+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-21857 | |||||||||||||||
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タイトル | 70S ribosome without free 5S rRNA and with a perturbed PTC | |||||||||||||||
マップデータ | Cryo-EM map of vacant 70S ribosome with 23S-cp5s rRNA and abberant PTC | |||||||||||||||
試料 |
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キーワード | Ribosome (リボソーム) / 23S-cp5S rRNA / engineering (工学) | |||||||||||||||
機能・相同性 | 機能・相同性情報 negative regulation of cytoplasmic translational initiation / stringent response / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity ...negative regulation of cytoplasmic translational initiation / stringent response / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / DnaA-L2 complex / four-way junction DNA binding / translation repressor activity / negative regulation of translational initiation / translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / ribosome assembly / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / positive regulation of RNA splicing / transcription elongation factor complex / response to reactive oxygen species / DNA endonuclease activity / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / transcription antitermination / regulation of cell growth / maintenance of translational fidelity / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / リボソーム生合成 / regulation of translation / small ribosomal subunit / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / molecular adaptor activity / リボソーム / structural constituent of ribosome / 翻訳 (生物学) / response to antibiotic / mRNA binding / negative regulation of DNA-templated transcription / DNA binding / RNA binding / zinc ion binding / 生体膜 / 細胞質基質 / 細胞質 類似検索 - 分子機能 | |||||||||||||||
生物種 | Escherichia coli (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: 3.5 Å | |||||||||||||||
データ登録者 | Loveland AB / Korostelev AA | |||||||||||||||
資金援助 | 米国, Estonia, 4件
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引用 | ジャーナル: Nat Commun / 年: 2020 タイトル: Ribosome engineering reveals the importance of 5S rRNA autonomy for ribosome assembly. 著者: Shijie Huang / Nikolay A Aleksashin / Anna B Loveland / Dorota Klepacki / Kaspar Reier / Amira Kefi / Teresa Szal / Jaanus Remme / Luc Jaeger / Nora Vázquez-Laslop / Andrei A Korostelev / Alexander S Mankin / 要旨: 5S rRNA is an indispensable component of cytoplasmic ribosomes in all species. The functions of 5S rRNA and the reasons for its evolutionary preservation as an independent molecule remain unclear. ...5S rRNA is an indispensable component of cytoplasmic ribosomes in all species. The functions of 5S rRNA and the reasons for its evolutionary preservation as an independent molecule remain unclear. Here we used ribosome engineering to investigate whether 5S rRNA autonomy is critical for ribosome function and cell survival. By linking circularly permutated 5S rRNA with 23S rRNA we generated a bacterial strain devoid of free 5S rRNA. Viability of the engineered cells demonstrates that autonomous 5S rRNA is dispensable for cell growth under standard conditions and is unlikely to have essential functions outside the ribosome. The fully assembled ribosomes carrying 23S-5S rRNA are highly active in translation. However, the engineered cells accumulate aberrant 50S subunits unable to form stable 70S ribosomes. Cryo-EM analysis revealed a malformed peptidyl transferase center in the misassembled 50S subunits. Our results argue that the autonomy of 5S rRNA is preserved due to its role in ribosome biogenesis. | |||||||||||||||
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_21857.map.gz | 794.7 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-21857-v30.xml emd-21857.xml | 73.6 KB 73.6 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_21857_fsc.xml | 20.7 KB | 表示 | FSCデータファイル |
画像 | emd_21857.png | 175.8 KB | ||
Filedesc metadata | emd-21857.cif.gz | 13.4 KB | ||
その他 | emd_21857_additional.map.gz emd_21857_half_map_1.map.gz emd_21857_half_map_2.map.gz | 794.9 MB 122.7 MB 122.7 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-21857 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21857 | 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_21857.map.gz / 形式: CCP4 / 大きさ: 857.4 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Cryo-EM map of vacant 70S ribosome with 23S-cp5s rRNA and abberant PTC | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.87 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
-追加マップ: Cryo-EM map with B-factor filtering of vacant 70S...
ファイル | emd_21857_additional.map | ||||||||||||
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注釈 | Cryo-EM map with B-factor filtering of vacant 70S ribosome with 23S-cp5s rRNA and abberant PTC | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Cryo-EM half map of vacant 70S ribosome with...
ファイル | emd_21857_half_map_1.map | ||||||||||||
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注釈 | Cryo-EM half map of vacant 70S ribosome with 23S-cp5s rRNA and abberant PTC | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Cryo-EM half map of vacant 70S ribosome with...
ファイル | emd_21857_half_map_2.map | ||||||||||||
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注釈 | Cryo-EM half map of vacant 70S ribosome with 23S-cp5s rRNA and abberant PTC | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
+全体 : 70S ribosome without free 5S rRNA and with perturbed PTC
+超分子 #1: 70S ribosome without free 5S rRNA and with perturbed PTC
+分子 #1: 50S ribosomal protein L2
+分子 #2: 50S ribosomal protein L3
+分子 #3: 50S ribosomal protein L4
+分子 #4: 50S ribosomal protein L5
+分子 #5: 50S ribosomal protein L6
+分子 #6: 50S ribosomal protein L9
+分子 #7: 50S ribosomal protein L10
+分子 #8: 50S ribosomal protein L11
+分子 #9: 50S ribosomal protein L13
+分子 #10: 50S ribosomal protein L14
+分子 #11: 50S ribosomal protein L15
+分子 #12: 50S ribosomal protein L17
+分子 #13: 50S ribosomal protein L18
+分子 #14: 50S ribosomal protein L19
+分子 #15: 50S ribosomal protein L20
+分子 #16: 50S ribosomal protein L21
+分子 #17: 50S ribosomal protein L22
+分子 #18: 50S ribosomal protein L23
+分子 #19: 50S ribosomal protein L24
+分子 #20: 50S ribosomal protein L25
+分子 #21: 50S ribosomal protein L27
+分子 #22: 50S ribosomal protein L28
+分子 #23: 50S ribosomal protein L29
+分子 #24: 50S ribosomal protein L30
+分子 #25: 50S ribosomal protein L31
+分子 #26: 50S ribosomal protein L32
+分子 #27: 50S ribosomal protein L34
+分子 #28: 50S ribosomal protein L35
+分子 #29: 50S ribosomal protein L36
+分子 #30: 30S ribosomal protein S2
+分子 #31: 30S ribosomal protein S3
+分子 #32: 30S ribosomal protein S4
+分子 #33: 30S ribosomal protein S5
+分子 #34: 30S ribosomal protein S6
+分子 #35: 30S ribosomal protein S7
+分子 #36: 30S ribosomal protein S8
+分子 #37: 30S ribosomal protein S9
+分子 #38: 30S ribosomal protein S10
+分子 #39: 30S ribosomal protein S11
+分子 #40: 30S ribosomal protein S12
+分子 #41: 30S ribosomal protein S13
+分子 #42: 30S ribosomal protein S14
+分子 #43: 30S ribosomal protein S15
+分子 #44: 30S ribosomal protein S16
+分子 #45: 30S ribosomal protein S17
+分子 #46: 30S ribosomal protein S18
+分子 #47: 30S ribosomal protein S19
+分子 #48: 30S ribosomal protein S20
+分子 #49: 30S ribosomal protein S21
+分子 #50: 50S ribosomal protein L1
+分子 #51: 16S ribosomal RNA
+分子 #52: 23s-5s joint ribosomal RNA
-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
濃度 | .1 mg/mL |
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緩衝液 | pH: 7 |
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | TFS TALOS |
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電子線 | 加速電圧: 200 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 |
撮影 | フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 平均電子線量: 30.0 e/Å2 |