+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-14454 | |||||||||
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タイトル | 70S E. coli ribosome with an extended uL23 loop from Candidatus marinimicrobia and a stalled filamin domain 5 nascent chain | |||||||||
マップデータ | Sharpened map | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 regulation of pseudopodium assembly / anterior cell cortex / Cell-extracellular matrix interactions / pseudopodium assembly / ISG15 antiviral mechanism / Platelet degranulation / sorocarp development / posterior cell cortex / chemotaxis to cAMP / lateral cell cortex ...regulation of pseudopodium assembly / anterior cell cortex / Cell-extracellular matrix interactions / pseudopodium assembly / ISG15 antiviral mechanism / Platelet degranulation / sorocarp development / posterior cell cortex / chemotaxis to cAMP / lateral cell cortex / phototaxis / macropinocytic cup / RHO GTPases activate PAKs / protein kinase B binding / actin crosslink formation / thermotaxis / hyperosmotic response / mitogen-activated protein kinase binding / lamellipodium assembly / cortical actin cytoskeleton / cell leading edge / pseudopodium / phagocytic cup / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / negative regulation of cytoplasmic translation / phagocytosis / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / response to cAMP / mRNA regulatory element binding translation repressor activity / extracellular matrix / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / response to reactive oxygen species / cell motility / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / small GTPase binding / actin filament binding / large ribosomal subunit / cell migration / ribosomal large subunit assembly / cell cortex / transferase activity / large ribosomal subunit rRNA binding / actin cytoskeleton organization / 5S 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 / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / plasma membrane / cytosol / cytoplasm 類似検索 - 分子機能 | |||||||||
生物種 | Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌) / Escherichia coli (大腸菌) / Dictyostelium discoideum (キイロタマホコリカビ) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.29 Å | |||||||||
データ登録者 | Mitropoulou A / Plessa E / Wlodarski T / Ahn M / Sidhu H / Becker TA / Beckmann R / Cabrita LD / Christodoulou J | |||||||||
資金援助 | 英国, 1件
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引用 | ジャーナル: Nat Commun / 年: 2022 タイトル: Modulating co-translational protein folding by rational design and ribosome engineering. 著者: Minkoo Ahn / Tomasz Włodarski / Alkistis Mitropoulou / Sammy H S Chan / Haneesh Sidhu / Elena Plessa / Thomas A Becker / Nediljko Budisa / Christopher A Waudby / Roland Beckmann / Anaïs M E ...著者: Minkoo Ahn / Tomasz Włodarski / Alkistis Mitropoulou / Sammy H S Chan / Haneesh Sidhu / Elena Plessa / Thomas A Becker / Nediljko Budisa / Christopher A Waudby / Roland Beckmann / Anaïs M E Cassaignau / Lisa D Cabrita / John Christodoulou / 要旨: Co-translational folding is a fundamental process for the efficient biosynthesis of nascent polypeptides that emerge through the ribosome exit tunnel. To understand how this process is modulated by ...Co-translational folding is a fundamental process for the efficient biosynthesis of nascent polypeptides that emerge through the ribosome exit tunnel. To understand how this process is modulated by the shape and surface of the narrow tunnel, we have rationally engineered three exit tunnel protein loops (uL22, uL23 and uL24) of the 70S ribosome by CRISPR/Cas9 gene editing, and studied the co-translational folding of an immunoglobulin-like filamin domain (FLN5). Our thermodynamics measurements employing F/N/methyl-TROSY NMR spectroscopy together with cryo-EM and molecular dynamics simulations reveal how the variations in the lengths of the loops present across species exert their distinct effects on the free energy of FLN5 folding. A concerted interplay of the uL23 and uL24 loops is sufficient to alter co-translational folding energetics, which we highlight by the opposite folding outcomes resulting from their extensions. These subtle modulations occur through a combination of the steric effects relating to the shape of the tunnel, the dynamic interactions between the ribosome surface and the unfolded nascent chain, and its altered exit pathway within the vestibule. These results illustrate the role of the exit tunnel structure in co-translational folding, and provide principles for how to remodel it to elicit a desired folding outcome. | |||||||||
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_14454.map.gz | 122 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-14454-v30.xml emd-14454.xml | 40 KB 40 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_14454.png | 172.5 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-14454 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14454 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_14454_validation.pdf.gz | 412.3 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_14454_full_validation.pdf.gz | 411.8 KB | 表示 | |
XML形式データ | emd_14454_validation.xml.gz | 7 KB | 表示 | |
CIF形式データ | emd_14454_validation.cif.gz | 8 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14454 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14454 | 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_14454.map.gz / 形式: CCP4 / 大きさ: 216 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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注釈 | Sharpened map | ||||||||||||||||||||||||||||||||||||
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: 1.067 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
-試料の構成要素
+全体 : ribosomal nascent chain of FLN5
+超分子 #1: ribosomal nascent chain of FLN5
+分子 #1: 50S ribosomal protein L28
+分子 #2: 50S ribosomal protein L29
+分子 #3: 50S ribosomal protein L30
+分子 #4: 50S ribosomal protein L32
+分子 #5: 50S ribosomal protein L33
+分子 #6: 50S ribosomal protein L34
+分子 #7: 50S ribosomal protein L35
+分子 #8: 50S ribosomal protein L36
+分子 #11: 50S ribosomal protein L2
+分子 #12: 50S ribosomal protein L3
+分子 #13: 50S ribosomal protein L4
+分子 #14: 50S ribosomal protein L5
+分子 #15: 50S ribosomal protein L6
+分子 #16: 50S ribosomal protein L9
+分子 #17: 50S ribosomal protein L13
+分子 #18: 50S ribosomal protein L14
+分子 #19: 50S ribosomal protein L15
+分子 #20: 50S ribosomal protein L16
+分子 #21: 50S ribosomal protein L17
+分子 #22: 50S ribosomal protein L18
+分子 #23: 50S ribosomal protein L19
+分子 #24: 50S ribosomal protein L20
+分子 #25: 50S ribosomal protein L21
+分子 #26: 50S ribosomal protein L22
+分子 #27: 50S ribosomal protein L23
+分子 #28: 50S ribosomal protein L24
+分子 #29: 50S ribosomal protein L25
+分子 #30: 50S ribosomal protein L27
+分子 #32: Gelation factor
+分子 #9: 5S rRNA
+分子 #10: 23S rRNA
+分子 #31: Pro-tRNA
-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: 7.5 |
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凍結 | 凍結剤: ETHANE / チャンバー内湿度: 95 % / チャンバー内温度: 277 K |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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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: 40.8 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 / 最大 デフォーカス(公称値): 2.5 µm / 最小 デフォーカス(公称値): 0.5 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 2.29 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 547000 |
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初期 角度割当 | タイプ: ANGULAR RECONSTITUTION |
最終 角度割当 | タイプ: ANGULAR RECONSTITUTION |