+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7wtt | ||||||
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タイトル | Cryo-EM structure of a human pre-40S ribosomal subunit - State RRP12-A1 (with CK1) | ||||||
要素 |
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キーワード | RIBOSOME / ribosome biogenesis / 40S 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 / Activation of SMO / intermediate filament cytoskeleton organization / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of NLRP3 inflammasome complex assembly / tRNA modification in the nucleus and cytosol ...peptidyl-glutamine methylation / regulation of protein localization to nucleolus / rRNA (guanine-N7)-methylation / tRNA methyltransferase activator activity / rRNA (guanine) methyltransferase activity / Activation of SMO / intermediate filament cytoskeleton organization / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of NLRP3 inflammasome complex assembly / tRNA modification in the nucleus and cytosol / Methylation / trophectodermal cell differentiation / protein methyltransferase activity / tRNA methylation / positive regulation of rRNA processing / cellular response to nutrient / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / positive regulation of respiratory burst involved in inflammatory response / beta-catenin destruction complex / nucleolus organization / 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 / negative regulation of RNA splicing / rRNA methylation / neural crest cell differentiation / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Maturation of nucleoprotein / 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 / preribosome, small subunit precursor / positive regulation of Rho protein signal transduction / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / snoRNA binding / Translation initiation complex formation / mammalian oogenesis stage / activation-induced cell death of T cells / fibroblast growth factor binding / monocyte chemotaxis / Golgi organization / Protein hydroxylation / 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 / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / 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 / 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 / 90S preribosome / T cell proliferation involved in immune response / regulation of translational fidelity / Major pathway of rRNA processing in the nucleolus and cytosol / erythrocyte development / 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 / stress granule assembly / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / cytosolic ribosome / rough endoplasmic reticulum / gastrulation / MDM2/MDM4 family protein binding / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Prevention of phagosomal-lysosomal fusion / translation initiation factor binding / Glycogen synthesis / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | 電子顕微鏡法 / 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
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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 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 7wtt.cif.gz | 1.9 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7wtt.ent.gz | 1.4 MB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7wtt.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 7wtt_validation.pdf.gz | 1.1 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 7wtt_full_validation.pdf.gz | 1.1 MB | 表示 | |
XML形式データ | 7wtt_validation.xml.gz | 163.3 KB | 表示 | |
CIF形式データ | 7wtt_validation.cif.gz | 284.8 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/wt/7wtt ftp://data.pdbj.org/pub/pdb/validation_reports/wt/7wtt | HTTPS FTP |
-関連構造データ
関連構造データ | 32800MC 7wtnC 7wtoC 7wtpC 7wtqC 7wtrC 7wtsC 7wtuC 7wtvC 7wtwC 7wtxC 7wtzC 7wu0C M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 (文献) |
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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
-集合体
登録構造単位 |
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1 |
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-要素
-RNA鎖 , 1種, 1分子 2
#1: RNA鎖 | 分子量: 604117.750 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) |
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+40S ribosomal protein ... , 23種, 23分子 RbBcEeFHGZYXWTSQPONLJIM
-タンパク質 , 10種, 10分子 xwutrqKfaz
#13: タンパク質 | 分子量: 27970.355 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q9NRX1 |
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#15: タンパク質 | 分子量: 49673.258 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q13895 |
#17: タンパク質 | 分子量: 91951.188 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q2NL82 |
#18: タンパク質 | 分子量: 54935.891 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q96GA3 |
#28: タンパク質 | 分子量: 14215.359 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q9UI30 |
#29: タンパク質 | 分子量: 31925.428 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) 参照: UniProt: O43709, 転移酵素; 一炭素原子の基を移すもの; メチル基を移すもの |
#30: タンパク質 | 分子量: 143916.516 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q5JTH9 |
#32: タンパク質 | 分子量: 18004.041 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P62979 |
#33: タンパク質 | 分子量: 38944.750 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) 参照: UniProt: P48729, non-specific serine/threonine protein kinase |
#34: タンパク質 | 分子量: 25503.346 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q9NSI2 |
-非ポリマー , 2種, 2分子
#35: 化合物 | ChemComp-SAH / |
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#36: 化合物 | ChemComp-ZN / |
-詳細
研究の焦点であるリガンドがあるか | N |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: Yeast pre-40S ribosomal subunit / タイプ: RIBOSOME / Entity ID: #1-#34 / 由来: NATURAL |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
緩衝液 | pH: 7.4 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 凍結剤: ETHANE |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2500 nm / 最小 デフォーカス(公称値): 800 nm |
撮影 | 電子線照射量: 44 e/Å2 / 検出モード: COUNTING フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) |
-解析
ソフトウェア |
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CTF補正 | 詳細: Relion / タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3次元再構成 | 解像度: 3.1 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 103616 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
精密化 | 交差検証法: NONE 立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 14.85 Å2 | ||||||||||||||||||||||||
拘束条件 |
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