+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-29273 | |||||||||
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タイトル | Human nuclear pre-60S ribosomal subunit (State K2) - Composite map | |||||||||
マップデータ | Human nuclear pre-60S ribosomal subunit (State K2) | |||||||||
試料 |
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キーワード | Pre-60S ribosomal subunit / Assembly intermediate / Ribosome / Nucleoprotein complex | |||||||||
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 / lamin filament / regulation of fatty acid biosynthetic process ...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 / 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 / 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 / negative regulation of formation of translation preinitiation complex / 90S preribosome assembly / blastocyst formation / positive regulation of protein K63-linked deubiquitination / 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 glycolytic process / maturation of 5.8S rRNA / A band / regulation of reactive oxygen species metabolic process / alpha-beta T cell differentiation / cytoplasmic side of rough endoplasmic reticulum membrane / 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 / negative regulation of cell-cell adhesion / positive regulation of dendritic spine development / homeostatic process / rRNA metabolic process / G1 to G0 transition / negative regulation of DNA replication / macrophage chemotaxis / lung morphogenesis / Protein hydroxylation / mitotic G2 DNA damage checkpoint signaling / ribosomal large subunit binding / Peptide chain elongation / rRNA transcription / preribosome, large subunit precursor / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / nuclear-transcribed mRNA catabolic process / Formation of a pool of free 40S subunits / blastocyst development / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / protein localization to nucleus / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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 targeting / negative regulation of protein-containing complex assembly / protein-RNA complex assembly / cellular response to interleukin-4 / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cellular response to actinomycin D / negative regulation of ubiquitin-dependent protein catabolic process / ribonucleoprotein complex binding / ribosomal subunit export from nucleus / rough endoplasmic reticulum / MDM2/MDM4 family protein binding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein ubiquitination / maturation of LSU-rRNA / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / cytosolic ribosome / embryo implantation / translation initiation factor activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ossification / assembly of large subunit precursor of preribosome / ribosomal large subunit biogenesis / cytosolic ribosome assembly / negative regulation of cell migration / regulation of signal transduction by p53 class mediator / innate immune response in mucosa 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) / human (ヒト) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.55 Å | |||||||||
データ登録者 | Vanden Broeck A / Klinge S | |||||||||
資金援助 | European Union, 米国, 2件
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引用 | ジャーナル: Science / 年: 2023 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
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_29273.map.gz | 137.5 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-29273-v30.xml emd-29273.xml | 78.6 KB 78.6 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_29273_fsc.xml | 15.8 KB | 表示 | FSCデータファイル |
画像 | emd_29273.png | 159.5 KB | ||
マスクデータ | emd_29273_msk_1.map | 421.9 MB | マスクマップ | |
その他 | emd_29273_half_map_1.map.gz emd_29273_half_map_2.map.gz | 391.1 MB 391.1 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-29273 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29273 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_29273_validation.pdf.gz | 1.2 MB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_29273_full_validation.pdf.gz | 1.2 MB | 表示 | |
XML形式データ | emd_29273_validation.xml.gz | 24.9 KB | 表示 | |
CIF形式データ | emd_29273_validation.cif.gz | 32.6 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29273 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29273 | HTTPS FTP |
-関連構造データ
関連構造データ | 8flbMC 8fkpC 8fkqC 8fkrC 8fksC 8fktC 8fkuC 8fkvC 8fkwC 8fkxC 8fkyC 8fkzC 8fl0C 8fl2C 8fl3C 8fl4C 8fl6C 8fl7C 8fl9C 8flaC 8flcC 8fldC 8fleC 8flfC C: 同じ文献を引用 (文献) M: このマップから作成された原子モデル |
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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_29273.map.gz / 形式: CCP4 / 大きさ: 421.9 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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注釈 | Human nuclear pre-60S ribosomal subunit (State K2) | ||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.072 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
-マスク #1
ファイル | emd_29273_msk_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half Map 1
ファイル | emd_29273_half_map_1.map | ||||||||||||
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注釈 | Half Map 1 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half Map 2
ファイル | emd_29273_half_map_2.map | ||||||||||||
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注釈 | Half Map 2 | ||||||||||||
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 : Human nuclear pre-60S ribosomal subunit (State K2)
+超分子 #1: Human nuclear pre-60S ribosomal subunit (State K2)
+分子 #1: 60S ribosomal protein L12
+分子 #5: 60S ribosomal protein L11
+分子 #6: 60S ribosomal protein L13
+分子 #7: 60S ribosomal protein L13a
+分子 #8: 60S ribosomal protein L14
+分子 #9: 60S ribosomal protein L15
+分子 #10: 60S ribosomal protein L17
+分子 #11: 60S ribosomal protein L18
+分子 #12: 60S ribosomal protein L18a
+分子 #13: 60S ribosomal protein L19
+分子 #14: 60S ribosomal protein L21
+分子 #15: 60S ribosomal protein L22
+分子 #16: 60S ribosomal protein L23
+分子 #17: 60S ribosomal protein L23a
+分子 #18: 60S ribosomal protein L26
+分子 #19: 60S ribosomal protein L27
+分子 #20: 60S ribosomal protein L27a
+分子 #21: 60S ribosomal protein L28
+分子 #22: 60S ribosomal protein L29
+分子 #23: 60S ribosomal protein L3
+分子 #24: 60S ribosomal protein L30
+分子 #25: 60S ribosomal protein L31
+分子 #26: 60S ribosomal protein L32
+分子 #27: 60S ribosomal protein L34
+分子 #28: 60S ribosomal protein L35
+分子 #29: 60S ribosomal protein L35a
+分子 #30: 60S ribosomal protein L36
+分子 #31: 60S ribosomal protein L36a
+分子 #32: 60S ribosomal protein L37
+分子 #33: 60S ribosomal protein L37a
+分子 #34: 60S ribosomal protein L38
+分子 #35: 60S ribosomal protein L39
+分子 #36: Protein LLP homolog
+分子 #37: Ribosome biogenesis protein NOP53
+分子 #38: Zinc finger protein 593
+分子 #39: Translation machinery-associated protein 16
+分子 #40: 60S ribosomal protein L4
+分子 #41: 60S ribosomal protein L5
+分子 #42: 60S ribosomal protein L6
+分子 #43: 60S ribosomal protein L7
+分子 #44: 60S ribosomal protein L7a
+分子 #45: 60S ribosomal protein L8
+分子 #46: 60S ribosomal protein L9
+分子 #47: MKI67 FHA domain-interacting nucleolar phosphoprotein
+分子 #48: 60S ribosomal protein L7-like 1
+分子 #49: Eukaryotic translation initiation factor 6
+分子 #50: Pescadillo homolog
+分子 #51: mRNA turnover protein 4 homolog
+分子 #52: GTP-binding protein 4
+分子 #53: Probable ribosome biogenesis protein RLP24
+分子 #54: Leydig cell tumor 10 kDa protein homolog
+分子 #2: 5.8S rRNA
+分子 #3: 28S rRNA
+分子 #4: 5S rRNA
+分子 #55: MAGNESIUM ION
+分子 #56: ZINC ION
+分子 #57: GUANOSINE-5'-DIPHOSPHATE
+分子 #58: 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: 7.6 |
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グリッド | モデル: Quantifoil R3.5/1 / 材質: GOLD / メッシュ: 400 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: CONTINUOUS / 支持フィルム - Film thickness: 2 / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 30 sec. |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 95 % / チャンバー内温度: 283 K / 装置: FEI VITROBOT MARK IV 詳細: Four applications with manual blotting before last blotting with the vitrobot.. |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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特殊光学系 | エネルギーフィルター - スリット幅: 20 eV |
撮影 | 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 / 平均露光時間: 2.0 sec. / 平均電子線量: 60.0 e/Å2 |
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: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2.5 µm / 最小 デフォーカス(公称値): 0.5 µm / 倍率(公称値): 64000 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
+画像解析
-原子モデル構築 1
精密化 | 空間: REAL |
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得られたモデル | PDB-8flb: |