+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-18320 | |||||||||
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タイトル | E. coli ApdP-stalled ribosomal complex | |||||||||
マップデータ | Postprocessed final map | |||||||||
試料 |
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キーワード | Stalling / nascent chain / translation arrest / regulation (規制) / 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 / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation ...mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / 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 / cytosolic ribosome assembly / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / ribosomal large subunit assembly / mRNA 5'-UTR binding / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit / ribosome binding / regulation of translation / 5S rRNA binding / large ribosomal subunit rRNA binding / small ribosomal subunit / cytosolic small ribosomal subunit / transferase activity / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / molecular adaptor activity / negative regulation of translation / rRNA binding / リボソーム / structural constituent of ribosome / 翻訳 (生物学) / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / 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 | Sinorhizobium medicae (根粒菌) / Escherichia coli BW25113 (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: 2.2 Å | |||||||||
データ登録者 | Morici M / Wilson DN | |||||||||
資金援助 | ドイツ, 1件
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引用 | ジャーナル: Nat Commun / 年: 2024 タイトル: RAPP-containing arrest peptides induce translational stalling by short circuiting the ribosomal peptidyltransferase activity. 著者: Martino Morici / Sara Gabrielli / Keigo Fujiwara / Helge Paternoga / Bertrand Beckert / Lars V Bock / Shinobu Chiba / Daniel N Wilson / 要旨: Arrest peptides containing RAPP (ArgAlaProPro) motifs have been discovered in both Gram-positive and Gram-negative bacteria, where they are thought to regulate expression of important protein ...Arrest peptides containing RAPP (ArgAlaProPro) motifs have been discovered in both Gram-positive and Gram-negative bacteria, where they are thought to regulate expression of important protein localization machinery components. Here we determine cryo-EM structures of ribosomes stalled on RAPP arrest motifs in both Bacillus subtilis and Escherichia coli. Together with molecular dynamics simulations, our structures reveal that the RAPP motifs allow full accommodation of the A-site tRNA, but prevent the subsequent peptide bond from forming. Our data support a model where the RAP in the P-site interacts and stabilizes a single hydrogen atom on the Pro-tRNA in the A-site, thereby preventing an optimal geometry for the nucleophilic attack required for peptide bond formation to occur. This mechanism to short circuit the ribosomal peptidyltransferase activity is likely to operate for the majority of other RAPP-like arrest peptides found across diverse bacterial phylogenies. | |||||||||
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_18320.map.gz | 49.8 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-18320-v30.xml emd-18320.xml | 71.1 KB 71.1 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_18320.png | 61.1 KB | ||
Filedesc metadata | emd-18320.cif.gz | 13.4 KB | ||
その他 | emd_18320_additional_1.map.gz emd_18320_additional_2.map.gz emd_18320_half_map_1.map.gz emd_18320_half_map_2.map.gz | 140 MB 95.3 MB 140.4 MB 140.4 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-18320 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18320 | 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_18320.map.gz / 形式: CCP4 / 大きさ: 178 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | Postprocessed final map | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.82 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
-追加マップ: Preprocessed map
ファイル | emd_18320_additional_1.map | ||||||||||||
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注釈 | Preprocessed map | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Filtered 3D map on the base of local...
ファイル | emd_18320_additional_2.map | ||||||||||||
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注釈 | Filtered 3D map on the base of local resolution as calculated by Bsoft | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half-map 1
ファイル | emd_18320_half_map_1.map | ||||||||||||
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注釈 | Half-map 1 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half-map 2
ファイル | emd_18320_half_map_2.map | ||||||||||||
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注釈 | Half-map 2 | ||||||||||||
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 : E. coli ApdP-stalled ribosomal complex
+超分子 #1: E. coli ApdP-stalled ribosomal complex
+分子 #1: 23S rRNA
+分子 #2: 5S rRNA
+分子 #30: 16S rRNA
+分子 #47: mRNA
+分子 #48: Pro-tRNA
+分子 #49: Ala-tRNA
+分子 #3: Large ribosomal subunit protein uL2
+分子 #4: 50S ribosomal protein L3
+分子 #5: Large ribosomal subunit protein uL4
+分子 #6: Large ribosomal subunit protein uL5
+分子 #7: Large ribosomal subunit protein uL6
+分子 #8: Large ribosomal subunit protein bL9
+分子 #9: Large ribosomal subunit protein uL13
+分子 #10: Large ribosomal subunit protein uL14
+分子 #11: 50S ribosomal protein L15
+分子 #12: 50S ribosomal protein L16
+分子 #13: Large ribosomal subunit protein bL17
+分子 #14: Large ribosomal subunit protein uL18
+分子 #15: Large ribosomal subunit protein bL19
+分子 #16: Large ribosomal subunit protein bL20
+分子 #17: Large ribosomal subunit protein bL21
+分子 #18: Large ribosomal subunit protein uL22
+分子 #19: Large ribosomal subunit protein uL23
+分子 #20: Large ribosomal subunit protein uL24
+分子 #21: 50S ribosomal protein L25
+分子 #22: Large ribosomal subunit protein bL27
+分子 #23: Large ribosomal subunit protein bL28
+分子 #24: Large ribosomal subunit protein uL29
+分子 #25: Large ribosomal subunit protein uL30
+分子 #26: Large ribosomal subunit protein bL32
+分子 #27: Large ribosomal subunit protein bL33
+分子 #28: Large ribosomal subunit protein bL34
+分子 #29: Large ribosomal subunit protein bL35
+分子 #31: 30S ribosomal protein S2
+分子 #32: Small ribosomal subunit protein uS5
+分子 #33: 30S ribosomal protein S6, fully modified isoform
+分子 #34: 30S ribosomal protein S7
+分子 #35: Small ribosomal subunit protein uS8
+分子 #36: Small ribosomal subunit protein uS9
+分子 #37: 30S ribosomal protein S11
+分子 #38: 30S ribosomal protein S12
+分子 #39: Small ribosomal subunit protein uS13
+分子 #40: Small ribosomal subunit protein uS14
+分子 #41: Small ribosomal subunit protein uS15
+分子 #42: Small ribosomal subunit protein uS17
+分子 #43: Small ribosomal subunit protein bS18
+分子 #44: Small ribosomal subunit protein uS19
+分子 #45: 30S ribosomal protein S20
+分子 #46: Small ribosomal subunit protein bS21
+分子 #50: Large ribosomal subunit protein bL36A
+分子 #51: ApdP nascent chain
+分子 #52: MAGNESIUM ION
+分子 #53: POTASSIUM ION
+分子 #54: PROLINE
+分子 #55: ZINC ION
+分子 #56: water
-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-PROPANE |
-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): 1.8 µm / 最小 デフォーカス(公称値): 0.6 µm |
撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 平均電子線量: 75.6 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期モデル | モデルのタイプ: OTHER 詳細: Exprimental unpublished map from our lab from an analogous ample, previously low-pass filtered |
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初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 2.2 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 205838 |