+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-35651 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | human nuclear pre-60S ribosomal particle - State D' | |||||||||
マップデータ | human nuclear pre-60S ribosomal particle - State D' - post processed | |||||||||
試料 |
| |||||||||
キーワード | GNL2 / nuclear / pre-60S / RIBOSOME | |||||||||
機能・相同性 | 機能・相同性情報 protein localization to nucleoplasm / inner cell mass cell differentiation / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / positive regulation of protein localization to chromosome, telomeric region / regulation of RIG-I signaling pathway / basal RNA polymerase II transcription machinery binding / negative regulation of collagen binding / hematopoietic stem cell homeostasis / dendrite extension ...protein localization to nucleoplasm / inner cell mass cell differentiation / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / positive regulation of protein localization to chromosome, telomeric region / regulation of RIG-I signaling pathway / basal RNA polymerase II transcription machinery binding / negative regulation of collagen binding / hematopoietic stem cell homeostasis / dendrite extension / preribosome binding / regulation of cellular senescence / lamin filament / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation / PeBoW complex / positive regulation of protein sumoylation / miRNA-mediated post-transcriptional gene silencing / stem cell division / negative regulation of signal transduction by p53 class mediator / miRNA-mediated gene silencing by inhibition of translation / eukaryotic 80S initiation complex / positive regulation of telomere maintenance / 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) / skeletal system morphogenesis / 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 / stem cell population maintenance / 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 / negative regulation of mitotic cell cycle / Viral mRNA Translation / protein localization to nucleus / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / ribosomal large subunit export from nucleus / 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 / somitogenesis / 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 / Notch signaling pathway / negative regulation of protein ubiquitination 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: 3.2 Å | |||||||||
データ登録者 | Zhang Y / Gao N | |||||||||
資金援助 | 中国, 1件
| |||||||||
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 |
|
-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_35651.map.gz | 12.7 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-35651-v30.xml emd-35651.xml | 82 KB 82 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_35651.png | 173.8 KB | ||
Filedesc metadata | emd-35651.cif.gz | 19.5 KB | ||
その他 | emd_35651_half_map_1.map.gz emd_35651_half_map_2.map.gz | 194.5 MB 194.3 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-35651 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35651 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_35651_validation.pdf.gz | 865.2 KB | 表示 | EMDB検証レポート |
---|---|---|---|---|
文書・詳細版 | emd_35651_full_validation.pdf.gz | 864.8 KB | 表示 | |
XML形式データ | emd_35651_validation.xml.gz | 15.5 KB | 表示 | |
CIF形式データ | emd_35651_validation.cif.gz | 18.6 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35651 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35651 | HTTPS FTP |
-関連構造データ
関連構造データ | 8ipyMC 8idtC 8idyC 8ie3C 8ineC 8infC 8inkC 8ipdC 8ipxC 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) |
---|---|
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_35651.map.gz / 形式: CCP4 / 大きさ: 244.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | human nuclear pre-60S ribosomal particle - State D' - post processed | ||||||||||||||||||||||||||||||||||||
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: 1.37 Å | ||||||||||||||||||||||||||||||||||||
密度 |
| ||||||||||||||||||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
|
-添付データ
-ハーフマップ: human nuclear pre-60S ribosomal particle - State D' - half1
ファイル | emd_35651_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | human nuclear pre-60S ribosomal particle - State D' - half1 | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-ハーフマップ: human nuclear pre-60S ribosomal particle - State D' - half2
ファイル | emd_35651_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | human nuclear pre-60S ribosomal particle - State D' - half2 | ||||||||||||
投影像・断面図 |
| ||||||||||||
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: Protein SDA1 homolog
+分子 #3: Eukaryotic translation initiation factor 6
+分子 #4: Probable ribosome biogenesis protein RLP24
+分子 #6: Zinc finger protein 593
+分子 #7: 60S ribosomal protein L29
+分子 #8: 60S ribosomal protein L3
+分子 #9: 60S ribosomal protein L4
+分子 #10: 60S ribosomal protein L30
+分子 #11: 60S ribosomal protein L7a
+分子 #12: 60S ribosomal protein L35
+分子 #13: 60S ribosomal protein L9
+分子 #14: Ribosome biogenesis protein NSA2 homolog
+分子 #15: 60S ribosomal protein L27a
+分子 #16: 60S ribosomal protein L37
+分子 #17: 60S ribosomal protein L39
+分子 #18: 60S ribosomal protein L13
+分子 #19: 60S ribosomal protein L14
+分子 #20: 60S ribosomal protein L15
+分子 #21: 60S ribosomal protein L13a
+分子 #22: 60S ribosomal protein L37a
+分子 #23: 60S ribosomal protein L18
+分子 #24: 60S ribosomal protein L19
+分子 #25: 60S ribosomal protein L18a
+分子 #26: 60S ribosomal protein L23
+分子 #27: 60S ribosomal protein L26
+分子 #28: 60S ribosomal protein L28
+分子 #29: 60S ribosomal protein L8
+分子 #30: 60S ribosomal protein L35a
+分子 #31: 60S ribosomal protein L6
+分子 #32: 60S ribosomal protein L7
+分子 #33: Coiled-coil domain-containing protein 86
+分子 #34: Guanine nucleotide-binding protein-like 3
+分子 #35: mRNA turnover protein 4 homolog
+分子 #36: G Protein Nucleolar 2
+分子 #37: 60S ribosomal protein L12
+分子 #38: Protein LLP homolog
+分子 #39: 60S ribosomal protein L11
+分子 #40: 60S ribosomal protein L5
+分子 #41: Notchless protein homolog 1
+分子 #42: 60S ribosomal protein L21
+分子 #43: GTP-binding protein 4
+分子 #44: 60S ribosomal protein L17
+分子 #45: 60S ribosomal protein L32
+分子 #46: 60S ribosomal protein L31
+分子 #47: 60S ribosomal protein L22
+分子 #48: MKI67 FHA domain-interacting nucleolar phosphoprotein
+分子 #50: Ribosomal L1 domain-containing protein 1
+分子 #51: 60S ribosomal protein L7-like 1
+分子 #52: 60S ribosomal protein L36
+分子 #53: 60S ribosomal protein L34
+分子 #54: 60S ribosomal protein L27
+分子 #55: 60S ribosomal protein L38
+分子 #57: Pescadillo homolog
+分子 #58: 60S ribosomal protein L23a
+分子 #59: Ribosome biogenesis protein NOP53
+分子 #2: 28S rRNA
+分子 #5: 5.8S rRNA
+分子 #49: ITS2
+分子 #56: 5S rRNA
+分子 #60: GUANOSINE-5'-TRIPHOSPHATE
+分子 #61: MAGNESIUM 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: 7.5 |
---|---|
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
---|---|
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 |
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 / 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 |
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 |
---|---|
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.2 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 26584 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |