+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-4351 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
タイトル | Cryo-EM structure of a late human pre-40S ribosomal subunit - State E | |||||||||||||||
マップデータ | ||||||||||||||||
試料 |
| |||||||||||||||
キーワード | 40S / pre-40S / ribosome biogenesis / RIBOSOME | |||||||||||||||
機能・相同性 | 機能・相同性情報 endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / protein tyrosine kinase inhibitor activity / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway ...endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / protein tyrosine kinase inhibitor activity / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / positive regulation of endodeoxyribonuclease activity / TNFR1-mediated ceramide production / negative regulation of DNA repair / negative regulation of RNA splicing / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / supercoiled DNA binding / neural crest cell differentiation / oxidized purine DNA binding / NF-kappaB complex / ubiquitin-like protein conjugating enzyme binding / negative regulation of phagocytosis / regulation of establishment of cell polarity / positive regulation of ubiquitin-protein transferase activity / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / U3 snoRNA binding / Formation of the ternary complex, and subsequently, the 43S complex / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / pigmentation / preribosome, small subunit precursor / 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 / positive regulation of mitochondrial depolarization / mammalian oogenesis stage / activation-induced cell death of T cells / positive regulation of T cell receptor signaling pathway / negative regulation of Wnt signaling pathway / fibroblast growth factor binding / iron-sulfur cluster binding / monocyte chemotaxis / positive regulation of activated T cell proliferation / Protein hydroxylation / regulation of cell division / negative regulation of peptidyl-serine phosphorylation / 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 / cysteine-type endopeptidase activator activity involved in apoptotic process / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / phagocytic cup / Eukaryotic Translation Termination / ubiquitin ligase inhibitor activity / negative regulation of respiratory burst involved in inflammatory response / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / T cell proliferation involved in immune response / regulation of translational fidelity / Major pathway of rRNA processing in the nucleolus and cytosol / spindle assembly / erythrocyte development / Protein methylation / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of ubiquitin-dependent protein catabolic process / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Nuclear events stimulated by ALK signaling in cancer / ribosomal small subunit export from nucleus / positive regulation of cell cycle / translation regulator activity / signaling adaptor activity / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of smoothened signaling pathway / stress granule assembly / Mitotic Prometaphase / laminin binding / antiviral innate immune response / EML4 and NUDC in mitotic spindle formation / cytosolic ribosome / rough endoplasmic reticulum / 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) / positive regulation of JUN kinase activity / gastrulation 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: 4.5 Å | |||||||||||||||
データ登録者 | Ameismeier M / Cheng J | |||||||||||||||
資金援助 | ドイツ, 4件
| |||||||||||||||
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 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
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_4351.map.gz | 15.9 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-4351-v30.xml emd-4351.xml | 48.2 KB 48.2 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_4351_fsc.xml | 12.8 KB | 表示 | FSCデータファイル |
画像 | emd_4351.png | 150.1 KB | ||
Filedesc metadata | emd-4351.cif.gz | 11.6 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-4351 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4351 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_4351_validation.pdf.gz | 256.8 KB | 表示 | EMDB検証レポート |
---|---|---|---|---|
文書・詳細版 | emd_4351_full_validation.pdf.gz | 255.9 KB | 表示 | |
XML形式データ | emd_4351_validation.xml.gz | 13.2 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4351 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4351 | HTTPS FTP |
-関連構造データ
関連構造データ | 6g53MC 4337C 4348C 4349C 4350C 4352C 4353C 6g18C 6g4sC 6g4wC 6g51C 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) |
---|---|
類似構造データ |
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
---|---|
「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_4351.map.gz / 形式: CCP4 / 大きさ: 178 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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: 1.084 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
|
-添付データ
-試料の構成要素
+全体 : Cryo-EM structure of a late human pre-40S ribosomal subunit - State E
+超分子 #1: Cryo-EM structure of a late human pre-40S ribosomal subunit - State E
+分子 #1: 18S ribosomal RNA
+分子 #2: 40S ribosomal protein S17
+分子 #3: 40S ribosomal protein SA
+分子 #4: 40S ribosomal protein S3a
+分子 #5: 40S ribosomal protein S2
+分子 #6: 40S ribosomal protein S4, X isoform
+分子 #7: 40S ribosomal protein S6
+分子 #8: 40S ribosomal protein S7
+分子 #9: 40S ribosomal protein S8
+分子 #10: 40S ribosomal protein S9
+分子 #11: 40S ribosomal protein S11
+分子 #12: 40S ribosomal protein S13
+分子 #13: 40S ribosomal protein S14
+分子 #14: 40S ribosomal protein S21
+分子 #15: 40S ribosomal protein S15a
+分子 #16: 40S ribosomal protein S23
+分子 #17: 40S ribosomal protein S24
+分子 #18: 40S ribosomal protein S27
+分子 #19: 40S ribosomal protein S30
+分子 #20: RNA-binding protein PNO1
+分子 #21: RNA-binding protein NOB1
+分子 #22: Pre-rRNA-processing protein TSR1 homolog
+分子 #23: Protein LTV1 homolog
+分子 #24: 40S ribosomal protein S29
+分子 #25: 40S ribosomal protein S3
+分子 #26: 40S ribosomal protein S5
+分子 #27: 40S ribosomal protein S10
+分子 #28: 40S ribosomal protein S12
+分子 #29: 40S ribosomal protein S15
+分子 #30: 40S ribosomal protein S16
+分子 #31: 40S ribosomal protein S18
+分子 #32: 40S ribosomal protein S19
+分子 #33: 40S ribosomal protein S20
+分子 #34: 40S ribosomal protein S25
+分子 #35: 40S ribosomal protein S28
+分子 #36: Ubiquitin-40S ribosomal protein S27a
+分子 #37: Receptor of activated protein C kinase 1
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
---|---|
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 |
---|---|
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
---|---|
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 |
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 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |