+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-21573 | |||||||||
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タイトル | 30S-Inactive-low-Mg2+ Class B | |||||||||
マップデータ | 30S-Inactive-low-Mg2+ Class A | |||||||||
試料 |
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キーワード | 30S subunit / conformations / inactive / activated / RIBOSOME (リボソーム) | |||||||||
機能・相同性 | 機能・相同性情報 mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / misfolded RNA binding / Group I intron splicing / RNA folding / negative regulation of translational initiation / four-way junction DNA binding / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing ...mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / misfolded RNA binding / Group I intron splicing / RNA folding / negative regulation of translational initiation / four-way junction DNA binding / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / transcription antitermination / DNA endonuclease activity / DNA-templated transcription termination / maintenance of translational fidelity / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / regulation of translation / small ribosomal subunit / cytoplasmic translation / tRNA binding / molecular adaptor activity / リボソーム / rRNA binding / structural constituent of ribosome / 翻訳 (生物学) / response to antibiotic / zinc ion binding / 細胞質基質 / 細胞質 類似検索 - 分子機能 | |||||||||
生物種 | Escherichia coli K-12 (大腸菌) / Escherichia coli (strain K12) (大腸菌) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.9 Å | |||||||||
データ登録者 | Jahagirdar D / Jha V | |||||||||
資金援助 | カナダ, 1件
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引用 | ジャーナル: RNA / 年: 2020 タイトル: Alternative conformations and motions adopted by 30S ribosomal subunits visualized by cryo-electron microscopy. 著者: Dushyant Jahagirdar / Vikash Jha / Kaustuv Basu / Josue Gomez-Blanco / Javier Vargas / Joaquin Ortega / 要旨: It is only after recent advances in cryo-electron microscopy that it is now possible to describe at high-resolution structures of large macromolecules that do not crystalize. Purified 30S subunits ...It is only after recent advances in cryo-electron microscopy that it is now possible to describe at high-resolution structures of large macromolecules that do not crystalize. Purified 30S subunits interconvert between an "active" and "inactive" conformation. The active conformation was described by crystallography in the early 2000s, but the structure of the inactive form at high resolution remains unsolved. Here we used cryo-electron microscopy to obtain the structure of the inactive conformation of the 30S subunit to 3.6 Å resolution and study its motions. In the inactive conformation, an alternative base-pairing of three nucleotides causes the region of helix 44, forming the decoding center to adopt an unlatched conformation and the 3' end of the 16S rRNA positions similarly to the mRNA during translation. Incubation of inactive 30S subunits at 42°C reverts these structural changes. The air-water interface to which ribosome subunits are exposed during sample preparation also peel off some ribosomal proteins. Extended exposures to low magnesium concentrations make the ribosomal particles more susceptible to the air-water interface causing the unfolding of large rRNA structural domains. Overall, this study provides new insights about the conformational space explored by the 30S ribosomal subunit when the ribosomal particles are free in solution. | |||||||||
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 | 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_21573.map.gz | 93.7 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-21573-v30.xml emd-21573.xml | 21.4 KB 21.4 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_21573_fsc.xml | 10.8 KB | 表示 | FSCデータファイル |
画像 | emd_21573.png | 83.2 KB | ||
Filedesc metadata | emd-21573.cif.gz | 6.7 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-21573 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21573 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「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_21573.map.gz / 形式: CCP4 / 大きさ: 107.2 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | 30S-Inactive-low-Mg2+ Class A | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.073 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-試料の構成要素
+全体 : 30S-Inactive-low-Mg2+ Class B
+超分子 #1: 30S-Inactive-low-Mg2+ Class B
+分子 #1: 16S rRNA
+分子 #2: 30S ribosomal protein S4
+分子 #3: 30S ribosomal protein S5
+分子 #4: 30S ribosomal protein S6
+分子 #5: 30S ribosomal protein S8
+分子 #6: 30S ribosomal protein S12
+分子 #7: 30S ribosomal protein S15
+分子 #8: 30S ribosomal protein S16
+分子 #9: 30S ribosomal protein S17
+分子 #10: 30S ribosomal protein S20
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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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: 7.4 |
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凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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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 FIELDBright-field microscopy |
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 |
撮影 | フィルム・検出器のモデル: FEI FALCON II (4k x 4k) 検出モード: INTEGRATING / 平均電子線量: 52.0 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |