[日本語] English
![](img/lk-miru.gif)
- EMDB-26259: State NE1 nucleolar 60S ribosome biogenesis intermediate - Overall map -
+
データを開く
-
基本情報
登録情報 | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
タイトル | State NE1 nucleolar 60S ribosome biogenesis intermediate - Overall map | ||||||||||||
![]() | Map of state NE1 | ||||||||||||
![]() |
| ||||||||||||
![]() | ribosome biogenesis / DEAD-box ATPases / methyltransferase / nucleolus / RIBOSOME | ||||||||||||
機能・相同性 | ![]() 27S pre-rRNA (guanosine2922-2'-O)-methyltransferase / rRNA (guanosine-2'-O-)-methyltransferase activity / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear exosome (RNase complex) / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / PeBoW complex / rRNA primary transcript binding / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...27S pre-rRNA (guanosine2922-2'-O)-methyltransferase / rRNA (guanosine-2'-O-)-methyltransferase activity / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear exosome (RNase complex) / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / PeBoW complex / rRNA primary transcript binding / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methylation / pre-mRNA 5'-splice site binding / nuclear-transcribed mRNA catabolic process / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / proteasome binding / maturation of 5.8S rRNA / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / ribosomal large subunit binding / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of mRNA splicing, via spliceosome / ATPase activator activity / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / ribosomal large subunit export from nucleus / regulation of translational fidelity / protein-RNA complex assembly / ribonucleoprotein complex binding / ribosomal subunit export from nucleus / translation initiation factor activity / proteasome complex / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / assembly of large subunit precursor of preribosome / maturation of LSU-rRNA / cytosolic ribosome assembly / ribosomal large subunit biogenesis / maturation of SSU-rRNA / macroautophagy / small-subunit processome / maintenance of translational fidelity / protein catabolic process / ribosomal large subunit assembly / rRNA processing / protein transport / ribosome biogenesis / protein-macromolecule adaptor activity / ATPase binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / GTPase activity / mRNA binding / nucleolus / GTP binding / RNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||||||||
生物種 | ![]() ![]() | ||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.76 Å | ||||||||||||
![]() | Cruz VE / Sekulski K / Peddada N / Erzberger JP | ||||||||||||
資金援助 | ![]()
| ||||||||||||
![]() | ![]() タイトル: Sequence-specific remodeling of a topologically complex RNP substrate by Spb4. 著者: Victor Emmanuel Cruz / Kamil Sekulski / Nagesh Peddada / Carolin Sailer / Sahana Balasubramanian / Christine S Weirich / Florian Stengel / Jan P Erzberger / ![]() ![]() ![]() 要旨: DEAD-box ATPases are ubiquitous enzymes essential in all aspects of RNA biology. However, the limited in vitro catalytic activities described for these enzymes are at odds with their complex cellular ...DEAD-box ATPases are ubiquitous enzymes essential in all aspects of RNA biology. However, the limited in vitro catalytic activities described for these enzymes are at odds with their complex cellular roles, most notably in driving large-scale RNA remodeling steps during the assembly of ribonucleoproteins (RNPs). We describe cryo-EM structures of 60S ribosomal biogenesis intermediates that reveal how context-specific RNA unwinding by the DEAD-box ATPase Spb4 results in extensive, sequence-specific remodeling of rRNA secondary structure. Multiple cis and trans interactions stabilize Spb4 in a post-catalytic, high-energy intermediate that drives the organization of the three-way junction at the base of rRNA domain IV. This mechanism explains how limited strand separation by DEAD-box ATPases is leveraged to provide non-equilibrium directionality and ensure efficient and accurate RNP assembly. | ||||||||||||
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 | ![]() | 229 MB | ![]() | |
---|---|---|---|---|
ヘッダ (付随情報) | ![]() ![]() | 77.4 KB 77.4 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 14.1 KB | 表示 | ![]() |
画像 | ![]() | 99 KB | ||
Filedesc metadata | ![]() | 16.3 KB | ||
その他 | ![]() ![]() | 194.1 MB 193.9 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 1.1 MB | 表示 | ![]() |
---|---|---|---|---|
文書・詳細版 | ![]() | 1.1 MB | 表示 | |
XML形式データ | ![]() | 21.8 KB | 表示 | |
CIF形式データ | ![]() | 28.7 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 7u0hMC ![]() 7nacC ![]() 7nadC ![]() 7nafC ![]() 7r6kC ![]() 7r6qC ![]() 7r72C ![]() 7r7aC ![]() 7r7cC C: 同じ文献を引用 ( 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 ![]() |
-
リンク
EMDBのページ | ![]() ![]() |
---|---|
「今月の分子」の関連する項目 |
-
マップ
ファイル | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Map of state NE1 | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.02885 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: Half-map 2 of state NE1
ファイル | emd_26259_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Half-map 2 of state NE1 | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-ハーフマップ: Half-map 1 of state NE1
ファイル | emd_26259_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Half-map 1 of state NE1 | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-
試料の構成要素
+全体 : Early nucleoplasmic 60S intermediate purified with tags on Nop53 ...
+超分子 #1: Early nucleoplasmic 60S intermediate purified with tags on Nop53 ...
+分子 #1: 25S rRNA
+分子 #2: 5.8S rRNA
+分子 #3: ITS2 rRNA
+分子 #4: 60S ribosomal protein L2-A
+分子 #5: 60S ribosomal protein L3
+分子 #6: 60S ribosomal protein L4-A
+分子 #7: 60S ribosomal protein L6-A
+分子 #8: 60S ribosomal protein L7-A
+分子 #9: 60S ribosomal protein L8-A
+分子 #10: 60S ribosomal protein L9-A
+分子 #11: Proteasome-interacting protein CIC1
+分子 #12: 60S ribosomal protein L13-A
+分子 #13: 60S ribosomal protein L14-A
+分子 #14: 60S ribosomal protein L15-A
+分子 #15: 60S ribosomal protein L16-A
+分子 #16: 60S ribosomal protein L17-A
+分子 #17: 60S ribosomal protein L18-A
+分子 #18: 60S ribosomal protein L19-A
+分子 #19: 60S ribosomal protein L20-A
+分子 #20: 60S ribosomal protein L21-A
+分子 #21: 60S ribosomal protein L22-A
+分子 #22: 60S ribosomal protein L23-A
+分子 #23: Ribosome assembly factor MRT4
+分子 #24: 60S ribosomal protein L25
+分子 #25: 60S ribosomal protein L26-A
+分子 #26: 60S ribosomal protein L27-A
+分子 #27: 60S ribosomal protein L28
+分子 #28: Nucleolar GTP-binding protein 1
+分子 #29: 60S ribosomal protein L30
+分子 #30: 60S ribosomal protein L31-A
+分子 #31: 60S ribosomal protein L32
+分子 #32: 60S ribosomal protein L33-A
+分子 #33: 60S ribosomal protein L34-A
+分子 #34: 60S ribosomal protein L35-A
+分子 #35: 60S ribosomal protein L36-A
+分子 #36: 60S ribosomal protein L37-A
+分子 #37: 60S ribosomal protein L38
+分子 #38: Nucleolar GTP-binding protein 2
+分子 #39: Pescadillo homolog
+分子 #40: Ribosome biogenesis protein 15
+分子 #41: 60S ribosomal protein L43-A
+分子 #42: Ribosome biogenesis protein NOP53
+分子 #43: Ribosome biogenesis protein NSA2
+分子 #44: Nuclear GTP-binding protein NUG1
+分子 #45: Ribosome biogenesis protein RLP7
+分子 #46: Ribosome biogenesis protein RLP24
+分子 #47: 27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase
+分子 #48: Eukaryotic translation initiation factor 6
+分子 #49: UPF0642 protein YBL028C
+分子 #50: MAGNESIUM ION
+分子 #51: ZINC ION
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
---|---|
![]() | 単粒子再構成法 |
試料の集合状態 | particle |
-
試料調製
濃度 | 0.2 mg/mL | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
緩衝液 | pH: 8 構成要素:
| ||||||||||||||||||
グリッド | モデル: Quantifoil R2/1 / 材質: COPPER / メッシュ: 300 / 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: 0.3 / 前処理 - タイプ: GLOW DISCHARGE | ||||||||||||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK IV |
-
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 K3 (6k x 4k) / 撮影したグリッド数: 1 / 実像数: 7398 / 平均露光時間: 0.05 sec. / 平均電子線量: 1.2 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | C2レンズ絞り径: 70.0 µm / 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): 2.2 µm / 最小 デフォーカス(公称値): 0.9 µm / 倍率(公称値): 81000 |
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 |
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 | プロトコル: RIGID BODY FIT |
---|---|
得られたモデル | ![]() PDB-7u0h: |