+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-4337 | |||||||||||||||
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タイトル | Cryo-EM structure of a late human pre-40S ribosomal subunit - State C | |||||||||||||||
マップデータ | ||||||||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 positive regulation of ribosomal small subunit export from nucleus / regulation of protein localization to nucleolus / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / trophectodermal cell differentiation / positive regulation of rRNA processing / negative regulation of endoplasmic reticulum unfolded protein response / protein tyrosine kinase inhibitor activity / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / IRE1-RACK1-PP2A complex ...positive regulation of ribosomal small subunit export from nucleus / regulation of protein localization to nucleolus / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / trophectodermal cell differentiation / positive regulation of rRNA processing / negative regulation of endoplasmic reticulum unfolded protein response / protein tyrosine kinase inhibitor activity / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / IRE1-RACK1-PP2A complex / nucleolus organization / response to extracellular stimulus / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of RNA splicing / laminin receptor activity / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / neural crest cell differentiation / rRNA modification in the nucleus and cytosol / negative regulation of phagocytosis / regulation of establishment of cell polarity / positive regulation of ubiquitin-protein transferase activity / regulation of mitotic metaphase/anaphase transition / U3 snoRNA binding / 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 / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / preribosome, small subunit precursor / Translation initiation complex formation / phagocytic cup / positive regulation of mitochondrial depolarization / snoRNA binding / negative regulation of Wnt signaling pathway / fibroblast growth factor binding / regulation of cell division / SARS-CoV-1 modulates host translation machinery / ヒドロキシル化 / 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) / Peptide chain elongation / Selenocysteine synthesis / 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 / Response of EIF2AK4 (GCN2) to amino acid deficiency / translation regulator activity / SRP-dependent cotranslational protein targeting to membrane / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / 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 / Major pathway of rRNA processing in the nucleolus and cytosol / gastrulation / 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) / regulation of translational fidelity / MDM2/MDM4 family protein binding / laminin binding / Protein methylation / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / 小胞体 / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Nuclear events stimulated by ALK signaling in cancer / negative regulation of smoothened signaling pathway / rescue of stalled ribosome / signaling adaptor activity / positive regulation of cell cycle / negative regulation of peptidyl-serine phosphorylation / stress granule assembly / translation initiation factor binding / maturation of SSU-rRNA / positive regulation of intrinsic apoptotic signaling pathway / Mitotic Prometaphase / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / EML4 and NUDC in mitotic spindle formation / negative regulation of ubiquitin-dependent protein catabolic process / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / RNA endonuclease activity / translational initiation / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / グリコーゲン合成 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 | Ameismeier M / Cheng J / Berninghausen O / Beckmann R | |||||||||||||||
資金援助 | ドイツ, 4件
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引用 | ジャーナル: Nature / 年: 2018 タイトル: Visualizing late states of human 40S ribosomal subunit maturation. 著者: Michael Ameismeier / Jingdong Cheng / Otto Berninghausen / Roland Beckmann / 要旨: The formation of eukaryotic ribosomal subunits extends from the nucleolus to the cytoplasm and entails hundreds of assembly factors. Despite differences in the pathways of ribosome formation, high- ...The formation of eukaryotic ribosomal subunits extends from the nucleolus to the cytoplasm and entails hundreds of assembly factors. Despite differences in the pathways of ribosome formation, high-resolution structural information has been available only from fungi. Here we present cryo-electron microscopy structures of late-stage human 40S assembly intermediates, representing one state reconstituted in vitro and five native states that range from nuclear to late cytoplasmic. The earliest particles reveal the position of the biogenesis factor RRP12 and distinct immature rRNA conformations that accompany the formation of the 40S subunit head. Molecular models of the late-acting assembly factors TSR1, RIOK1, RIOK2, ENP1, LTV1, PNO1 and NOB1 provide mechanistic details that underlie their contribution to a sequential 40S subunit assembly. The NOB1 architecture displays an inactive nuclease conformation that requires rearrangement of the PNO1-bound 3' rRNA, thereby coordinating the final rRNA folding steps with site 3 cleavage. | |||||||||||||||
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_4337.map.gz | 19.5 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-4337-v30.xml emd-4337.xml | 48.8 KB 48.8 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_4337_fsc.xml | 12.8 KB | 表示 | FSCデータファイル |
画像 | emd_4337.png | 165.3 KB | ||
その他 | emd_4337_half_map_1.map.gz emd_4337_half_map_2.map.gz | 139.8 MB 139.8 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-4337 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4337 | HTTPS FTP |
-関連構造データ
関連構造データ | 6g18MC 4348C 4349C 4350C 4351C 4352C 4353C 6g4sC 6g4wC 6g51C 6g53C 6g5hC 6g5iC 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 |
-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_4337.map.gz / 形式: CCP4 / 大きさ: 178 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 1.084 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
-ハーフマップ: #1
ファイル | emd_4337_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #2
ファイル | emd_4337_half_map_2.map | ||||||||||||
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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 : Cryo-EM structure of a human pre-40S ribosomal subunit with bound...
+超分子 #1: Cryo-EM structure of a human pre-40S ribosomal subunit with bound...
+分子 #1: pre-18S ribosomal RNA
+分子 #2: 40S ribosomal protein S5
+分子 #3: 40S ribosomal protein S12
+分子 #4: 40S ribosomal protein S15
+分子 #5: 40S ribosomal protein S16
+分子 #6: 40S ribosomal protein S17
+分子 #7: 40S ribosomal protein S18
+分子 #8: 40S ribosomal protein S19
+分子 #9: 40S ribosomal protein S25
+分子 #10: 40S ribosomal protein S28
+分子 #11: Ubiquitin-40S ribosomal protein S27a
+分子 #12: Receptor of activated protein C kinase 1
+分子 #13: 40S ribosomal protein SA
+分子 #14: 40S ribosomal protein S3a
+分子 #15: 40S ribosomal protein S2
+分子 #16: 40S ribosomal protein S4, X isoform
+分子 #17: 40S ribosomal protein S6
+分子 #18: 40S ribosomal protein S7
+分子 #19: 40S ribosomal protein S8
+分子 #20: 40S ribosomal protein S9
+分子 #21: 40S ribosomal protein S11
+分子 #22: 40S ribosomal protein S13
+分子 #23: 40S ribosomal protein S14
+分子 #24: 40S ribosomal protein S21
+分子 #25: 40S ribosomal protein S15a
+分子 #26: 40S ribosomal protein S23
+分子 #27: 40S ribosomal protein S24
+分子 #28: 40S ribosomal protein S27
+分子 #29: 40S ribosomal protein S30
+分子 #30: RNA-binding protein PNO1
+分子 #31: RNA-binding protein NOB1
+分子 #32: Pre-rRNA-processing protein TSR1 homolog
+分子 #33: Bystin
+分子 #34: Serine/threonine-protein kinase RIO2
+分子 #35: Protein LTV1 homolog
+分子 #36: ZINC ION
-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: 7.6 |
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凍結 | 凍結剤: ETHANE |
-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 |
撮影 | フィルム・検出器のモデル: FEI FALCON II (4k x 4k) 平均電子線量: 2.5 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |