+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-15113 | |||||||||
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タイトル | Human mature large subunit of the ribosome with eIF6 and homoharringtonine bound | |||||||||
マップデータ | Postprocessed map. Masked, and sharpened at -40 A2. Must be upsampled 768x768x768 (0.55267 pixel size) for best visualisation and alignment with supplied structure. | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 lamin filament / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation / miRNA-mediated post-transcriptional gene silencing / embryonic brain development / eukaryotic 80S initiation complex / negative regulation of protein neddylation / miRNA-mediated gene silencing by inhibition of translation / translation at presynapse / axial mesoderm development ...lamin filament / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation / miRNA-mediated post-transcriptional gene silencing / embryonic brain development / eukaryotic 80S initiation complex / negative regulation of protein neddylation / miRNA-mediated gene silencing by inhibition of translation / translation at presynapse / axial mesoderm development / regulation of G1 to G0 transition / negative regulation of formation of translation preinitiation complex / 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 / exit from mitosis / protein-DNA complex disassembly / 90S preribosome assembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / optic nerve development / TORC2 complex binding / GAIT complex / G1 to G0 transition / retinal ganglion cell axon guidance / middle ear morphogenesis / cytoplasmic side of rough endoplasmic reticulum membrane / A band / regulation of reactive oxygen species metabolic process / positive regulation of signal transduction by p53 class mediator / alpha-beta T cell differentiation / ubiquitin ligase inhibitor activity / regulation of glycolytic process / negative regulation of ubiquitin protein ligase activity / response to aldosterone / maturation of 5.8S rRNA / homeostatic process / lung morphogenesis / macrophage chemotaxis / ribosomal subunit export from nucleus / ヒドロキシル化 / Peptide chain elongation / ribosomal large subunit binding / Selenocysteine synthesis / protein-RNA complex assembly / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / blastocyst development / preribosome, large subunit precursor / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / translation regulator activity / Viral mRNA Translation / protein localization to nucleus / cellular response to actinomycin D / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / protein targeting / Major pathway of rRNA processing in the nucleolus and cytosol / 小胞体 / MDM2/MDM4 family protein binding / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / negative regulation of ubiquitin-dependent protein catabolic process / ribosomal large subunit biogenesis / 着床 / cellular response to interleukin-4 / translation initiation factor activity / 骨化 / assembly of large subunit precursor of preribosome / cytosolic ribosome / cytosolic ribosome assembly / positive regulation of translation / innate immune response in mucosa / regulation of signal transduction by p53 class mediator / skeletal system development / mRNA 3'-UTR binding / sensory perception of sound / response to insulin / cellular response to gamma radiation / 骨 / mRNA 5'-UTR binding / ribosomal large subunit assembly / transcription coactivator binding / cytoplasmic ribonucleoprotein granule / rRNA processing / Regulation of expression of SLITs and ROBOs / cellular response to type II interferon / cellular response to UV / antimicrobial humoral immune response mediated by antimicrobial peptide / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / presynapse / regulation of translation / retina development in camera-type eye / cell body 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: 1.67 Å | |||||||||
データ登録者 | Faille A / Warren AJ / Dent KC | |||||||||
資金援助 | 英国, 1件
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引用 | ジャーナル: bioRxiv / 年: 2023 タイトル: The chemical landscape of the human ribosome at 1.67 Å resolution. 著者: Alexandre Faille / Kyle C Dent / Simone Pellegrino / Pekka Jaako / Alan J Warren 要旨: The ability of ribosomes to translate the genetic code into protein requires a finely tuned ion and solvent ecosystem. However, the lack of high-resolution structures has precluded accurate ...The ability of ribosomes to translate the genetic code into protein requires a finely tuned ion and solvent ecosystem. However, the lack of high-resolution structures has precluded accurate positioning of all the functional elements of the ribosome and limited our understanding of the specific role of ribosomal RNA chemical modifications in modulating ribosome function in health and disease. Here, using a new sample preparation methodology based on functionalised pristine graphene-coated grids, we solve the cryo-EM structure of the human large ribosomal subunit to a resolution of 1.67 Å. The accurate assignment of water molecules, magnesium and potassium ions in our model highlights the fundamental biological role of ribosomal RNA methylation in harnessing unconventional carbon-oxygen hydrogen bonds to establish chemical interactions with the environment and fine-tune the functional interplay with tRNA. In addition, the structures of three translational inhibitors bound to the human large ribosomal subunit at better than 2 Å resolution provide mechanistic insights into how three key druggable pockets of the ribosome are targeted and illustrate the potential of this methodology to accelerate high-throughput structure-based design of anti-cancer therapeutics. | |||||||||
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
-EMDBアーカイブ
マップデータ | emd_15113.map.gz | 58.7 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-15113-v30.xml emd-15113.xml | 68 KB 68 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_15113_fsc.xml | 17.8 KB | 表示 | FSCデータファイル |
画像 | emd_15113.png | 81 KB | ||
マスクデータ | emd_15113_msk_1.map | 512 MB | マスクマップ | |
その他 | emd_15113_additional_1.map.gz emd_15113_half_map_1.map.gz emd_15113_half_map_2.map.gz | 405.2 MB 409.1 MB 409.1 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-15113 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15113 | HTTPS FTP |
-関連構造データ
関連構造データ | 8a3dMC 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 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-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_15113.map.gz / 形式: CCP4 / 大きさ: 512 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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注釈 | Postprocessed map. Masked, and sharpened at -40 A2. Must be upsampled 768x768x768 (0.55267 pixel size) for best visualisation and alignment with supplied structure. | ||||||||||||||||||||||||||||||||||||
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: 0.829 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
-マスク #1
ファイル | emd_15113_msk_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: Final refinement map.
ファイル | emd_15113_additional_1.map | ||||||||||||
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注釈 | Final refinement map. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Final refinement half-map 1.
ファイル | emd_15113_half_map_1.map | ||||||||||||
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注釈 | Final refinement half-map 1. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Final refinement half-map 2.
ファイル | emd_15113_half_map_2.map | ||||||||||||
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注釈 | Final refinement half-map 2. | ||||||||||||
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 mature large subunit of the ribosome with eIF6 bound
+超分子 #1: Human mature large subunit of the ribosome with eIF6 bound
+分子 #1: 28S ribosomal RNA
+分子 #2: 5S ribosomal RNA
+分子 #3: 5.8S 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
+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: 60S ribosomal protein L29
+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: Ribosomal protein uL29
+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 L36a
+分子 #43: 60S ribosomal protein L37a
+分子 #44: 60S ribosomal protein L28
+分子 #45: Eukaryotic translation initiation factor 6
+分子 #46: MAGNESIUM ION
+分子 #47: POTASSIUM ION
+分子 #48: SODIUM ION
+分子 #49: (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methy...
+分子 #50: SPERMINE
+分子 #51: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
+分子 #52: ZINC ION
+分子 #53: 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
緩衝液 | pH: 7.5 構成要素:
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グリッド | モデル: Quantifoil R2/2 / 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: 2.0 nm 詳細: Grid was functionalised with 1-pyrenemethylamine. See methods section in published article. | |||||||||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK IV / 詳細: 30 seconds 'wait' time. |
-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 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / 最大 デフォーカス(公称値): 1.8 µm / 最小 デフォーカス(公称値): 1.0 µm / 倍率(公称値): 105000 |
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 |
撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 撮影したグリッド数: 1 / 実像数: 9973 / 平均露光時間: 2.2 sec. / 平均電子線量: 51.0 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
粒子像選択 | 選択した数: 1147785 |
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初期モデル | モデルのタイプ: PDB ENTRY PDBモデル - PDB ID: 6ek0 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD / ソフトウェア - 名称: cryoSPARC (ver. 3) |
最終 3次元分類 | クラス数: 3 / ソフトウェア - 名称: cryoSPARC (ver. 3.1) 詳細: Used to filter out very few bad particles, mostly due to ice contamination. |
最終 角度割当 | タイプ: OTHER / ソフトウェア - 名称: RELION (ver. 3.1) |
最終 再構成 | 使用したクラス数: 1 / 解像度のタイプ: BY AUTHOR / 解像度: 1.67 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: RELION (ver. 3.1) / 使用した粒子像数: 1088709 |
FSC曲線 (解像度の算出) |