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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: 8ink | ||||||
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タイトル | human nuclear pre-60S ribosomal particle - State D | ||||||
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![]() | RIBOSOME / GNL2 / nuclear / pre-60S | ||||||
機能・相同性 | ![]() inner cell mass cell differentiation / negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / positive regulation of protein localization to chromosome, telomeric region / basal RNA polymerase II transcription machinery binding / negative regulation of collagen binding / hematopoietic stem cell homeostasis / dendrite extension / preribosome binding / lamin filament / regulation of fatty acid biosynthetic process ...inner cell mass cell differentiation / negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / positive regulation of protein localization to chromosome, telomeric region / basal RNA polymerase II transcription machinery binding / negative regulation of collagen binding / hematopoietic stem cell homeostasis / dendrite extension / preribosome binding / lamin filament / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation / positive regulation of protein sumoylation / miRNA-mediated post-transcriptional gene silencing / stem cell division / miRNA-mediated gene silencing by inhibition of translation / eukaryotic 80S initiation complex / negative regulation of protein neddylation / positive regulation of telomere maintenance / translation at presynapse / axial mesoderm development / ribosomal protein import into nucleus / negative regulation of formation of translation preinitiation complex / 90S preribosome assembly / TORC2 complex binding / GAIT complex / middle ear morphogenesis / skeletal system 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 / response to aldosterone / stem cell population maintenance / regulation of cyclin-dependent protein serine/threonine kinase activity / G1 to G0 transition / negative regulation of cell-cell adhesion / homeostatic process / positive regulation of dendritic spine development / maturation of 5.8S rRNA / negative regulation of DNA replication / macrophage chemotaxis / lung morphogenesis / 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 / 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 mitotic cell cycle / protein localization to nucleus / ribosomal large subunit export from nucleus / 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 / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of ubiquitin-dependent protein catabolic process / ribosomal subunit export from nucleus / cellular response to actinomycin D / somitogenesis / cytosolic ribosome / rough endoplasmic reticulum / MDM2/MDM4 family protein binding / Notch signaling pathway / 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 / ossification / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / assembly of large subunit precursor of preribosome / negative regulation of cell migration / innate immune response in mucosa / cytosolic ribosome assembly / regulation of signal transduction by p53 class mediator / ribosomal large subunit biogenesis / kidney development / skeletal system development / ribosomal large subunit assembly / mRNA 3'-UTR binding 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: 3.2 Å | ||||||
![]() | Zhang, Y. / Gao, N. | ||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Visualizing the nucleoplasmic maturation of human pre-60S ribosomal particles. 著者: Yunyang Zhang / Xiaomeng Liang / Sha Luo / Yan Chen / Yu Li / Chengying Ma / Ningning Li / Ning Gao / ![]() 要旨: Eukaryotic ribosome assembly is a highly orchestrated process that involves over two hundred protein factors. After early assembly events on nascent rRNA in the nucleolus, pre-60S particles undergo ...Eukaryotic ribosome assembly is a highly orchestrated process that involves over two hundred protein factors. After early assembly events on nascent rRNA in the nucleolus, pre-60S particles undergo continuous maturation steps in the nucleoplasm, and prepare for nuclear export. Here, we report eleven cryo-EM structures of the nuclear pre-60S particles isolated from human cells through epitope-tagged GNL2, at resolutions of 2.8-4.3 Å. These high-resolution snapshots provide fine details for several major structural remodeling events at a virtual temporal resolution. Two new human nuclear factors, L10K and C11orf98, were also identified. Comparative structural analyses reveal that many assembly factors act as successive place holders to control the timing of factor association/dissociation events. They display multi-phasic binding properties for different domains and generate complex binding inter-dependencies as a means to guide the rRNA maturation process towards its mature conformation. Overall, our data reveal that nuclear assembly of human pre-60S particles is generally hierarchical with short branch pathways, and a few factors display specific roles as rRNA chaperones by confining rRNA helices locally to facilitate their folding, such as the C-terminal domain of SDAD1. | ||||||
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 | ![]() | 3.4 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 | ![]() 35599MC ![]() 8idtC ![]() 8idyC ![]() 8ie3C ![]() 8ineC ![]() 8infC ![]() 8ipdC ![]() 8ipxC ![]() 8ipyC ![]() 8ir1C ![]() 8ir3C 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 ( |
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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
-タンパク質 , 12種, 12分子 N679JruwzW4v
#1: タンパク質 | 分子量: 80005.492 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
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#2: 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) ![]() |
#3: 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) ![]() |
#5: 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) ![]() |
#14: タンパク質 | 分子量: 30136.703 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
#37: タンパク質 | 分子量: 40312.742 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
#38: タンパク質 | 分子量: 62098.242 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: 83796.094 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
#41: 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) ![]() |
#44: タンパク質 | 分子量: 53387.141 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
#46: 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) ![]() |
#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) ![]() |
-RNA鎖 , 3種, 3分子 832
#4: RNA鎖 | 分子量: 50157.676 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
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#51: RNA鎖 | 分子量: 38651.887 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
#53: RNA鎖 | 分子量: 1636466.500 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: NCBI Reference Sequence: NR_146154.1 / 由来: (天然) ![]() |
+60S ribosomal protein ... , 38種, 38分子 ABDEFGHIKLMOPQSUVXZabeghilmnop...
-非ポリマー , 2種, 2分子 ![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MG.gif)
#54: 化合物 | ChemComp-GTP / |
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#55: 化合物 | ChemComp-MG / |
-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: cryo-EM structure of human nuclear pre-60S ribosomal particle - State D タイプ: RIBOSOME / Entity ID: #1-#53 / 由来: NATURAL |
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由来(天然) | 生物種: ![]() |
緩衝液 | pH: 7.5 |
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 |
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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: DIFFRACTION / 最大 デフォーカス(公称値): 1800 nm / 最小 デフォーカス(公称値): 1200 nm |
撮影 | 電子線照射量: 1.8 e/Å2 フィルム・検出器のモデル: GATAN K2 QUANTUM (4k x 4k) |
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解析
EMソフトウェア | 名称: PHENIX / バージョン: 1.19.2_4158: / カテゴリ: モデル精密化 | ||||||||||||||||||||||||
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3次元再構成 | 解像度: 3.2 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 24229 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
拘束条件 |
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