+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-4070 | |||||||||
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タイトル | Structure-function insights reveal the human ribosome as a cancer target for antibiotics | |||||||||
マップデータ | Chimera contour level | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / eukaryotic 80S initiation complex / protein tyrosine kinase inhibitor activity / negative regulation of protein neddylation / translation at presynapse / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage ...positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / eukaryotic 80S initiation complex / protein tyrosine kinase inhibitor activity / negative regulation of protein neddylation / translation at presynapse / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / axial mesoderm development / regulation of G1 to G0 transition / negative regulation of formation of translation preinitiation complex / IRE1-RACK1-PP2A complex / nucleolus organization / ribosomal protein import into nucleus / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / : / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / exit from mitosis / protein-DNA complex disassembly / TNFR1-mediated ceramide production / 90S preribosome assembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of RNA splicing / negative regulation of DNA repair / laminin receptor activity / optic nerve development / TORC2 complex binding / oxidized purine DNA binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / supercoiled DNA binding / GAIT complex / G1 to G0 transition / neural crest cell differentiation / rRNA modification in the nucleus and cytosol / retinal ganglion cell axon guidance / negative regulation of phagocytosis / NF-kappaB complex / middle ear morphogenesis / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / positive regulation of ubiquitin-protein transferase activity / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / A band / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / alpha-beta T cell differentiation / 顔料 / protein kinase A binding / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / Translation initiation complex formation / phagocytic cup / positive regulation of mitochondrial depolarization / response to aldosterone / negative regulation of Wnt signaling pathway / homeostatic process / positive regulation of T cell receptor signaling pathway / lung morphogenesis / macrophage chemotaxis / positive regulation of activated T cell proliferation / fibroblast growth factor binding / regulation of cell division / SARS-CoV-1 modulates host translation machinery / ヒドロキシル化 / iron-sulfur cluster binding / male meiosis I / MTOR / BH3 domain binding / mTORC1-mediated signalling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Peptide chain elongation / Selenocysteine synthesis / protein-RNA complex assembly / monocyte chemotaxis / cysteine-type endopeptidase activator activity involved in apoptotic process / Formation of a pool of free 40S subunits / ribosomal small subunit export from nucleus / positive regulation of cyclic-nucleotide phosphodiesterase activity / Eukaryotic Translation Termination / blastocyst development / Response of EIF2AK4 (GCN2) to amino acid deficiency / translation regulator activity / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / protein localization to nucleus / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / cellular response to actinomycin D / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of respiratory burst involved in inflammatory response 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: 3.6 Å | |||||||||
データ登録者 | Myasnikov AG / Natchiar SK / Nebout M / Hazemann I / Imbert V / Khatter H / Peyron J-F / Klaholz BP | |||||||||
引用 | ジャーナル: Nature / 年: 2015 タイトル: Structure of the human 80S ribosome. 著者: Heena Khatter / Alexander G Myasnikov / S Kundhavai Natchiar / Bruno P Klaholz / 要旨: Ribosomes are translational machineries that catalyse protein synthesis. Ribosome structures from various species are known at the atomic level, but obtaining the structure of the human ribosome has ...Ribosomes are translational machineries that catalyse protein synthesis. Ribosome structures from various species are known at the atomic level, but obtaining the structure of the human ribosome has remained a challenge; efforts to address this would be highly relevant with regard to human diseases. Here we report the near-atomic structure of the human ribosome derived from high-resolution single-particle cryo-electron microscopy and atomic model building. The structure has an average resolution of 3.6 Å, reaching 2.9 Å resolution in the most stable regions. It provides unprecedented insights into ribosomal RNA entities and amino acid side chains, notably of the transfer RNA binding sites and specific molecular interactions with the exit site tRNA. It reveals atomic details of the subunit interface, which is seen to remodel strongly upon rotational movements of the ribosomal subunits. Furthermore, the structure paves the way for analysing antibiotic side effects and diseases associated with deregulated protein synthesis. | |||||||||
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_4070.map.gz | 23.4 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-4070-v30.xml emd-4070.xml | 95.4 KB 95.4 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_4070.png | 140.7 KB | ||
その他 | emd_4070_additional.map.gz | 23.1 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-4070 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4070 | 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_4070.map.gz / 形式: CCP4 / 大きさ: 371.3 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Chimera contour level | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.1 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
-追加マップ: Chimera contour level
ファイル | emd_4070_additional.map | ||||||||||||
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注釈 | Chimera contour level | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
+全体 : Human 80S ribsome
+超分子 #1: Human 80S ribsome
+分子 #1: 28S ribosomal RNA
+分子 #2: 5S ribosomal RNA
+分子 #3: 5.8S ribosomal RNA
+分子 #47: 18S ribosomal RNA
+分子 #4: 60S ribosomal protein L8
+分子 #5: 60S ribosomal protein L3
+分子 #6: 60S ribosomal protein L4
+分子 #7: 60S ribosomal protein L5
+分子 #8: 60S ribosomal protein L6
+分子 #9: 60S ribosomal protein L7
+分子 #10: 60S ribosomal protein L7a
+分子 #11: 60S ribosomal protein L9
+分子 #12: 60S ribosomal protein L10-like
+分子 #13: 60S ribosomal protein L11
+分子 #14: 60S ribosomal protein L13
+分子 #15: 60S ribosomal protein L14
+分子 #16: 60S ribosomal protein L15
+分子 #17: 60S ribosomal protein L13a
+分子 #18: 60S ribosomal protein L17
+分子 #19: 60S ribosomal protein L18
+分子 #20: 60S ribosomal protein L19
+分子 #21: 60S ribosomal protein L18a
+分子 #22: 60S ribosomal protein L21
+分子 #23: 60S ribosomal protein L22
+分子 #24: 60S ribosomal protein L23
+分子 #25: 60S ribosomal protein L24
+分子 #26: 60S ribosomal protein L23a
+分子 #27: 60S ribosomal protein L26
+分子 #28: 60S ribosomal protein L27
+分子 #29: 60S ribosomal protein L27a
+分子 #30: Ribosomal protein L29, isoform CRA_a
+分子 #31: 60S ribosomal protein L30
+分子 #32: 60S ribosomal protein L31
+分子 #33: 60S ribosomal protein L32
+分子 #34: 60S ribosomal protein L35a
+分子 #35: 60S ribosomal protein L34
+分子 #36: 60S ribosomal protein L35
+分子 #37: 60S ribosomal protein L36
+分子 #38: 60S ribosomal protein L37
+分子 #39: 60S ribosomal protein L38
+分子 #40: 60S ribosomal protein L39
+分子 #41: Ubiquitin-60S ribosomal protein L40
+分子 #42: 60S ribosomal protein L41
+分子 #43: 60S ribosomal protein L36a
+分子 #44: 60S ribosomal protein L37a
+分子 #45: 60S ribosomal protein L28
+分子 #46: 60S ribosomal protein L10a
+分子 #48: 40S ribosomal protein SA
+分子 #49: 40S ribosomal protein S3a
+分子 #50: 40S ribosomal protein S3
+分子 #51: 40S ribosomal protein S4, X isoform
+分子 #52: 40S ribosomal protein S5
+分子 #53: 40S ribosomal protein S7
+分子 #54: 40S ribosomal protein S8
+分子 #55: 40S ribosomal protein S10
+分子 #56: 40S ribosomal protein S11
+分子 #57: 40S ribosomal protein S15
+分子 #58: 40S ribosomal protein S16
+分子 #59: 40S ribosomal protein S17
+分子 #60: 40S ribosomal protein S18
+分子 #61: 40S ribosomal protein S19
+分子 #62: 40S ribosomal protein S20
+分子 #63: 40S ribosomal protein S21
+分子 #64: 40S ribosomal protein S23
+分子 #65: 40S ribosomal protein S26
+分子 #66: 40S ribosomal protein S28
+分子 #67: 40S ribosomal protein S29
+分子 #68: Receptor of activated protein C kinase 1
+分子 #69: 40S ribosomal protein S2
+分子 #70: 40S ribosomal protein S6
+分子 #71: 40S ribosomal protein S9
+分子 #72: 40S ribosomal protein S12
+分子 #73: 40S ribosomal protein S13
+分子 #74: 40S ribosomal protein S14
+分子 #75: 40S ribosomal protein S15a
+分子 #76: 40S ribosomal protein S24
+分子 #77: 40S ribosomal protein S25
+分子 #78: 40S ribosomal protein S27
+分子 #79: Ribosomal protein S30
+分子 #80: Ubiquitin-40S ribosomal protein S27a
+分子 #81: 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethy...
+分子 #82: MAGNESIUM ION
+分子 #83: ZINC ION
+分子 #84: 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 |
-試料調製
濃度 | 0.5 mg/mL |
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緩衝液 | pH: 7.5 |
グリッド | モデル: Quantifoil R2/2 / 材質: COPPER/RHODIUM / 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: HOLEY / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 雰囲気: AIR |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 283 K / 装置: FEI VITROBOT MARK IV |
-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: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 50.0 µm / 最大 デフォーカス(補正後): 3.0 µm / 最小 デフォーカス(補正後): 0.5 µm / 照射モード: SPOT SCAN / 撮影モード: BRIGHT FIELDBright-field microscopy / Cs: 0.001 mm / 最大 デフォーカス(公称値): 2.5 µm / 最小 デフォーカス(公称値): 0.4 µm / 倍率(公称値): 79000 |
特殊光学系 | 球面収差補正装置: CS corrected microscope |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
温度 | 最低: 79.0 K / 最高: 105.0 K |
撮影 | フィルム・検出器のモデル: FEI FALCON II (4k x 4k) 検出モード: OTHER / デジタル化 - サンプリング間隔: 14.0 µm / デジタル化 - 画像ごとのフレーム数: 3-9 / 撮影したグリッド数: 4 / 実像数: 6600 / 平均露光時間: 1.0 sec. / 平均電子線量: 50.0 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: CTFFIND (ver. CTFFIND 4) / 詳細: Relion |
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初期 角度割当 | タイプ: NOT APPLICABLE |
最終 3次元分類 | クラス数: 2 / ソフトウェア - 名称: RELION (ver. RELION1.4) / ソフトウェア - 詳細: LMB |
最終 角度割当 | タイプ: OTHER / ソフトウェア - 名称: RELION (ver. RELION1.4) / ソフトウェア - 詳細: LMB |
最終 再構成 | 使用したクラス数: 1 / アルゴリズム: FOURIER SPACE / 解像度のタイプ: BY AUTHOR / 解像度: 3.6 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 詳細: RELION / 使用した粒子像数: 19000 |
-原子モデル構築 1
精密化 | プロトコル: RIGID BODY FIT / 当てはまり具合の基準: Maximum likelihood |
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得られたモデル | PDB-5lks: |