[日本語] English
万見- EMDB-71745: Composite map of hypomethylated 80S ribosome treated with hygromycin B -
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データを開く
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基本情報
| 登録情報 | ![]() | |||||||||
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| タイトル | Composite map of hypomethylated 80S ribosome treated with hygromycin B | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | 2'-O-methylation / ribosome / rRNA modification | |||||||||
| 機能・相同性 | 機能・相同性情報maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / translational readthrough / positive regulation of translational fidelity / RMTs methylate histone arginines / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / positive regulation of protein kinase activity ...maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / translational readthrough / positive regulation of translational fidelity / RMTs methylate histone arginines / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / positive regulation of protein kinase activity / ribosome-associated ubiquitin-dependent protein catabolic process / pre-mRNA 5'-splice site binding / GDP-dissociation inhibitor activity / cytosolic large ribosomal subunit assembly / nonfunctional rRNA decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Ribosomal scanning and start codon recognition / response to cycloheximide / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA destabilization / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of mRNA splicing, via spliceosome / preribosome, large subunit precursor / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / negative regulation of translational frameshifting / translational elongation / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / 90S preribosome / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal subunit export from nucleus / translational termination / regulation of translational fidelity / maturation of LSU-rRNA / protein-RNA complex assembly / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator activity / ribosomal small subunit export from nucleus / DNA-(apurinic or apyrimidinic site) endonuclease activity / rescue of stalled cytosolic ribosome / cellular response to amino acid starvation / protein kinase C binding / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / macroautophagy / maturation of SSU-rRNA / translational initiation / small-subunit processome / maintenance of translational fidelity / modification-dependent protein catabolic process / cytoplasmic stress granule / protein tag activity / rRNA processing / ribosomal small subunit assembly / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / structural constituent of ribosome / protein ubiquitination / ribosome / translation / G protein-coupled receptor signaling pathway / negative regulation of gene expression / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol 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: 1.75 Å | |||||||||
データ登録者 | Zhao Y / Li H | |||||||||
| 資金援助 | 米国, 2件
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引用 | ジャーナル: Acta Crystallogr D Struct Biol / 年: 2019 タイトル: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. 著者: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / ...著者: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams / ![]() 要旨: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks. | |||||||||
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構造の表示
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ダウンロードとリンク
-EMDBアーカイブ
| マップデータ | emd_71745.map.gz | 766.3 MB | EMDBマップデータ形式 | |
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| ヘッダ (付随情報) | emd-71745-v30.xml emd-71745.xml | 101.3 KB 101.3 KB | 表示 表示 | EMDBヘッダ |
| 画像 | emd_71745.png | 35.8 KB | ||
| Filedesc metadata | emd-71745.cif.gz | 19.7 KB | ||
| アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-71745 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-71745 | HTTPS FTP |
-関連構造データ
| 関連構造データ | ![]() 9pn5MC ![]() 71722 ![]() 71723 ![]() 71724 ![]() 71725 M: このマップから作成された原子モデル C: 同じ文献を引用 ( |
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| 類似構造データ | 類似検索 - 機能・相同性 F&H 検索 |
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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 |
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マップ
| ファイル | ダウンロード / ファイル: emd_71745.map.gz / 形式: CCP4 / 大きさ: 824 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: 0.73 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
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試料の構成要素
+全体 : Hypomethylated 80S treated with hygromycin B
+超分子 #1: Hypomethylated 80S treated with hygromycin B
+分子 #1: Small ribosomal subunit protein uS2A
+分子 #2: Small ribosomal subunit protein eS1A
+分子 #3: Small ribosomal subunit protein uS5
+分子 #4: Small ribosomal subunit protein eS4A
+分子 #5: Small ribosomal subunit protein eS6A
+分子 #6: Small ribosomal subunit protein eS7A
+分子 #7: Small ribosomal subunit protein eS8A
+分子 #8: Small ribosomal subunit protein uS4A
+分子 #9: Small ribosomal subunit protein uS17A
+分子 #10: Small ribosomal subunit protein uS15
+分子 #11: Small ribosomal subunit protein uS11A
+分子 #12: Small ribosomal subunit protein eS21A
+分子 #13: Small ribosomal subunit protein uS8A
+分子 #14: Small ribosomal subunit protein uS12A
+分子 #15: Small ribosomal subunit protein eS24A
+分子 #16: Small ribosomal subunit protein eS26B
+分子 #17: Small ribosomal subunit protein eS27A
+分子 #18: Small ribosomal subunit protein eS30A
+分子 #19: Small ribosomal subunit protein uS3
+分子 #20: Small ribosomal subunit protein uS7
+分子 #21: Small ribosomal subunit protein eS10A
+分子 #22: Small ribosomal subunit protein uS19
+分子 #23: Small ribosomal subunit protein uS9A
+分子 #24: Small ribosomal subunit protein eS17A
+分子 #25: Small ribosomal subunit protein uS13A
+分子 #26: Small ribosomal subunit protein eS19A
+分子 #27: Small ribosomal subunit protein uS10
+分子 #28: Small ribosomal subunit protein eS25A
+分子 #29: Small ribosomal subunit protein eS28A
+分子 #30: Small ribosomal subunit protein uS14A
+分子 #31: Small ribosomal subunit protein RACK1
+分子 #32: Ubiquitin-ribosomal protein eS31 fusion protein
+分子 #33: Small ribosomal subunit protein eS12
+分子 #35: 60S ribosomal protein L2-A
+分子 #36: Large ribosomal subunit protein uL3
+分子 #37: 60S ribosomal protein L4-A
+分子 #41: 60S ribosomal protein L5
+分子 #42: Large ribosomal subunit protein eL6A
+分子 #43: 60S ribosomal protein L7-A
+分子 #44: Large ribosomal subunit protein eL8A
+分子 #45: Large ribosomal subunit protein uL6A
+分子 #46: Large ribosomal subunit protein uL16
+分子 #47: 60S ribosomal protein L11-A
+分子 #48: 60S ribosomal protein L13-A
+分子 #49: 60S ribosomal protein L14-A
+分子 #50: Large ribosomal subunit protein eL15A
+分子 #51: Large ribosomal subunit protein uL13A
+分子 #52: 60S ribosomal protein L17-A
+分子 #53: 60S ribosomal protein L18-A
+分子 #54: 60S ribosomal protein L19-A
+分子 #55: Large ribosomal subunit protein eL20A
+分子 #56: 60S ribosomal protein L21-A
+分子 #57: 60S ribosomal protein L22-A
+分子 #58: 60S ribosomal protein L23-A
+分子 #59: Large ribosomal subunit protein eL24A
+分子 #60: 60S ribosomal protein L25
+分子 #61: 60S ribosomal protein L26-A
+分子 #62: 60S ribosomal protein L27-A
+分子 #63: 60S ribosomal protein L28
+分子 #64: Large ribosomal subunit protein eL29
+分子 #65: 60S ribosomal protein L30
+分子 #66: 60S ribosomal protein L31-A
+分子 #67: 60S ribosomal protein L32
+分子 #68: 60S ribosomal protein L33-A
+分子 #69: 60S ribosomal protein L34-A
+分子 #70: 60S ribosomal protein L35-A
+分子 #71: 60S ribosomal protein L36-A
+分子 #72: 60S ribosomal protein L37-A
+分子 #73: 60S ribosomal protein L38
+分子 #74: 60S ribosomal protein L39
+分子 #75: Ubiquitin-ribosomal protein eL40A fusion protein
+分子 #76: Small ribosomal subunit protein eS32A
+分子 #77: Large ribosomal subunit protein eL42A
+分子 #78: 60S ribosomal protein L43-A
+分子 #34: 18S rRNA
+分子 #38: 25S rRNA
+分子 #39: 5S rRNA
+分子 #40: 5.8S rRNA
+分子 #79: MAGNESIUM ION
+分子 #80: POTASSIUM ION
+分子 #81: ZINC ION
+分子 #82: 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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解析 | 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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| グリッド | モデル: Quantifoil R1.2/1.3 / 材質: COPPER / メッシュ: 300 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: CONTINUOUS / 支持フィルム - Film thickness: 2 / 前処理 - タイプ: PLASMA CLEANING |
| 凍結 | 凍結剤: ETHANE |
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電子顕微鏡法
| 顕微鏡 | TFS KRIOS |
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| 撮影 | フィルム・検出器のモデル: FEI FALCON IV (4k x 4k) 平均電子線量: 55.0 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: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2.0 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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万見について



キーワード
データ登録者
米国, 2件
引用












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解析
FIELD EMISSION GUN
