+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-19076 | |||||||||
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タイトル | Cryo-EM structure of P. urativorans 70S ribosome in complex with hibernation factor Balon, mRNA and P-site tRNA (structure 2). | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | Ribosome (リボソーム) / Hibernation factor / Dormancy / Balon | |||||||||
機能・相同性 | 機能・相同性情報 guanosine tetraphosphate binding / translation elongation factor activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / small ribosomal subunit / 5S rRNA binding ...guanosine tetraphosphate binding / translation elongation factor activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / small ribosomal subunit / 5S rRNA binding / transferase activity / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / リボソーム / structural constituent of ribosome / ribonucleoprotein complex / 翻訳 (生物学) / mRNA binding / GTPase activity / GTP binding / RNA binding / 細胞質基質 / 細胞質 類似検索 - 分子機能 | |||||||||
生物種 | Psychrobacter urativorans (バクテリア) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.6 Å | |||||||||
データ登録者 | Helena-Bueno K / Rybak MY / Gagnon MG / Hill CH / Melnikov SV | |||||||||
資金援助 | 英国, 1件
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引用 | ジャーナル: Nature / 年: 2024 タイトル: A new family of bacterial ribosome hibernation factors. 著者: Karla Helena-Bueno / Mariia Yu Rybak / Chinenye L Ekemezie / Rudi Sullivan / Charlotte R Brown / Charlotte Dingwall / Arnaud Baslé / Claudia Schneider / James P R Connolly / James N Blaza / ...著者: Karla Helena-Bueno / Mariia Yu Rybak / Chinenye L Ekemezie / Rudi Sullivan / Charlotte R Brown / Charlotte Dingwall / Arnaud Baslé / Claudia Schneider / James P R Connolly / James N Blaza / Bálint Csörgő / Patrick J Moynihan / Matthieu G Gagnon / Chris H Hill / Sergey V Melnikov / 要旨: To conserve energy during starvation and stress, many organisms use hibernation factor proteins to inhibit protein synthesis and protect their ribosomes from damage. In bacteria, two families of ...To conserve energy during starvation and stress, many organisms use hibernation factor proteins to inhibit protein synthesis and protect their ribosomes from damage. In bacteria, two families of hibernation factors have been described, but the low conservation of these proteins and the huge diversity of species, habitats and environmental stressors have confounded their discovery. Here, by combining cryogenic electron microscopy, genetics and biochemistry, we identify Balon, a new hibernation factor in the cold-adapted bacterium Psychrobacter urativorans. We show that Balon is a distant homologue of the archaeo-eukaryotic translation factor aeRF1 and is found in 20% of representative bacteria. During cold shock or stationary phase, Balon occupies the ribosomal A site in both vacant and actively translating ribosomes in complex with EF-Tu, highlighting an unexpected role for EF-Tu in the cellular stress response. Unlike typical A-site substrates, Balon binds to ribosomes in an mRNA-independent manner, initiating a new mode of ribosome hibernation that can commence while ribosomes are still engaged in protein synthesis. Our work suggests that Balon-EF-Tu-regulated ribosome hibernation is a ubiquitous bacterial stress-response mechanism, and we demonstrate that putative Balon homologues in Mycobacteria bind to ribosomes in a similar fashion. This finding calls for a revision of the current model of ribosome hibernation inferred from common model organisms and holds numerous implications for how we understand and study ribosome hibernation. #1: ジャーナル: Biorxiv / 年: 2023 タイトル: A bacterial ribosome hibernation factor with evolutionary connections to eukaryotic protein synthesis 著者: Helena-Bueno K / Ekemezie CL / Brown CR / Basle A / Blaza JN / Hill CH / Melnikov SV | |||||||||
履歴 |
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-構造の表示
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_19076.map.gz | 352.7 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-19076-v30.xml emd-19076.xml | 72.6 KB 72.6 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_19076_fsc.xml | 19.1 KB | 表示 | FSCデータファイル |
画像 | emd_19076.png | 111.8 KB | ||
マスクデータ | emd_19076_msk_1.map | 600.7 MB | マスクマップ | |
Filedesc metadata | emd-19076.cif.gz | 14.2 KB | ||
その他 | emd_19076_half_map_1.map.gz emd_19076_half_map_2.map.gz | 483.5 MB 483.6 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-19076 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19076 | 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_19076.map.gz / 形式: CCP4 / 大きさ: 600.7 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 0.723 Å | ||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-マスク #1
ファイル | emd_19076_msk_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #2
ファイル | emd_19076_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_19076_half_map_2.map | ||||||||||||
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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 : Ribosomes isolated from ice-treated cultures of Psychrobacter ura...
+超分子 #1: Ribosomes isolated from ice-treated cultures of Psychrobacter ura...
+分子 #1: Methyl-accepting chemotaxis protein
+分子 #2: Small ribosomal subunit protein uS9
+分子 #3: Elongation factor Tu
+分子 #5: Small ribosomal subunit protein bS18
+分子 #6: Small ribosomal subunit protein uS2
+分子 #7: Small ribosomal subunit protein uS5
+分子 #8: Small ribosomal subunit protein uS12
+分子 #9: Large ribosomal subunit protein uL5
+分子 #11: Large ribosomal subunit protein uL4
+分子 #12: Large ribosomal subunit protein bL32
+分子 #13: Large ribosomal subunit protein bL17
+分子 #14: Large ribosomal subunit protein bL25
+分子 #15: Large ribosomal subunit protein bL28
+分子 #16: Large ribosomal subunit protein uL29
+分子 #17: Large ribosomal subunit protein uL22
+分子 #18: Small ribosomal subunit protein bS6
+分子 #19: Large ribosomal subunit protein bL27
+分子 #20: Large ribosomal subunit protein uL24
+分子 #21: Large ribosomal subunit protein bL31B
+分子 #22: Small ribosomal subunit protein uS14
+分子 #23: Small ribosomal subunit protein uS15
+分子 #24: Small ribosomal subunit protein uS13
+分子 #25: Large ribosomal subunit protein bL20
+分子 #26: Small ribosomal subunit protein uS19
+分子 #27: Small ribosomal subunit protein uS8
+分子 #28: Large ribosomal subunit protein uL6
+分子 #29: Small ribosomal subunit protein uS7
+分子 #30: Small ribosomal subunit protein uS3
+分子 #31: Small ribosomal subunit protein uS11
+分子 #32: Small ribosomal subunit protein bS21
+分子 #33: Large ribosomal subunit protein uL30
+分子 #34: Large ribosomal subunit protein uL13
+分子 #35: Small ribosomal subunit protein uS10
+分子 #36: Small ribosomal subunit protein uS17
+分子 #37: Large ribosomal subunit protein bL34
+分子 #38: Large ribosomal subunit protein bL21
+分子 #39: Large ribosomal subunit protein uL18
+分子 #40: Large ribosomal subunit protein uL15
+分子 #41: Large ribosomal subunit protein uL14
+分子 #42: Large ribosomal subunit protein uL3
+分子 #43: Large ribosomal subunit protein uL16
+分子 #44: Large ribosomal subunit protein bL35
+分子 #45: Large ribosomal subunit protein bL19
+分子 #46: Small ribosomal subunit protein bS16
+分子 #47: Large ribosomal subunit protein bL33
+分子 #48: Large ribosomal subunit protein uL2
+分子 #49: Small ribosomal subunit protein uS4
+分子 #50: Large ribosomal subunit protein uL23
+分子 #51: Small ribosomal subunit protein bS20
+分子 #52: Large ribosomal subunit protein bL36
+分子 #55: Large ribosomal subunit protein bL9
+分子 #4: 23S rRNA
+分子 #10: 5S rRNA
+分子 #53: Heterogenous tRNA
+分子 #54: Heterogenous mRNA
+分子 #56: 16S rRNA
-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 | 0.75 mg/mL |
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緩衝液 | pH: 7.5 |
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | TFS 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 / 最大 デフォーカス(公称値): 2.4 µm / 最小 デフォーカス(公称値): 0.9 µm |
撮影 | フィルム・検出器のモデル: FEI FALCON IV (4k x 4k) 平均電子線量: 40.0 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |