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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 8fld | |||||||||
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タイトル | Human nuclear pre-60S ribosomal subunit (State L1) | |||||||||
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![]() | RIBOSOME / Pre-60S ribosomal subunit / Assembly intermediate / Nucleoprotein complex | |||||||||
機能・相同性 | ![]() protein localization to nucleoplasm / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / regulation of RIG-I signaling pathway / basal RNA polymerase II transcription machinery binding / negative regulation of collagen binding / dendrite extension / preribosome binding / regulation of cellular senescence / lamin filament ...protein localization to nucleoplasm / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / regulation of RIG-I signaling pathway / basal RNA polymerase II transcription machinery binding / negative regulation of collagen binding / dendrite extension / preribosome binding / regulation of cellular senescence / lamin filament / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation / miRNA-mediated post-transcriptional gene silencing / negative regulation of signal transduction by p53 class mediator / PeBoW complex / miRNA-mediated gene silencing by inhibition of translation / eukaryotic 80S initiation complex / negative regulation of protein neddylation / embryonic brain development / translation at presynapse / axial mesoderm development / ribosomal protein import into nucleus / negative regulation of formation of translation preinitiation complex / 90S preribosome assembly / positive regulation of protein K63-linked deubiquitination / blastocyst formation / protein localization to nucleolus / TORC2 complex binding / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / GAIT complex / middle ear morphogenesis / regulation of reactive oxygen species metabolic process / regulation of glycolytic process / A band / cytoplasmic side of rough endoplasmic reticulum membrane / alpha-beta T cell differentiation / regulation of G1 to G0 transition / 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 / negative regulation of ubiquitin protein ligase activity / regulation of aerobic respiration / response to aldosterone / regulation of cyclin-dependent protein serine/threonine kinase activity / rRNA metabolic process / negative regulation of cell-cell adhesion / G1 to G0 transition / positive regulation of dendritic spine development / homeostatic process / maturation of 5.8S rRNA / negative regulation of DNA replication / macrophage chemotaxis / lung morphogenesis / Protein hydroxylation / ribosomal large subunit binding / mitotic G2 DNA damage checkpoint signaling / Peptide chain elongation / Selenocysteine synthesis / rRNA transcription / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / nuclear-transcribed mRNA catabolic process / Eukaryotic Translation Termination / blastocyst development / preribosome, large subunit precursor / ubiquitin ligase inhibitor activity / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein localization to nucleus / condensed nuclear chromosome / 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 / protein-RNA complex assembly / Major pathway of rRNA processing in the nucleolus and cytosol / protein targeting / cellular response to interleukin-4 / negative regulation of protein-containing complex assembly / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ribosomal subunit export from nucleus / negative regulation of ubiquitin-dependent protein catabolic process / ossification / translation regulator activity / cellular response to actinomycin D / ribonucleoprotein complex binding / cytosolic ribosome / rough endoplasmic reticulum / MDM2/MDM4 family protein binding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein ubiquitination / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / translation initiation factor activity / embryo implantation / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / assembly of large subunit precursor of preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) 類似検索 - 分子機能 | |||||||||
生物種 | ![]() | |||||||||
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: 2.58 Å | |||||||||
![]() | Vanden Broeck, A. / Klinge, S. | |||||||||
資金援助 | European Union, ![]()
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![]() | ![]() タイトル: Principles of human pre-60 biogenesis. 著者: Arnaud Vanden Broeck / Sebastian Klinge / ![]() 要旨: During the early stages of human large ribosomal subunit (60) biogenesis, an ensemble of assembly factors establishes and fine-tunes the essential RNA functional centers of pre-60 particles by an ...During the early stages of human large ribosomal subunit (60) biogenesis, an ensemble of assembly factors establishes and fine-tunes the essential RNA functional centers of pre-60 particles by an unknown mechanism. Here, we report a series of cryo-electron microscopy structures of human nucleolar and nuclear pre-60 assembly intermediates at resolutions of 2.5 to 3.2 angstroms. These structures show how protein interaction hubs tether assembly factor complexes to nucleolar particles and how guanosine triphosphatases and adenosine triphosphatase couple irreversible nucleotide hydrolysis steps to the installation of functional centers. Nuclear stages highlight how a conserved RNA-processing complex, the rixosome, couples large-scale RNA conformational changes with pre-ribosomal RNA processing by the RNA degradation machinery. Our ensemble of human pre-60 particles provides a rich foundation with which to elucidate the molecular principles of ribosome formation. | |||||||||
履歴 |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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ダウンロード
PDBx/mmCIF形式 | ![]() | 3.3 MB | 表示 | ![]() |
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PDB形式 | ![]() | 表示 | ![]() | |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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-関連構造データ
関連構造データ | ![]() 29275MC ![]() 8fkpC ![]() 8fkqC ![]() 8fkrC ![]() 8fksC ![]() 8fktC ![]() 8fkuC ![]() 8fkvC ![]() 8fkwC ![]() 8fkxC ![]() 8fkyC ![]() 8fkzC ![]() 8fl0C ![]() 8fl2C ![]() 8fl3C ![]() 8fl4C ![]() 8fl6C ![]() 8fl7C ![]() 8fl9C ![]() 8flaC ![]() 8flbC ![]() 8flcC ![]() 8fleC ![]() 8flfC C: 同じ文献を引用 ( M: このデータのモデリングに利用したマップデータ |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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リンク
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集合体
登録構造単位 | ![]()
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要素
+60S ribosomal protein ... , 40種, 40分子 BEL5L6L7L8L9LALBLCLDLELFLGLHLILJLKLLLMLNLOLPLQLRLSLTLULVLWLX...
-RNA鎖 , 4種, 4分子 L1L2L3L4
#2: RNA鎖 | 分子量: 50463.840 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
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#3: RNA鎖 | 分子量: 376425.312 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
#4: RNA鎖 | 分子量: 1641203.750 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
#5: RNA鎖 | 分子量: 38998.078 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
-タンパク質 , 10種, 10分子 NKNLNPSHSKSLSMSQSRSV
#37: タンパク質 | 分子量: 15268.361 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
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#38: タンパク質 | 分子量: 54498.402 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
#39: タンパク質 | 分子量: 15230.225 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
#47: タンパク質 | 分子量: 34285.309 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
#49: 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) ![]() |
#50: タンパク質 | 分子量: 55089.750 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
#51: タンパク質 | 分子量: 68114.727 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
#52: タンパク質 | 分子量: 27602.535 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
#53: タンパク質 | 分子量: 74107.820 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
#54: タンパク質 | 分子量: 19666.258 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
-非ポリマー , 2種, 93分子 ![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/ZN.gif)
#55: 化合物 | ChemComp-MG / #56: 化合物 | ChemComp-ZN / |
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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 |
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試料調製
構成要素 | 名称: Human nuclear pre-60S ribosomal subunit (State L1) / タイプ: RIBOSOME / Entity ID: #1-#54 / 由来: NATURAL |
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分子量 | 実験値: NO |
由来(天然) | 生物種: ![]() |
緩衝液 | pH: 7.6 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | グリッドの材料: GOLD / グリッドのサイズ: 400 divisions/in. / グリッドのタイプ: Quantifoil R3.5/1 |
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 95 % / 凍結前の試料温度: 283 K 詳細: Four applications with manual blotting before last blotting with the Vitrobot. |
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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: ![]() |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 64000 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): 500 nm |
撮影 | 平均露光時間: 2 sec. / 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: 4 / 実像数: 172699 |
電子光学装置 | エネルギーフィルタースリット幅: 20 eV |
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解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 15679142 | ||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 2.58 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 88174 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | 空間: REAL |