+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-5643 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Cryo-EM structures of the late-stage assembly intermediates of 50S ribosome subunit from YlqF-deficient Bacillus subtilis strain. | |||||||||
マップデータ | 3D classification of the assembly intermediates of 50S ribosome subunit from YlqF-deficient Bacillus subtilis strain | |||||||||
試料 |
| |||||||||
キーワード | Ribosome biogenesis / ribosome assembly intermediate / RNA folding | |||||||||
機能・相同性 | 機能・相同性情報 positive regulation of rRNA processing / nucleoid / rRNA processing / large ribosomal subunit / regulation of translation / ribosomal large subunit assembly / transferase activity / large ribosomal subunit rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit ...positive regulation of rRNA processing / nucleoid / rRNA processing / large ribosomal subunit / regulation of translation / ribosomal large subunit assembly / transferase activity / large ribosomal subunit rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / mRNA binding / DNA binding / RNA binding / cytoplasm 類似検索 - 分子機能 | |||||||||
生物種 | Bacillus subtilis (枯草菌) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 10.7 Å | |||||||||
データ登録者 | Li N / Chen Y / Guo Q / Zhang Y / Yuan Y / Ma C / Deng H / Lei J / Gao N | |||||||||
引用 | ジャーナル: Nucleic Acids Res / 年: 2013 タイトル: Cryo-EM structures of the late-stage assembly intermediates of the bacterial 50S ribosomal subunit. 著者: Ningning Li / Yuling Chen / Qiang Guo / Yixiao Zhang / Yi Yuan / Chengying Ma / Haiteng Deng / Jianlin Lei / Ning Gao / 要旨: Ribosome assembly is a process fundamental for all cellular activities. The efficiency and accuracy of the subunit assembly are tightly regulated and closely monitored. In the present work, we ...Ribosome assembly is a process fundamental for all cellular activities. The efficiency and accuracy of the subunit assembly are tightly regulated and closely monitored. In the present work, we characterized, both compositionally and structurally, a set of in vivo 50S subunit precursors (45S), isolated from a mutant bacterial strain. Our qualitative mass spectrometry data indicate that L28, L16, L33, L36 and L35 are dramatically underrepresented in the 45S particles. This protein spectrum shows interesting similarity to many qualitatively analyzed 50S precursors from different genetic background, indicating the presence of global rate-limiting steps in the late-stage assembly of 50S subunit. Our structural data reveal two major intermediate states for the 45S particles. Consistently, both states severally lack those proteins, but they also differ in the stability of the functional centers of the 50S subunit, demonstrating that they are translationally inactive. Detailed analysis indicates that the orientation of H38 accounts for the global conformational differences in these intermediate structures, and suggests that the reorientation of H38 to its native position is rate-limiting during the late-stage assembly. Especially, H38 plays an essential role in stabilizing the central protuberance, through the interaction with the 5S rRNA, and the correctly orientated H38 is likely a prerequisite for further maturation of the 50S subunit. | |||||||||
履歴 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
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_5643.map.gz | 54.2 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-5643-v30.xml emd-5643.xml | 11.7 KB 11.7 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_5643_1.jpg emd_5643_2.tif | 71.7 KB 533.9 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-5643 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5643 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_5643_validation.pdf.gz | 320.6 KB | 表示 | EMDB検証レポート |
---|---|---|---|---|
文書・詳細版 | emd_5643_full_validation.pdf.gz | 320.2 KB | 表示 | |
XML形式データ | emd_5643_validation.xml.gz | 6.1 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5643 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5643 | HTTPS FTP |
-関連構造データ
-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_5643.map.gz / 形式: CCP4 / 大きさ: 62.5 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | 3D classification of the assembly intermediates of 50S ribosome subunit from YlqF-deficient Bacillus subtilis strain | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
|
-添付データ
-試料の構成要素
-全体 : Assembly intermediate of 50S ribosome subunit from YlqF-deficient...
全体 | 名称: Assembly intermediate of 50S ribosome subunit from YlqF-deficient Bacillus subtilis strain |
---|---|
要素 |
|
-超分子 #1000: Assembly intermediate of 50S ribosome subunit from YlqF-deficient...
超分子 | 名称: Assembly intermediate of 50S ribosome subunit from YlqF-deficient Bacillus subtilis strain タイプ: sample / ID: 1000 / Number unique components: 1 |
---|
-超分子 #1: assembly intermediate of 50S ribosome subunit from YlqF-deficient...
超分子 | 名称: assembly intermediate of 50S ribosome subunit from YlqF-deficient Bacillus subtilis strain タイプ: complex / ID: 1 / Name.synonym: immature 50S ribosome / 組換発現: No / データベース: NCBI / Ribosome-details: ribosome-prokaryote: LSU 50S |
---|---|
由来(天然) | 生物種: Bacillus subtilis (枯草菌) / 株: Bacillus subtilis subsp. subtilis str. 168 |
-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 / 詳細: 100mM NH4Cl, 20mM Tris-HCl, 10mM MgOAc2, 1mM TCEP |
---|---|
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / 装置: FEI VITROBOT MARK IV / 手法: Blot for 20 seconds before plunging |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
---|---|
日付 | 2011年12月6日 |
撮影 | カテゴリ: CCD / フィルム・検出器のモデル: FEI EAGLE (4k x 4k) / 平均電子線量: 20 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 / Cs: 2.7 mm / 最大 デフォーカス(公称値): 4.0 µm / 最小 デフォーカス(公称値): 1.0 µm / 倍率(公称値): 59000 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
詳細 | This is one of the classified groups with the software RELION |
---|---|
CTF補正 | 詳細: Each particle |
最終 再構成 | アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 10.7 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: RELION / 使用した粒子像数: 27652 |
-原子モデル構築 1
初期モデル | PDB ID: 2aw4 |
---|---|
ソフトウェア | 名称: S2S, modeRNA, MODELLER, MDFF |
詳細 | Atom models of the 23S and 5S rRNAs were built using the software S2S and modeRNA, with the crystal structures of the 50S subunits from E. coli (PDB ID: 2AW4) and Thermus thermophilus (PDB ID: 2J01) as template. Models of ribosomal proteins, L1, L3, L4, L6, L10, L13, L14, L15, L17, L19, L20, L21, L22, L23, L24, L27, L29, L30, L31, L32, L33, L34, L35 and L36 were downloaded from the SWISS-MODEL Repository. The others, including L2, L5, L11, L16, L18 and L28 were modeled using MODELLER with crystal structures of E. coli and T. thermophilus 50S subunits as templates.The combined atomic model of the B. subtilis 50S subunit was docked into a high resolution mature 50S density map and optimized using MDFF. This optimized model was docked into the EM density using Chimera and flexible fitted into the density using MDFF |
精密化 | 空間: REAL / プロトコル: FLEXIBLE FIT 当てはまり具合の基準: Cross-correlation coefficient |
得られたモデル | PDB-3j3w: |
-原子モデル構築 2
初期モデル | PDB ID: 2j01 |
---|---|
ソフトウェア | 名称: S2S, modeRNA, MODELLER, MDFF |
詳細 | Atom models of the 23S and 5S rRNAs were built using the software S2S and modeRNA, with the crystal structures of the 50S subunits from E. coli (PDB ID: 2AW4) and Thermus thermophilus (PDB ID: 2J01) as template. Models of ribosomal proteins, L1, L3, L4, L6, L10, L13, L14, L15, L17, L19, L20, L21, L22, L23, L24, L27, L29, L30, L31, L32, L33, L34, L35 and L36 were downloaded from the SWISS-MODEL Repository. The others, including L2, L5, L11, L16, L18 and L28 were modeled using MODELLER with crystal structures of E. coli and T. thermophilus 50S subunits as templates.The combined atomic model of the B. subtilis 50S subunit was docked into a high resolution mature 50S density map and optimized using MDFF. This optimized model was docked into the EM density using Chimera and flexible fitted into the density using MDFF |
精密化 | 空間: REAL 当てはまり具合の基準: Cross-correlation coefficient |
得られたモデル | PDB-3j3w: |