似検索 - 分子機能 | ||||||||||||||||||
生物種 | ![]() | ||||||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.85 Å | ||||||||||||||||||
![]() | Singh V / Itoh Y / Amunts A | ||||||||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Structural basis of LRPPRC-SLIRP-dependent translation by the mitoribosome. 著者: Vivek Singh / J Conor Moran / Yuzuru Itoh / Iliana C Soto / Flavia Fontanesi / Mary Couvillion / Martijn A Huynen / L Stirling Churchman / Antoni Barrientos / Alexey Amunts / ![]() ![]() ![]() ![]() ![]() 要旨: In mammalian mitochondria, mRNAs are cotranscriptionally stabilized by the protein factor LRPPRC (leucine-rich pentatricopeptide repeat-containing protein). Here, we characterize LRPPRC as an mRNA ...In mammalian mitochondria, mRNAs are cotranscriptionally stabilized by the protein factor LRPPRC (leucine-rich pentatricopeptide repeat-containing protein). Here, we characterize LRPPRC as an mRNA delivery factor and report its cryo-electron microscopy structure in complex with SLIRP (SRA stem-loop-interacting RNA-binding protein), mRNA and the mitoribosome. The structure shows that LRPPRC associates with the mitoribosomal proteins mS39 and the N terminus of mS31 through recognition of the LRPPRC helical repeats. Together, the proteins form a corridor for handoff of the mRNA. The mRNA is directly bound to SLIRP, which also has a stabilizing function for LRPPRC. To delineate the effect of LRPPRC on individual mitochondrial transcripts, we used RNA sequencing, metabolic labeling and mitoribosome profiling, which showed a transcript-specific influence on mRNA translation efficiency, with cytochrome c oxidase subunit 1 and 2 translation being the most affected. Our data suggest that LRPPRC-SLIRP acts in recruitment of mitochondrial mRNAs to modulate their translation. Collectively, the data define LRPPRC-SLIRP as a regulator of the mitochondrial gene expression system. | ||||||||||||||||||
履歴 |
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構造の表示
添付画像 |
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ダウンロードとリンク
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マップデータ | ![]() | 571.8 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 118.4 KB 118.4 KB | 表示 表示 | ![]() |
画像 | ![]() | 104.2 KB | ||
Filedesc metadata | ![]() | 24.2 KB | ||
その他 | ![]() ![]() | 559.4 MB 558.2 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 454.7 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 454.3 KB | 表示 | |
XML形式データ | ![]() | 8.5 KB | 表示 | |
CIF形式データ | ![]() | 10 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 8anyMC C: 同じ文献を引用 ( 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 | 類似検索 - 機能・相同性 ![]() |
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||
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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: 0.83 Å | ||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-追加マップ: #1
ファイル | emd_15544_additional_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-追加マップ: consensus unsharpened
ファイル | emd_15544_additional_2.map | ||||||||||||
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注釈 | consensus unsharpened | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
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試料の構成要素
+全体 : Human mitochondrial ribosome bound to LRPPRC-SLIRP, mRNA and tRNA...
+超分子 #1: Human mitochondrial ribosome bound to LRPPRC-SLIRP, mRNA and tRNA...
+分子 #1: 12S mitochondrial rRNA
+分子 #30: A/A-tRNA
+分子 #31: P/P-tRNA
+分子 #32: E/E-tRNA
+分子 #33: 16S mitochondrial rRNA
+分子 #34: mitochondrial tRNAVal
+分子 #91: mRNA
+分子 #2: 28S ribosomal protein S2, mitochondrial
+分子 #3: 28S ribosomal protein S24, mitochondrial
+分子 #4: 28S ribosomal protein S5, mitochondrial
+分子 #5: 28S ribosomal protein S6, mitochondrial
+分子 #6: 28S ribosomal protein S7, mitochondrial
+分子 #7: 28S ribosomal protein S9, mitochondrial
+分子 #8: 28S ribosomal protein S10, mitochondrial
+分子 #9: 28S ribosomal protein S11, mitochondrial
+分子 #10: 28S ribosomal protein S12, mitochondrial
+分子 #11: 28S ribosomal protein S14, mitochondrial
+分子 #12: 28S ribosomal protein S15, mitochondrial
+分子 #13: 28S ribosomal protein S16, mitochondrial
+分子 #14: 28S ribosomal protein S17, mitochondrial
+分子 #15: 28S ribosomal protein S18b, mitochondrial
+分子 #16: 28S ribosomal protein S18c, mitochondrial
+分子 #17: 28S ribosomal protein S21, mitochondrial
+分子 #18: 28S ribosomal protein S22, mitochondrial
+分子 #19: 28S ribosomal protein S23, mitochondrial
+分子 #20: 28S ribosomal protein S25, mitochondrial
+分子 #21: 28S ribosomal protein S26, mitochondrial
+分子 #22: 28S ribosomal protein S27, mitochondrial
+分子 #23: 28S ribosomal protein S28, mitochondrial
+分子 #24: 28S ribosomal protein S29, mitochondrial
+分子 #25: 28S ribosomal protein S33, mitochondrial
+分子 #26: 28S ribosomal protein S34, mitochondrial
+分子 #27: 28S ribosomal protein S35, mitochondrial
+分子 #28: Coiled-coil-helix-coiled-coil-helix domain-containing protein 1
+分子 #29: Aurora kinase A-interacting protein
+分子 #35: 39S ribosomal protein L2, mitochondrial
+分子 #36: 39S ribosomal protein L3, mitochondrial
+分子 #37: 39S ribosomal protein L4, mitochondrial
+分子 #38: 39S ribosomal protein L10, mitochondrial
+分子 #39: 39S ribosomal protein L11, mitochondrial
+分子 #40: 39S ribosomal protein L13, mitochondrial
+分子 #41: 39S ribosomal protein L14, mitochondrial
+分子 #42: 39S ribosomal protein L15, mitochondrial
+分子 #43: 39S ribosomal protein L16, mitochondrial
+分子 #44: 39S ribosomal protein L17, mitochondrial
+分子 #45: 39S ribosomal protein L18, mitochondrial
+分子 #46: 39S ribosomal protein L19, mitochondrial
+分子 #47: 39S ribosomal protein L20, mitochondrial
+分子 #48: 39S ribosomal protein L21, mitochondrial
+分子 #49: 39S ribosomal protein L22, mitochondrial
+分子 #50: 39S ribosomal protein L23, mitochondrial
+分子 #51: 39S ribosomal protein L24, mitochondrial
+分子 #52: 39S ribosomal protein L27, mitochondrial
+分子 #53: 39S ribosomal protein L28, mitochondrial
+分子 #54: 39S ribosomal protein L47, mitochondrial
+分子 #55: 39S ribosomal protein L30, mitochondrial
+分子 #56: 39S ribosomal protein L32, mitochondrial
+分子 #57: 39S ribosomal protein L33, mitochondrial
+分子 #58: 39S ribosomal protein L34, mitochondrial
+分子 #59: 39S ribosomal protein L35, mitochondrial
+分子 #60: 39S ribosomal protein L36, mitochondrial
+分子 #61: 39S ribosomal protein L37, mitochondrial
+分子 #62: 39S ribosomal protein L38, mitochondrial
+分子 #63: 39S ribosomal protein L39, mitochondrial
+分子 #64: 39S ribosomal protein L40, mitochondrial
+分子 #65: 39S ribosomal protein L41, mitochondrial
+分子 #66: 39S ribosomal protein L42, mitochondrial
+分子 #67: Large ribosomal subunit protein mL43
+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 #83: 39S ribosomal protein S30, mitochondrial
+分子 #84: 39S ribosomal protein L12, mitochondrial
+分子 #85: 39S ribosomal protein L9, mitochondrial
+分子 #86: 39S ribosomal protein L1, mitochondrial
+分子 #87: 28S ribosomal protein S31, mitochondrial
+分子 #88: Leucine-rich PPR motif-containing protein, mitochondrial
+分子 #89: Pentatricopeptide repeat domain-containing protein 3, mitochondrial
+分子 #90: SRA stem-loop-interacting RNA-binding protein, mitochondrial
+分子 #92: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
+分子 #93: SPERMINE
+分子 #94: SPERMIDINE
+分子 #95: MAGNESIUM ION
+分子 #96: POTASSIUM ION
+分子 #97: ZINC ION
+分子 #98: FE2/S2 (INORGANIC) CLUSTER
+分子 #99: ADENOSINE-5'-TRIPHOSPHATE
+分子 #100: GUANOSINE-5'-DIPHOSPHATE
+分子 #101: 1,4-DIAMINOBUTANE
+分子 #102: VALINE
+分子 #103: water
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
緩衝液 | pH: 7.5 |
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凍結 | 凍結剤: ETHANE |
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電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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特殊光学系 | エネルギーフィルター - スリット幅: 20 eV |
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: 30.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 照射モード: SPOT SCAN / 撮影モード: BRIGHT FIELD 最大 デフォーカス(公称値): 2.8000000000000003 µm 最小 デフォーカス(公称値): 0.6 µm |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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画像解析
初期モデル | モデルのタイプ: PDB ENTRY PDBモデル - PDB ID: |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 2.85 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 82522 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |