+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-14317 | |||||||||||||||
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タイトル | Cryo-EM reconstruction of the human 40S ribosomal subunit - Full map | |||||||||||||||
マップデータ | ||||||||||||||||
試料 |
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キーワード | Ribosome (リボソーム) / rRNA modifications / post-translational modifications / cryo-EM (低温電子顕微鏡法) | |||||||||||||||
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 / protein tyrosine kinase inhibitor activity / 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 / IRE1-RACK1-PP2A complex ...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 / protein tyrosine kinase inhibitor activity / 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 / IRE1-RACK1-PP2A complex / nucleolus organization / : / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of RNA splicing / negative regulation of DNA repair / laminin receptor activity / oxidized purine DNA binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / supercoiled DNA binding / neural crest cell differentiation / negative regulation of phagocytosis / NF-kappaB complex / rRNA modification in the nucleus and cytosol / 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 / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / 顔料 / protein kinase A binding / Ribosomal scanning and start codon recognition / negative regulation of ubiquitin protein ligase activity / ion channel inhibitor activity / Translation initiation complex formation / phagocytic cup / positive regulation of mitochondrial depolarization / negative regulation of Wnt signaling pathway / positive regulation of T cell receptor signaling pathway / fibroblast growth factor binding / positive regulation of activated T cell proliferation / regulation of cell division / ヒドロキシル化 / MTOR / iron-sulfur cluster binding / BH3 domain binding / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Selenocysteine synthesis / monocyte chemotaxis / Formation of a pool of free 40S subunits / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of cyclic-nucleotide phosphodiesterase activity / Eukaryotic Translation Termination / ribosomal small subunit export from nucleus / organelle membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / translation regulator activity / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of respiratory burst involved in inflammatory response / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / L13a-mediated translational silencing of Ceruloplasmin expression / gastrulation / Major pathway of rRNA processing in the nucleolus and cytosol / 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) / 小胞体 / regulation of translational fidelity / spindle assembly / MDM2/MDM4 family protein binding / laminin binding / Protein methylation / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Nuclear events stimulated by ALK signaling in cancer / rescue of stalled ribosome / signaling adaptor activity / negative regulation of smoothened signaling pathway / positive regulation of cell cycle / translation initiation factor binding / negative regulation of peptidyl-serine phosphorylation / maturation of SSU-rRNA / positive regulation of intrinsic apoptotic signaling pathway / Mitotic Prometaphase / positive regulation of apoptotic signaling pathway / EML4 and NUDC in mitotic spindle formation / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / positive regulation of JUN kinase activity / Maturation of protein E / positive regulation of microtubule polymerization 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: 2.15 Å | |||||||||||||||
データ登録者 | Pellegrino S / Dent KC / Spikes T / Warren AJ | |||||||||||||||
資金援助 | 英国, 4件
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引用 | ジャーナル: Nucleic Acids Res / 年: 2023 タイトル: Cryo-EM reconstruction of the human 40S ribosomal subunit at 2.15 Å resolution. 著者: Simone Pellegrino / Kyle C Dent / Tobias Spikes / Alan J Warren / 要旨: The chemical modification of ribosomal RNA and proteins is critical for ribosome assembly, for protein synthesis and may drive ribosome specialisation in development and disease. However, the ...The chemical modification of ribosomal RNA and proteins is critical for ribosome assembly, for protein synthesis and may drive ribosome specialisation in development and disease. However, the inability to accurately visualise these modifications has limited mechanistic understanding of the role of these modifications in ribosome function. Here we report the 2.15 Å resolution cryo-EM reconstruction of the human 40S ribosomal subunit. We directly visualise post-transcriptional modifications within the 18S rRNA and four post-translational modifications of ribosomal proteins. Additionally, we interpret the solvation shells in the core regions of the 40S ribosomal subunit and reveal how potassium and magnesium ions establish both universally conserved and eukaryote-specific coordination to promote the stabilisation and folding of key ribosomal elements. This work provides unprecedented structural details for the human 40S ribosomal subunit that will serve as an important reference for unravelling the functional role of ribosomal RNA modifications. | |||||||||||||||
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_14317.map.gz | 44.4 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-14317-v30.xml emd-14317.xml | 48.3 KB 48.3 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_14317_fsc.xml | 18 KB | 表示 | FSCデータファイル |
画像 | emd_14317.png | 59.5 KB | ||
Filedesc metadata | emd-14317.cif.gz | 11.7 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-14317 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14317 | HTTPS FTP |
-関連構造データ
関連構造データ | 7r4xMC 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 | 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_14317.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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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: 0.8267 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
-試料の構成要素
+全体 : Human 40S ribosomal subunit
+超分子 #1: Human 40S ribosomal subunit
+分子 #1: 60S ribosomal protein L41
+分子 #3: 40S ribosomal protein S3a
+分子 #4: 40S ribosomal protein S3
+分子 #5: 40S ribosomal protein S4, X isoform
+分子 #6: 40S ribosomal protein S5
+分子 #7: 40S ribosomal protein S7
+分子 #8: 40S ribosomal protein S8
+分子 #9: 40S ribosomal protein S10
+分子 #10: 40S ribosomal protein S11
+分子 #11: 40S ribosomal protein S15
+分子 #12: 40S ribosomal protein S16
+分子 #13: 40S ribosomal protein S17
+分子 #14: 40S ribosomal protein S18
+分子 #15: 40S ribosomal protein S19
+分子 #16: 40S ribosomal protein S20
+分子 #17: 40S ribosomal protein S21
+分子 #18: 40S ribosomal protein S23
+分子 #19: 40S ribosomal protein S26
+分子 #20: 40S ribosomal protein S28
+分子 #21: 40S ribosomal protein S29
+分子 #22: 40S ribosomal protein S2
+分子 #23: 40S ribosomal protein S6
+分子 #24: 40S ribosomal protein S9
+分子 #25: 40S ribosomal protein S12
+分子 #26: 40S ribosomal protein S13
+分子 #27: 40S ribosomal protein S14
+分子 #28: 40S ribosomal protein S15a
+分子 #29: 40S ribosomal protein S24
+分子 #30: 40S ribosomal protein S25
+分子 #31: 40S ribosomal protein S27
+分子 #32: 40S ribosomal protein S30
+分子 #33: Ubiquitin-40S ribosomal protein S27a
+分子 #34: Receptor of activated protein C kinase 1
+分子 #35: 40S ribosomal protein SA
+分子 #2: 18S ribosomal RNA
+分子 #36: POTASSIUM ION
+分子 #37: MAGNESIUM ION
+分子 #38: ZINC ION
+分子 #39: 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 |
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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 |
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 |
-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 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy 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): 1.0 µm |
撮影 | フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 平均電子線量: 40.56 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |