+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-29263 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Human nucleolar pre-60S ribosomal subunit (State H) - Composite map | |||||||||
マップデータ | ||||||||||
試料 |
| |||||||||
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 inner cell mass cell differentiation / 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 ...inner cell mass cell differentiation / 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 / negative regulation of protein neddylation / positive regulation of telomere maintenance / ribosomal protein import into nucleus / negative regulation of formation of translation preinitiation complex / protein localization to nucleolus / GAIT complex / skeletal system morphogenesis / regulation of reactive oxygen species metabolic process / regulation of glycolytic process / regulation of G1 to G0 transition / nuclear-transcribed mRNA catabolic process / protein-DNA complex disassembly / negative regulation of ubiquitin protein ligase activity / mitotic metaphase chromosome alignment / stem cell population maintenance / regulation of cyclin-dependent protein serine/threonine kinase activity / G1 to G0 transition / positive regulation of dendritic spine development / homeostatic process / negative regulation of cell-cell adhesion / negative regulation of DNA replication / maturation of 5.8S rRNA / lung morphogenesis / macrophage chemotaxis / Peptide chain elongation / ribosomal large subunit binding / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / 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 / negative regulation of mitotic cell cycle / 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 / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / 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) / hematopoietic progenitor cell differentiation / cellular response to actinomycin D / somitogenesis / ribosomal subunit export from nucleus / cytosolic ribosome / rough endoplasmic reticulum / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Notch signaling pathway / negative regulation of protein ubiquitination / translation initiation factor activity / negative regulation of ubiquitin-dependent protein catabolic process / negative regulation of cell migration / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / assembly of large subunit precursor of preribosome / regulation of signal transduction by p53 class mediator / condensed nuclear chromosome / maturation of LSU-rRNA / cytosolic ribosome assembly / ribosomal large subunit biogenesis / kidney development / mRNA 3'-UTR binding / positive regulation of translation / response to insulin / ribosomal large subunit assembly / mRNA 5'-UTR binding / transcription coactivator binding / Regulation of expression of SLITs and ROBOs / positive regulation of miRNA transcription / cellular response to type II interferon / cytoplasmic ribonucleoprotein granule / osteoblast differentiation / rRNA processing / large ribosomal subunit / positive regulation of canonical Wnt signaling pathway / ribosome biogenesis / positive regulation of protein binding / ribosome binding / chromosome / mitotic cell cycle / regulation of cell population proliferation / midbody 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: 2.91 Å | |||||||||
データ登録者 | Vanden Broeck A / Klinge S | |||||||||
資金援助 | European Union, 米国, 2件
| |||||||||
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 |
|
-構造の表示
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_29263.map.gz | 37.9 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-29263-v30.xml emd-29263.xml | 57 KB 57 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_29263_fsc.xml | 15.9 KB | 表示 | FSCデータファイル |
画像 | emd_29263.png | 133.6 KB | ||
マスクデータ | emd_29263_msk_1.map | 421.9 MB | マスクマップ | |
Filedesc metadata | emd-29263.cif.gz | 14.6 KB | ||
その他 | emd_29263_half_map_1.map.gz emd_29263_half_map_2.map.gz | 390.9 MB 390.9 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-29263 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29263 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_29263_validation.pdf.gz | 1.1 MB | 表示 | EMDB検証レポート |
---|---|---|---|---|
文書・詳細版 | emd_29263_full_validation.pdf.gz | 1.1 MB | 表示 | |
XML形式データ | emd_29263_validation.xml.gz | 25.1 KB | 表示 | |
CIF形式データ | emd_29263_validation.cif.gz | 32.7 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29263 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29263 | HTTPS FTP |
-関連構造データ
関連構造データ | 8fl0MC 8fkpC 8fkqC 8fkrC 8fksC 8fktC 8fkuC 8fkvC 8fkwC 8fkxC 8fkyC 8fkzC 8fl2C 8fl3C 8fl4C 8fl6C 8fl7C 8fl9C 8flaC 8flbC 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 |
---|---|
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 |
---|---|
「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_29263.map.gz / 形式: CCP4 / 大きさ: 421.9 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ボクセルのサイズ | X=Y=Z: 1.072 Å | ||||||||||||||||||||
密度 |
| ||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
|
-添付データ
-マスク #1
ファイル | emd_29263_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-ハーフマップ: #2
ファイル | emd_29263_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_29263_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-試料の構成要素
+全体 : Human nucleolar pre-60S ribosomal subunit (State H)
+超分子 #1: Human nucleolar pre-60S ribosomal subunit (State H)
+分子 #1: 60S ribosomal protein L12
+分子 #4: 60S ribosomal protein L11
+分子 #5: 60S ribosomal protein L13a
+分子 #6: 60S ribosomal protein L14
+分子 #7: 60S ribosomal protein L18
+分子 #8: 60S ribosomal protein L18a
+分子 #9: 60S ribosomal protein L21
+分子 #10: 60S ribosomal protein L23
+分子 #11: 60S ribosomal protein L28
+分子 #12: 60S ribosomal protein L3
+分子 #13: 60S ribosomal protein L32
+分子 #14: 60S ribosomal protein L35a
+分子 #15: Guanine nucleotide-binding protein-like 3
+分子 #16: Nucleolar GTP-binding protein 2
+分子 #17: Ribosome production factor 2 homolog
+分子 #18: Ribosome biogenesis protein NSA2 homolog
+分子 #19: Notchless protein homolog 1
+分子 #20: Protein LLP homolog
+分子 #21: Coiled-coil domain-containing protein 86
+分子 #22: 60S ribosomal protein L4
+分子 #23: 60S ribosomal protein L5
+分子 #24: 60S ribosomal protein L6
+分子 #25: 60S ribosomal protein L7
+分子 #26: 60S ribosomal protein L9
+分子 #27: Eukaryotic translation initiation factor 6
+分子 #28: mRNA turnover protein 4 homolog
+分子 #29: GTP-binding protein 4
+分子 #30: Ribosome biogenesis regulatory protein homolog
+分子 #31: Probable ribosome biogenesis protein RLP24
+分子 #2: 28S rRNA
+分子 #3: 5S rRNA
+分子 #32: MAGNESIUM ION
+分子 #33: GUANOSINE-5'-TRIPHOSPHATE
+分子 #34: POTASSIUM ION
+分子 #35: GUANOSINE-5'-DIPHOSPHATE
+分子 #36: ZINC ION
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
---|---|
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 |
---|---|
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 |
---|---|
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 |
---|---|
得られたモデル | PDB-8fl0: |