+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-0964 | |||||||||
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タイトル | Cryo-EM structure of a pre-60S ribosomal subunit - state preA | |||||||||
マップデータ | Cryo-em structure of a human pre-60S ribosomal subunit state - preA | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / 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 / miRNA-mediated post-transcriptional gene silencing / eukaryotic 80S initiation complex ...negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / 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 / miRNA-mediated post-transcriptional gene silencing / eukaryotic 80S initiation complex / negative regulation of protein neddylation / miRNA-mediated gene silencing by inhibition of translation / translation at presynapse / axial mesoderm development / regulation of G1 to G0 transition / negative regulation of formation of translation preinitiation complex / ribosomal protein import into nucleus / 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 / 90S preribosome assembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / TORC2 complex binding / GAIT complex / G1 to G0 transition / middle ear morphogenesis / cytoplasmic side of rough endoplasmic reticulum membrane / A band / regulation of reactive oxygen species metabolic process / positive regulation of signal transduction by p53 class mediator / alpha-beta T cell differentiation / ubiquitin ligase inhibitor activity / regulation of glycolytic process / negative regulation of ubiquitin protein ligase activity / response to aldosterone / maturation of 5.8S rRNA / homeostatic process / positive regulation of dendritic spine development / lung morphogenesis / macrophage chemotaxis / negative regulation of DNA replication / negative regulation of cell-cell adhesion / ribosomal subunit export from nucleus / ヒドロキシル化 / regulation of cyclin-dependent protein serine/threonine kinase activity / Peptide chain elongation / ribosomal large subunit binding / Selenocysteine synthesis / protein-RNA complex assembly / Formation of a pool of free 40S subunits / 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 localization to nucleus / cellular response to actinomycin D / 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 / L13a-mediated translational silencing of Ceruloplasmin expression / protein targeting / Major pathway of rRNA processing in the nucleolus and cytosol / 小胞体 / MDM2/MDM4 family protein binding / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / negative regulation of ubiquitin-dependent protein catabolic process / ribosomal large subunit biogenesis / negative regulation of protein ubiquitination / 着床 / cellular response to interleukin-4 / translation initiation factor activity / 骨化 / assembly of large subunit precursor of preribosome / cytosolic ribosome / negative regulation of cell migration / cytosolic ribosome assembly / positive regulation of translation / innate immune response in mucosa / regulation of signal transduction by p53 class mediator / skeletal system development / mRNA 3'-UTR binding / sensory perception of sound / response to insulin / cellular response to gamma radiation / 骨 / mRNA 5'-UTR binding / ribosomal large subunit assembly / transcription coactivator binding / cytoplasmic ribonucleoprotein granule / osteoblast differentiation / rRNA processing / Regulation of expression of SLITs and ROBOs / cellular response to type II interferon / cellular response to UV / antimicrobial humoral immune response mediated by antimicrobial peptide 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: 3.23 Å | |||||||||
データ登録者 | Liang X / Zuo M / Zhang Y / Li N / Ma C / Dong M / Gao N | |||||||||
資金援助 | 中国, 1件
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引用 | ジャーナル: Nat Commun / 年: 2020 タイトル: Structural snapshots of human pre-60S ribosomal particles before and after nuclear export. 著者: Xiaomeng Liang / Mei-Qing Zuo / Yunyang Zhang / Ningning Li / Chengying Ma / Meng-Qiu Dong / Ning Gao / 要旨: Ribosome biogenesis is an elaborate and energetically expensive program that involve two hundred protein factors in eukaryotes. Nuclear export of pre-ribosomal particles is one central step which ...Ribosome biogenesis is an elaborate and energetically expensive program that involve two hundred protein factors in eukaryotes. Nuclear export of pre-ribosomal particles is one central step which also serves as an internal structural checkpoint to ensure the proper completion of nuclear assembly events. Here we present four structures of human pre-60S particles isolated through a nuclear export factor NMD3, representing assembly stages immediately before and after nuclear export. These structures reveal locations of a dozen of human factors, including an uncharacterized factor TMA16 localized between the 5S RNA and the P0 stalk. Comparison of these structures shows a progressive maturation for the functional regions, such as peptidyl transferase centre and peptide exit tunnel, and illustrate a sequence of factor-assisted rRNA maturation events. These data facilitate our understanding of the global conservation of ribosome assembly in eukaryotes and species-specific features of human assembly factors. | |||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_0964.map.gz | 38.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-0964-v30.xml emd-0964.xml | 58.8 KB 58.8 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_0964.png | 87.7 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-0964 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0964 | HTTPS FTP |
-関連構造データ
-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_0964.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 | Cryo-em structure of a human pre-60S ribosomal subunit state - preA | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.058 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-試料の構成要素
+全体 : Cryo-EM structure of a human pre-60S ribosomal subunit state - preA
+超分子 #1: Cryo-EM structure of a human pre-60S ribosomal subunit state - preA
+分子 #1: Nucleolar GTP-binding protein 2
+分子 #3: Nucleolar GTP-binding protein 1
+分子 #5: Eukaryotic translation initiation factor 6
+分子 #6: Probable ribosome biogenesis protein RLP24
+分子 #8: Zinc finger protein 593
+分子 #9: 60S ribosomal protein L3
+分子 #10: 60S ribosomal protein L29
+分子 #11: 60S ribosomal protein L4
+分子 #12: 60S ribosomal protein L30
+分子 #13: 60S ribosomal protein L34
+分子 #14: 60S ribosomal protein L7a
+分子 #15: 60S ribosomal protein L35
+分子 #16: 60S ribosomal protein L9
+分子 #17: 60S ribosomal protein L36
+分子 #18: 60S ribosomal protein L27a
+分子 #19: 60S ribosomal protein L37
+分子 #20: 60S ribosomal protein L11
+分子 #21: 60S ribosomal protein L38
+分子 #22: 60S ribosomal protein L39
+分子 #23: 60S ribosomal protein L13
+分子 #24: Translation machinery-associated protein 16
+分子 #25: 60S ribosomal protein L14
+分子 #26: 60S ribosomal protein L15
+分子 #27: 60S ribosomal protein L13a
+分子 #28: 60S ribosomal protein L36a
+分子 #29: 60S ribosomal protein L37a
+分子 #30: 60S ribosomal protein L17
+分子 #31: 60S ribosomal protein L18
+分子 #32: 60S ribosomal protein L19
+分子 #33: 60S ribosomal protein L18a
+分子 #34: 60S ribosomal protein L21
+分子 #35: 60S ribosomal protein L22
+分子 #36: 60S ribosomal protein L23
+分子 #37: 60S ribosomal protein L23a
+分子 #38: 60S ribosomal protein L26
+分子 #39: 60S ribosomal protein L27
+分子 #40: 60S ribosomal protein L31
+分子 #41: 60S ribosomal protein L32
+分子 #42: 60S ribosomal protein L28
+分子 #43: 60S ribosomal protein L8
+分子 #44: 60S ribosomal protein L35a
+分子 #45: 60S ribosomal protein L6
+分子 #46: 60S ribosomal protein L7
+分子 #47: 60S ribosomal protein L5
+分子 #48: Protein LLP homolog
+分子 #2: 28S rRNA
+分子 #4: 5S rRNA
+分子 #7: 28S rRNA
+分子 #49: MAGNESIUM ION
+分子 #50: water
-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: 7.8 |
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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: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 平均電子線量: 64.0 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期 角度割当 | タイプ: NOT APPLICABLE |
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最終 角度割当 | タイプ: PROJECTION MATCHING |
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.23 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 10277 |