+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-32800 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Cryo-EM structure of a human pre-40S ribosomal subunit - State RRP12-A1 (with CK1) | |||||||||
マップデータ | ||||||||||
試料 |
| |||||||||
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 / Activation of SMO / tRNA modification in the nucleus and cytosol / intermediate filament cytoskeleton organization / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of NLRP3 inflammasome complex assembly ...peptidyl-glutamine methylation / regulation of protein localization to nucleolus / rRNA (guanine-N7)-methylation / tRNA methyltransferase activator activity / rRNA (guanine) methyltransferase activity / Activation of SMO / tRNA modification in the nucleus and cytosol / intermediate filament cytoskeleton organization / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of NLRP3 inflammasome complex assembly / メチル化 / trophectodermal cell differentiation / protein methyltransferase activity / tRNA methylation / positive regulation of rRNA processing / cellular response to nutrient / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / : / beta-catenin destruction complex / negative regulation of RNA splicing / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / neural crest cell differentiation / rRNA methylation / Formation of the ternary complex, and subsequently, the 43S complex / Disassembly of the destruction complex and recruitment of AXIN to the membrane / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / Maturation of nucleoprotein / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / U3 snoRNA binding / Ribosomal scanning and start codon recognition / negative regulation of ubiquitin protein ligase activity / preribosome, small subunit precursor / positive regulation of Rho protein signal transduction / Translation initiation complex formation / snoRNA binding / fibroblast growth factor binding / ヒドロキシル化 / Golgi organization / MTOR / 90S preribosome / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Selenocysteine synthesis / monocyte chemotaxis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / ribosomal small subunit export from nucleus / 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 / L13a-mediated translational silencing of Ceruloplasmin expression / 小胞体 / regulation of translational fidelity / Major pathway of rRNA processing in the nucleolus and cytosol / MDM2/MDM4 family protein binding / 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 / positive regulation of cell cycle / translation initiation factor binding / stress granule assembly / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / Maturation of protein E / negative regulation of ubiquitin-dependent protein catabolic process / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / translational initiation / 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 / グリコーゲン合成 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / Resolution of Sister Chromatid Cohesion 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: 3.1 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_32800.map.gz | 106.2 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-32800-v30.xml emd-32800.xml | 50 KB 50 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_32800_fsc.xml | 12.7 KB | 表示 | FSCデータファイル |
画像 | emd_32800.png | 163.9 KB | ||
その他 | emd_32800_additional_1.map.gz emd_32800_additional_2.map.gz emd_32800_additional_3.map.gz | 107.8 MB 107.8 MB 116.7 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-32800 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32800 | HTTPS FTP |
-関連構造データ
関連構造データ | 7wttMC 7wtnC 7wtoC 7wtpC 7wtqC 7wtrC 7wtsC 7wtuC 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_32800.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: #3
ファイル | emd_32800_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-追加マップ: #2
ファイル | emd_32800_additional_2.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_32800_additional_3.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: Casein kinase I isoform alpha
+分子 #34: Ribosome biogenesis protein SLX9 homolog
+分子 #35: S-ADENOSYL-L-HOMOCYSTEINE
+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 |
---|---|
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 |
---|---|
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): 2.5 µm / 最小 デフォーカス(公称値): 0.8 µm |
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 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |