+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6lss | ||||||
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タイトル | Cryo-EM structure of a pre-60S ribosomal subunit - state preA | ||||||
要素 |
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キーワード | RIBOSOME (リボソーム) / 60S / pre-60S / pre-ribosome / human 60S / human pre-ribosome / NMD3 / human NMD3 | ||||||
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 / positive regulation of signal transduction by p53 class mediator / regulation of reactive oxygen species metabolic process / ubiquitin ligase inhibitor activity / alpha-beta T cell differentiation / positive regulation of dendritic spine development / negative regulation of ubiquitin protein ligase activity / regulation of glycolytic process / maturation of 5.8S rRNA / response to aldosterone / homeostatic process / 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 / ribosomal large subunit binding / Peptide chain elongation / Selenocysteine synthesis / protein-RNA complex assembly / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / preribosome, large subunit precursor / blastocyst development / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / protein localization to nucleus / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / cellular response to actinomycin D / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / protein targeting / 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 / translation initiation factor activity / cellular response to interleukin-4 / 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 / mRNA 3'-UTR binding / skeletal system development / sensory perception of sound / response to insulin / cellular response to gamma radiation / mRNA 5'-UTR binding / 骨 / ribosomal large subunit assembly / transcription coactivator binding / cytoplasmic ribonucleoprotein granule / rRNA processing / osteoblast differentiation / 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) | ||||||
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: 3.23 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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 6lss.cif.gz | 3.1 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6lss.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 6lss.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ls/6lss ftp://data.pdbj.org/pub/pdb/validation_reports/ls/6lss | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
-Nucleolar GTP-binding protein ... , 2種, 2分子 14
#1: 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) Homo sapiens (ヒト) / 参照: UniProt: Q13823 |
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#3: 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) Homo sapiens (ヒト) / 参照: UniProt: Q9BZE4 |
-RNA鎖 , 3種, 3分子 258
#2: RNA鎖 | 分子量: 1641892.625 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) |
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#4: RNA鎖 | 分子量: 38691.914 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: GenBank: 23898 |
#7: RNA鎖 | 分子量: 50157.676 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) |
-タンパク質 , 5種, 5分子 679Rz
#5: 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) Homo sapiens (ヒト) / 参照: UniProt: P56537 |
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#6: 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) Homo sapiens (ヒト) / 参照: UniProt: Q9UHA3 |
#8: 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) Homo sapiens (ヒト) / 参照: UniProt: O00488 |
#24: タンパク質 | 分子量: 23912.414 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q96EY4 |
#48: 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) Homo sapiens (ヒト) / 参照: UniProt: Q9BRT6 |
+60S ribosomal protein ... , 38種, 38分子 BCDEFGHIKLMNOPQSUVWXYZabcdeghi...
-非ポリマー , 2種, 266分子
#49: 化合物 | ChemComp-MG / #50: 水 | ChemComp-HOH / | |
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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 |
-試料調製
構成要素 | 名称: Cryo-EM structure of a human pre-60S ribosomal subunit state - preA タイプ: RIBOSOME / Entity ID: #1-#48 / 由来: MULTIPLE SOURCES |
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分子量 | 実験値: NO |
由来(天然) | 生物種: Homo sapiens (ヒト) |
緩衝液 | pH: 7.8 |
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 |
-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: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELDBright-field microscopy / アライメント法: COMA FREE |
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
撮影 | 電子線照射量: 64 e/Å2 フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) |
-解析
CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3次元再構成 | 解像度: 3.23 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 10277 / 対称性のタイプ: POINT |