+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-35597 | |||||||||
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タイトル | human nuclear pre-60S ribosomal particle - State F' | |||||||||
マップデータ | human nuclear pre-60S ribosomal particle - State F' - post processed | |||||||||
試料 |
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キーワード | GNL2 / nuclear / pre-60S / RIBOSOME (リボソーム) | |||||||||
機能・相同性 | 機能・相同性情報 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 / PeBoW complex / miRNA-mediated post-transcriptional gene silencing / negative regulation of signal transduction by p53 class mediator / eukaryotic 80S initiation complex / miRNA-mediated gene silencing by inhibition of translation / negative regulation of protein neddylation / translation at presynapse / axial mesoderm development / negative regulation of formation of translation preinitiation complex / ribosomal protein import into nucleus / 90S preribosome assembly / blastocyst formation / positive regulation of protein K63-linked deubiquitination / TORC2 complex binding / protein localization to nucleolus / GAIT complex / middle ear morphogenesis / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytoplasmic side of rough endoplasmic reticulum membrane / A band / regulation of reactive oxygen species metabolic process / nuclear-transcribed mRNA catabolic process / regulation of G1 to G0 transition / alpha-beta T cell differentiation / regulation of glycolytic process / 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 / G1 to G0 transition / rRNA metabolic process / maturation of 5.8S rRNA / homeostatic process / positive regulation of dendritic spine development / negative regulation of cell-cell adhesion / lung morphogenesis / negative regulation of DNA replication / ヒドロキシル化 / macrophage chemotaxis / regulation of cyclin-dependent protein serine/threonine kinase activity / Peptide chain elongation / mitotic G2 DNA damage checkpoint signaling / ribosomal large subunit binding / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / rRNA transcription / Formation of a pool of free 40S subunits / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / blastocyst development / preribosome, large subunit precursor / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / protein-RNA complex assembly / protein localization to nucleus / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / GTP hydrolysis and joining of the 60S ribosomal subunit / ribosomal large subunit export from nucleus / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein targeting / cellular response to interleukin-4 / negative regulation of protein-containing complex assembly / ribosomal subunit export from nucleus / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cellular response to actinomycin D / ribonucleoprotein complex binding / 90S preribosome / 小胞体 / MDM2/MDM4 family protein binding / cytosolic ribosome / negative regulation of protein ubiquitination / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / translation initiation factor activity / 着床 / negative regulation of ubiquitin-dependent protein catabolic process / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 骨化 / maturation of LSU-rRNA / negative regulation of cell migration / assembly of large subunit precursor of preribosome / ribosomal large subunit biogenesis 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.0 Å | |||||||||
データ登録者 | Zhang Y / Gao N | |||||||||
資金援助 | 中国, 1件
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引用 | ジャーナル: Cell Res / 年: 2023 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
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_35597.map.gz | 13.1 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-35597-v30.xml emd-35597.xml | 82.3 KB 82.3 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_35597.png | 165.2 KB | ||
Filedesc metadata | emd-35597.cif.gz | 19 KB | ||
その他 | emd_35597_half_map_1.map.gz emd_35597_half_map_2.map.gz | 194.5 MB 194.4 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-35597 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35597 | HTTPS FTP |
-関連構造データ
関連構造データ | 8infMC 8idtC 8idyC 8ie3C 8ineC 8inkC 8ipdC 8ipxC 8ipyC 8ir1C 8ir3C 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) |
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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
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「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_35597.map.gz / 形式: CCP4 / 大きさ: 244.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | human nuclear pre-60S ribosomal particle - State F' - post processed | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.37 Å | ||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-ハーフマップ: human nuclear pre-60S ribosomal particle - State F' - half1
ファイル | emd_35597_half_map_1.map | ||||||||||||
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注釈 | human nuclear pre-60S ribosomal particle - State F' - half1 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: human nuclear pre-60S ribosomal particle - State F' - half2
ファイル | emd_35597_half_map_2.map | ||||||||||||
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注釈 | human nuclear pre-60S ribosomal particle - State F' - half2 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
+全体 : cryo-EM structure of human nuclear pre-60S ribosomal particle - S...
+超分子 #1: cryo-EM structure of human nuclear pre-60S ribosomal particle - S...
+分子 #1: Ribosomal L1 domain-containing protein 1
+分子 #2: Protein SDA1 homolog
+分子 #3: 60S ribosomal protein L10a
+分子 #4: MKI67 FHA domain-interacting nucleolar phosphoprotein
+分子 #5: 60S ribosomal protein L7-like 1
+分子 #7: GTP-binding protein 4
+分子 #9: Eukaryotic translation initiation factor 6
+分子 #10: Probable ribosome biogenesis protein RLP24
+分子 #11: Zinc finger protein 593
+分子 #12: 60S ribosomal protein L3
+分子 #13: 60S ribosomal protein L29
+分子 #14: 60S ribosomal protein L4
+分子 #15: 60S ribosomal protein L30
+分子 #16: 60S ribosomal protein L34
+分子 #17: 60S ribosomal protein L7a
+分子 #18: 60S ribosomal protein L35
+分子 #19: 60S ribosomal protein L9
+分子 #20: 60S ribosomal protein L36
+分子 #21: 60S ribosomal protein L27a
+分子 #22: 60S ribosomal protein L37
+分子 #23: 60S ribosomal protein L11
+分子 #24: 60S ribosomal protein L38
+分子 #25: 60S ribosomal protein L39
+分子 #26: 60S ribosomal protein L13
+分子 #27: 60S ribosomal protein L14
+分子 #28: 60S ribosomal protein L15
+分子 #29: 60S ribosomal protein L13a
+分子 #30: 60S ribosomal protein L36a
+分子 #31: 60S ribosomal protein L37a
+分子 #32: 60S ribosomal protein L17
+分子 #33: 60S ribosomal protein L18
+分子 #34: 60S ribosomal protein L19
+分子 #35: 60S ribosomal protein L18a
+分子 #36: 60S ribosomal protein L21
+分子 #37: 60S ribosomal protein L22
+分子 #38: 60S ribosomal protein L23
+分子 #39: 60S ribosomal protein L23a
+分子 #40: 60S ribosomal protein L26
+分子 #41: 60S ribosomal protein L27
+分子 #42: 60S ribosomal protein L31
+分子 #43: 60S ribosomal protein L32
+分子 #44: 60S ribosomal protein L28
+分子 #45: 60S ribosomal protein L8
+分子 #46: 60S ribosomal protein L35a
+分子 #47: 60S ribosomal protein L6
+分子 #48: 60S ribosomal protein L7
+分子 #49: 60S ribosomal protein L5
+分子 #50: Protein LLP homolog
+分子 #51: G Protein Nucleolar 2
+分子 #52: Translation machinery-associated protein 16
+分子 #53: mRNA turnover protein 4 homolog
+分子 #54: Leydig cell tumor 10 kDa protein homolog
+分子 #55: 60S ribosomal protein L12
+分子 #56: Pescadillo homolog
+分子 #58: Uncharacterized protein C11orf98
+分子 #59: Ribosome biogenesis protein NSA2 homolog
+分子 #60: Ribosome biogenesis protein NOP53
+分子 #6: 28S rRNA
+分子 #8: 5S rRNA
+分子 #57: 5.8S rRNA
+分子 #61: Internal Transcribed Spacer 2
+分子 #62: GUANOSINE-5'-DIPHOSPHATE
+分子 #63: MAGNESIUM ION
+分子 #64: POTASSIUM ION
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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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: 7.5 |
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凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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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: OTHER / 撮影モード: DIFFRACTION回折 / 最大 デフォーカス(公称値): 1.8 µm / 最小 デフォーカス(公称値): 1.2 µm |
撮影 | フィルム・検出器のモデル: GATAN K2 QUANTUM (4k x 4k) 平均電子線量: 1.8 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期モデル | モデルのタイプ: INSILICO MODEL |
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初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.0 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 45905 |