+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-32801 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Cryo-EM structure of a human pre-40S ribosomal subunit - State RRP12-A1 (without CK1) | |||||||||
マップデータ | ||||||||||
試料 |
| |||||||||
キーワード | ribosome biogenesis / 40S ribosome / RIBOSOME | |||||||||
機能・相同性 | 機能・相同性情報 peptidyl-glutamine methylation / regulation of protein localization to nucleolus / rRNA (guanine-N7)-methylation / tRNA methyltransferase activator activity / rRNA (guanine) methyltransferase activity / tRNA modification in the nucleus and cytosol / Methylation / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / trophectodermal cell differentiation / protein methyltransferase activity ...peptidyl-glutamine methylation / regulation of protein localization to nucleolus / rRNA (guanine-N7)-methylation / tRNA methyltransferase activator activity / rRNA (guanine) methyltransferase activity / tRNA modification in the nucleus and cytosol / Methylation / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / trophectodermal cell differentiation / protein methyltransferase activity / positive regulation of rRNA processing / tRNA methylation / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / : / negative regulation of RNA splicing / neural crest cell differentiation / rRNA methylation / Formation of the ternary complex, and subsequently, the 43S complex / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / U3 snoRNA binding / Ribosomal scanning and start codon recognition / negative regulation of ubiquitin protein ligase activity / preribosome, small subunit precursor / Translation initiation complex formation / mammalian oogenesis stage / snoRNA binding / activation-induced cell death of T cells / fibroblast growth factor binding / Protein hydroxylation / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / monocyte chemotaxis / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / negative regulation of respiratory burst involved in inflammatory response / 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 / T cell proliferation involved in immune response / Major pathway of rRNA processing in the nucleolus and cytosol / regulation of translational fidelity / ribosomal small subunit export from nucleus / negative regulation of ubiquitin-dependent protein catabolic process / erythrocyte development / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translation regulator activity / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Nuclear events stimulated by ALK signaling in cancer / positive regulation of cell cycle / cytosolic ribosome / stress granule assembly / Mitotic Prometaphase / rough endoplasmic reticulum / EML4 and NUDC in mitotic spindle formation / Maturation of protein E / Maturation of protein E / gastrulation / ER Quality Control Compartment (ERQC) / MDM2/MDM4 family protein binding / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / transcription initiation-coupled chromatin remodeling / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / translation initiation factor binding / Resolution of Sister Chromatid Cohesion / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy 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: 3.0 Å | |||||||||
データ登録者 | Cheng J / Lau B / Thoms M / Ameismeier M / Berninghausen O / Hurt E / Beckmann R | |||||||||
資金援助 | 1件
| |||||||||
引用 | ジャーナル: Nucleic Acids Res / 年: 2022 タイトル: The nucleoplasmic phase of pre-40S formation prior to nuclear export. 著者: Jingdong Cheng / Benjamin Lau / Matthias Thoms / Michael Ameismeier / Otto Berninghausen / Ed Hurt / Roland Beckmann / 要旨: Biogenesis of the small ribosomal subunit in eukaryotes starts in the nucleolus with the formation of a 90S precursor and ends in the cytoplasm. Here, we elucidate the enigmatic structural ...Biogenesis of the small ribosomal subunit in eukaryotes starts in the nucleolus with the formation of a 90S precursor and ends in the cytoplasm. Here, we elucidate the enigmatic structural transitions of assembly intermediates from human and yeast cells during the nucleoplasmic maturation phase. After dissociation of all 90S factors, the 40S body adopts a close-to-mature conformation, whereas the 3' major domain, later forming the 40S head, remains entirely immature. A first coordination is facilitated by the assembly factors TSR1 and BUD23-TRMT112, followed by re-positioning of RRP12 that is already recruited early to the 90S for further head rearrangements. Eventually, the uS2 cluster, CK1 (Hrr25 in yeast) and the export factor SLX9 associate with the pre-40S to provide export competence. These exemplary findings reveal the evolutionary conserved mechanism of how yeast and humans assemble the 40S ribosomal subunit, but reveal also a few minor differences. | |||||||||
履歴 |
|
-構造の表示
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_32801.map.gz | 106.1 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-32801-v30.xml emd-32801.xml | 49.7 KB 49.7 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_32801_fsc.xml | 12.8 KB | 表示 | FSCデータファイル |
画像 | emd_32801.png | 155.1 KB | ||
Filedesc metadata | emd-32801.cif.gz | 12.2 KB | ||
その他 | emd_32801_additional_1.map.gz emd_32801_additional_2.map.gz | 105.6 MB 89.7 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-32801 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32801 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_32801_validation.pdf.gz | 454.6 KB | 表示 | EMDB検証レポート |
---|---|---|---|---|
文書・詳細版 | emd_32801_full_validation.pdf.gz | 454.2 KB | 表示 | |
XML形式データ | emd_32801_validation.xml.gz | 13.2 KB | 表示 | |
CIF形式データ | emd_32801_validation.cif.gz | 17.8 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32801 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32801 | HTTPS FTP |
-関連構造データ
関連構造データ | 7wtuMC 7wtnC 7wtoC 7wtpC 7wtqC 7wtrC 7wtsC 7wttC 7wtvC 7wtwC 7wtxC 7wtzC 7wu0C 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 | 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 |
---|---|
「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_32801.map.gz / 形式: CCP4 / 大きさ: 178 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ボクセルのサイズ | X=Y=Z: 1.059 Å | ||||||||||||||||||||
密度 |
| ||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
|
-添付データ
-追加マップ: #2
ファイル | emd_32801_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-追加マップ: #1
ファイル | emd_32801_additional_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-試料の構成要素
+全体 : Yeast pre-40S ribosomal subunit
+超分子 #1: Yeast pre-40S ribosomal subunit
+分子 #1: 18S rRNA
+分子 #2: 40S ribosomal protein S17
+分子 #3: 40S ribosomal protein S27
+分子 #4: 40S ribosomal protein S3a
+分子 #5: 40S ribosomal protein S28
+分子 #6: 40S ribosomal protein S4, X isoform
+分子 #7: 40S ribosomal protein S30
+分子 #8: 40S ribosomal protein S5
+分子 #9: 40S ribosomal protein S7
+分子 #10: 40S ribosomal protein S6
+分子 #11: 40S ribosomal protein S25
+分子 #12: 40S ribosomal protein S24
+分子 #13: RNA-binding protein PNO1
+分子 #14: 40S ribosomal protein S23
+分子 #15: Bystin
+分子 #16: 40S ribosomal protein S15a
+分子 #17: Pre-rRNA-processing protein TSR1 homolog
+分子 #18: Protein LTV1 homolog
+分子 #19: 40S ribosomal protein S19
+分子 #20: 40S ribosomal protein S18
+分子 #21: 40S ribosomal protein S16
+分子 #22: 40S ribosomal protein S15
+分子 #23: 40S ribosomal protein S14
+分子 #24: 40S ribosomal protein S13
+分子 #25: 40S ribosomal protein S11
+分子 #26: 40S ribosomal protein S9
+分子 #27: 40S ribosomal protein S8
+分子 #28: Multifunctional methyltransferase subunit TRM112-like protein
+分子 #29: Probable 18S rRNA (guanine-N(7))-methyltransferase
+分子 #30: RRP12-like protein
+分子 #31: 40S ribosomal protein S12
+分子 #32: Ubiquitin-40S ribosomal protein S27a
+分子 #33: Ribosome biogenesis protein SLX9 homolog
+分子 #34: S-ADENOSYL-L-HOMOCYSTEINE
+分子 #35: ZINC ION
-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: 7.4 |
---|---|
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: GATAN K2 SUMMIT (4k x 4k) 検出モード: COUNTING / 平均電子線量: 44.0 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 / 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): 0.8 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |