+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 9gmo | |||||||||
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タイトル | eIF6-bound pre-60S large ribosomal subunit incorporating mutant uL16 | |||||||||
要素 |
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キーワード | RIBOSOME / Complex / pre-60S / uL16 | |||||||||
機能・相同性 | 機能・相同性情報 preribosome binding / lamin filament / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation / miRNA-mediated post-transcriptional gene silencing / miRNA-mediated gene silencing by inhibition of translation / eukaryotic 80S initiation complex / negative regulation of protein neddylation / translation at presynapse / axial mesoderm development ...preribosome binding / lamin filament / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation / miRNA-mediated post-transcriptional gene silencing / miRNA-mediated gene silencing by inhibition of translation / eukaryotic 80S initiation complex / negative regulation of protein neddylation / translation at presynapse / axial mesoderm development / ribosomal protein import into nucleus / embryonic brain development / negative regulation of formation of translation preinitiation complex / 90S preribosome assembly / positive regulation of kinase activity / GAIT complex / middle ear morphogenesis / regulation of glycolytic process / regulation of reactive oxygen species metabolic process / A band / alpha-beta T cell differentiation / cytoplasmic side of rough endoplasmic reticulum membrane / regulation of G1 to G0 transition / exit from mitosis / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / optic nerve development / negative regulation of ubiquitin protein ligase activity / intrinsic apoptotic signaling pathway in response to oxidative stress / response to aldosterone / retinal ganglion cell axon guidance / homeostatic process / G1 to G0 transition / maturation of 5.8S rRNA / lung morphogenesis / macrophage chemotaxis / Protein hydroxylation / ribosomal large subunit binding / Peptide chain elongation / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / preribosome, large subunit precursor / blastocyst development / Eukaryotic Translation Termination / ubiquitin ligase inhibitor activity / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / protein localization to nucleus / 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 / Major pathway of rRNA processing in the nucleolus and cytosol / protein-RNA complex assembly / cellular response to interleukin-4 / protein targeting / ribosomal subunit export from nucleus / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cellular response to actinomycin D / negative regulation of ubiquitin-dependent protein catabolic process / translation regulator activity / cytosolic ribosome / rough endoplasmic reticulum / MDM2/MDM4 family protein binding / Maturation of protein E / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / 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 / Glycogen synthesis / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Endosomal Sorting Complex Required For Transport (ESCRT) / TICAM1,TRAF6-dependent induction of TAK1 complex / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of FZD by ubiquitination / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / p75NTR recruits signalling complexes / APC/C:Cdc20 mediated degradation of Cyclin B / embryo implantation / translation initiation factor activity / maturation of LSU-rRNA / Downregulation of ERBB4 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling 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: 2.59 Å | |||||||||
データ登録者 | Bothe, A. / Ban, N. / Kostova, K. | |||||||||
資金援助 | スイス, 2件
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引用 | ジャーナル: bioRxiv / 年: 2024 タイトル: ZNF574 is a Quality Control Factor For Defective Ribosome Biogenesis Intermediates. 著者: Jared Akers / Adrian Bothe / Hanna Suh / Carmen Jung / Zachary Stolp / Tanushree Ghosh / Liewei Yan / Yuming Wang / Tarabryn Grismer / Andreas Reyes / Tianyi Hu / Shouling Xu / Nenad Ban / Kamena Kostova 要旨: Eukaryotic ribosome assembly is an intricate process that involves four ribosomal RNAs, 80 ribosomal proteins, and over 200 biogenesis factors that take part in numerous interdependent steps. This ...Eukaryotic ribosome assembly is an intricate process that involves four ribosomal RNAs, 80 ribosomal proteins, and over 200 biogenesis factors that take part in numerous interdependent steps. This complexity creates a large genetic space in which pathogenic mutations can occur. Dead-end ribosome intermediates that result from biogenesis errors are rapidly degraded, affirming the existence of quality control pathway(s) that monitor ribosome assembly. However, the factors that differentiate between on-path and dead-end intermediates are unknown. We engineered a system to perturb ribosome assembly in human cells and discovered that faulty ribosomes are degraded via the ubiquitin proteasome system. We identified ZNF574 as a key component of a novel quality control pathway, which we term the Ribosome Assembly Surveillance Pathway (RASP). Loss of ZNF574 results in the accumulation of faulty biogenesis intermediates that interfere with global ribosome production, further emphasizing the role of RASP in protein homeostasis and cellular health. | |||||||||
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 | 9gmo.cif.gz | 4.1 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb9gmo.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 9gmo.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 | 9gmo_validation.pdf.gz | 1.7 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 9gmo_full_validation.pdf.gz | 1.8 MB | 表示 | |
XML形式データ | 9gmo_validation.xml.gz | 223.5 KB | 表示 | |
CIF形式データ | 9gmo_validation.cif.gz | 368.6 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/gm/9gmo ftp://data.pdbj.org/pub/pdb/validation_reports/gm/9gmo | HTTPS FTP |
-関連構造データ
関連構造データ | 51452MC 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 , 3種, 3分子 ABC
#1: RNA鎖 | 分子量: 1639262.250 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) |
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#2: RNA鎖 | 分子量: 38346.707 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: GenBank: 23898 |
#3: RNA鎖 | 分子量: 50463.840 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: GenBank: 555853 |
+60S ribosomal protein ... , 36種, 36分子 DEFGIJKLMNOPQRTUVWXYZabcdefijk...
-Large ribosomal subunit protein ... , 4種, 4分子 HSmp
#8: タンパク質 | 分子量: 32810.176 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q02878 |
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#19: タンパク質 | 分子量: 17303.363 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P61254 |
#39: タンパク質 | 分子量: 29290.973 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P18124 |
#42: タンパク質 | 分子量: 23610.838 Da / 分子数: 1 / 由来タイプ: 天然 詳細: residues 102-111 (wild type numbering) are not present in this variant 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P27635 |
-タンパク質 , 3種, 3分子 gh0
#33: タンパク質 | 分子量: 14758.394 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P62987 |
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#34: タンパク質 | 分子量: 26620.010 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P56537 |
#46: タンパク質 | 分子量: 54357.090 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q969S3 |
-非ポリマー , 7種, 396分子
#47: 化合物 | ChemComp-MG / #48: 化合物 | ChemComp-K / #49: 化合物 | #50: 化合物 | ChemComp-GTP / | #51: 化合物 | ChemComp-EPE / | #52: 化合物 | ChemComp-ZN / #53: 水 | ChemComp-HOH / | |
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-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: pre-60S-eIF6 complex incorporating uL16 protein with an internal deletion タイプ: RIBOSOME / Entity ID: #1-#46 / 由来: NATURAL |
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分子量 | 実験値: NO |
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-PROPANE / 湿度: 100 % / 凍結前の試料温度: 277.15 K |
-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 / 倍率(公称値): 81000 X / 最大 デフォーカス(公称値): 2500 nm / 最小 デフォーカス(公称値): 1000 nm |
撮影 | 電子線照射量: 60 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 撮影したグリッド数: 1 / 実像数: 6360 |
-解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3次元再構成 | 解像度: 2.59 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 193000 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
原子モデル構築 | 空間: REAL | ||||||||||||||||||||||||
原子モデル構築 | PDB-ID: 8a3d Accession code: 8a3d / Source name: PDB / タイプ: experimental model | ||||||||||||||||||||||||
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: 113.06 Å2 | ||||||||||||||||||||||||
拘束条件 |
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