+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-8505 | |||||||||
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タイトル | Structural Basis of Co-translational Quality Control by ArfA and RF2 Bound to Ribosome | |||||||||
マップデータ | ||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 translation release factor activity, codon specific / stringent response / ribosomal large subunit binding / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / misfolded RNA binding / transcription antitermination factor activity, RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation ...translation release factor activity, codon specific / stringent response / ribosomal large subunit binding / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / misfolded RNA binding / transcription antitermination factor activity, 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 / rescue of stalled ribosome / translational termination / DnaA-L2 complex / four-way junction DNA binding / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / ribosome assembly / mRNA regulatory element binding translation repressor activity / response to reactive oxygen species / assembly of large subunit precursor of preribosome / transcription elongation factor complex / positive regulation of RNA splicing / 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 / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / ribosomal large 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 / 5S rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / 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) / 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: 3.5 Å | |||||||||
データ登録者 | Zeng F / Chen Y / Remis J / Shekhar M / Phillips JC / Tajkhorshid E / Jin H | |||||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Nature / 年: 2017 タイトル: Structural basis of co-translational quality control by ArfA and RF2 bound to ribosome. 著者: Fuxing Zeng / Yanbo Chen / Jonathan Remis / Mrinal Shekhar / James C Phillips / Emad Tajkhorshid / Hong Jin / 要旨: Quality control mechanisms intervene appropriately when defective translation events occur, in order to preserve the integrity of protein synthesis. Rescue of ribosomes translating on messenger RNAs ...Quality control mechanisms intervene appropriately when defective translation events occur, in order to preserve the integrity of protein synthesis. Rescue of ribosomes translating on messenger RNAs that lack stop codons is one of the co-translational quality control pathways. In many bacteria, ArfA recognizes stalled ribosomes and recruits the release factor RF2, which catalyses the termination of protein synthesis. Although an induced-fit mechanism of nonstop mRNA surveillance mediated by ArfA and RF2 has been reported, the molecular interaction between ArfA and RF2 in the ribosome that is responsible for the mechanism is unknown. Here we report an electron cryo-microscopy structure of ArfA and RF2 in complex with the 70S ribosome bound to a nonstop mRNA. The structure, which is consistent with our kinetic and biochemical data, reveals the molecular interactions that enable ArfA to specifically recruit RF2, not RF1, into the ribosome and to enable RF2 to release the truncated protein product in this co-translational quality control pathway. The positively charged C-terminal domain of ArfA anchors in the mRNA entry channel of the ribosome. Furthermore, binding of ArfA and RF2 induces conformational changes in the ribosomal decoding centre that are similar to those seen in other protein-involved decoding processes. Specific interactions between residues in the N-terminal domain of ArfA and RF2 help RF2 to adopt a catalytically competent conformation for peptide release. Our findings provide a framework for understanding recognition of the translational state of the ribosome by new proteins, and expand our knowledge of the decoding potential of the ribosome. | |||||||||
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_8505.map.gz | 202.4 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-8505-v30.xml emd-8505.xml | 116.6 KB 116.6 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_8505_fsc.xml | 13.4 KB | 表示 | FSCデータファイル |
画像 | emd_8505.png | 99.8 KB | ||
その他 | emd_8505_half_map_1.map.gz emd_8505_half_map_2.map.gz | 171.5 MB 171.5 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-8505 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8505 | 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_8505.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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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: 1.193 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
-ハーフマップ: #1
ファイル | emd_8505_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: #2
ファイル | emd_8505_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 : Non-stop ribosomal complex with ArfA and RF2
+超分子 #1: Non-stop ribosomal complex with ArfA and RF2
+超分子 #2: 30S subunit
+超分子 #3: 50S subunit
+超分子 #11: 30S ribosomal protein S2
+超分子 #49: 50S ribosomal protein L25
+超分子 #4: Alternative ribosome-rescue factor A
+超分子 #5: Peptide chain release factor 2
+超分子 #6: P-site or E-site fMet-tRNA(fMet)
+超分子 #7: mRNA
+超分子 #8: 23S rRNA
+超分子 #9: 50S ribosomal protein L2
+超分子 #10: 16S rRNA
+超分子 #12: 30S ribosomal protein S3
+超分子 #13: 30S ribosomal protein S4
+超分子 #14: 30S ribosomal protein S5
+超分子 #15: 30S ribosomal protein S6
+超分子 #16: 30S ribosomal protein S7
+超分子 #17: 30S ribosomal protein S8
+超分子 #18: 30S ribosomal protein S9
+超分子 #19: 30S ribosomal protein S10
+超分子 #20: 30S ribosomal protein S11
+超分子 #21: 30S ribosomal protein S12
+超分子 #22: 30S ribosomal protein S13
+超分子 #23: 30S ribosomal protein S14
+超分子 #24: 30S ribosomal protein S15
+超分子 #25: 30S ribosomal protein S16
+超分子 #26: 30S ribosomal protein S17
+超分子 #27: 30S ribosomal protein S18
+超分子 #28: 30S ribosomal protein S19
+超分子 #29: 30S ribosomal protein S20
+超分子 #30: 30S ribosomal protein S21
+超分子 #31: 50S ribosomal protein L3
+超分子 #32: 50S ribosomal protein L4
+超分子 #33: 50S ribosomal protein L5
+超分子 #34: 50S ribosomal protein L6
+超分子 #35: 50S ribosomal protein L9
+超分子 #36: 50S ribosomal protein L11
+超分子 #37: 50S ribosomal protein L13
+超分子 #38: 50S ribosomal protein L14
+超分子 #39: 50S ribosomal protein L15
+超分子 #40: 50S ribosomal protein L16
+超分子 #41: 50S ribosomal protein L17
+超分子 #42: 50S ribosomal protein L18
+超分子 #43: 50S ribosomal protein L19
+超分子 #44: 50S ribosomal protein L20
+超分子 #45: 50S ribosomal protein L21
+超分子 #46: 50S ribosomal protein L22
+超分子 #47: 50S ribosomal protein L23
+超分子 #48: 50S ribosomal protein L24
+超分子 #50: 50S ribosomal protein L27
+超分子 #51: 50S ribosomal protein L28
+超分子 #52: 50S ribosomal protein L29
+超分子 #53: 50S ribosomal protein L30
+超分子 #54: 50S ribosomal protein L32
+超分子 #55: 50S ribosomal protein L33
+超分子 #56: 50S ribosomal protein L34
+超分子 #57: 50S ribosomal protein L35
+超分子 #58: 50S ribosomal protein L36
+超分子 #59: 5S rRNA
+分子 #1: 23S rRNA
+分子 #2: 5S rRNA
+分子 #32: 16S rRNA
+分子 #55: P-site or E-site fMet-tRNA(fMet)
+分子 #56: mRNA
+分子 #3: 50S ribosomal protein L2
+分子 #4: 50S ribosomal protein L3
+分子 #5: 50S ribosomal protein L4
+分子 #6: 50S ribosomal protein L5
+分子 #7: 50S ribosomal protein L6
+分子 #8: 50S ribosomal protein L9
+分子 #9: 50S ribosomal protein L11
+分子 #10: 50S ribosomal protein L13
+分子 #11: 50S ribosomal protein L14
+分子 #12: 50S ribosomal protein L15
+分子 #13: 50S ribosomal protein L16
+分子 #14: 50S ribosomal protein L17
+分子 #15: 50S ribosomal protein L18
+分子 #16: 50S ribosomal protein L19
+分子 #17: 50S ribosomal protein L20
+分子 #18: 50S ribosomal protein L21
+分子 #19: 50S ribosomal protein L22
+分子 #20: 50S ribosomal protein L23
+分子 #21: 50S ribosomal protein L24
+分子 #22: 50S ribosomal protein L25
+分子 #23: 50S ribosomal protein L27
+分子 #24: 50S ribosomal protein L28
+分子 #25: 50S ribosomal protein L29
+分子 #26: 50S ribosomal protein L30
+分子 #27: 50S ribosomal protein L32
+分子 #28: 50S ribosomal protein L33
+分子 #29: 50S ribosomal protein L34
+分子 #30: 50S ribosomal protein L35
+分子 #31: 50S ribosomal protein L36
+分子 #33: 30S ribosomal protein S2
+分子 #34: 30S ribosomal protein S3
+分子 #35: 30S ribosomal protein S4
+分子 #36: 30S ribosomal protein S5
+分子 #37: 30S ribosomal protein S6
+分子 #38: 30S ribosomal protein S7
+分子 #39: 30S ribosomal protein S8
+分子 #40: 30S ribosomal protein S9
+分子 #41: 30S ribosomal protein S10
+分子 #42: 30S ribosomal protein S11
+分子 #43: 30S ribosomal protein S12
+分子 #44: 30S ribosomal protein S13
+分子 #45: 30S ribosomal protein S14
+分子 #46: 30S ribosomal protein S15
+分子 #47: 30S ribosomal protein S16
+分子 #48: 30S ribosomal protein S17
+分子 #49: 30S ribosomal protein S18
+分子 #50: 30S ribosomal protein S19
+分子 #51: 30S ribosomal protein S20
+分子 #52: 30S ribosomal protein S21
+分子 #53: Peptide chain release factor 2
+分子 #54: Alternative ribosome-rescue factor A
+分子 #57: MAGNESIUM ION
+分子 #58: ZINC ION
-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 | 0.2 mg/mL | |||||||||||||||||||||
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緩衝液 | pH: 7.5 構成要素:
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グリッド | モデル: C-flat-2/0.5 4C / 材質: COPPER / メッシュ: 400 / 前処理 - タイプ: GLOW DISCHARGE | |||||||||||||||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK IV |
-電子顕微鏡法
顕微鏡 | JEOL 3200FSC |
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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 | 倍率(補正後): 83822 / 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): 3.0 µm / 最小 デフォーカス(公称値): 0.7 µm |
試料ステージ | ホルダー冷却材: NITROGEN |
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: SUPER-RESOLUTION / デジタル化 - 画像ごとのフレーム数: 4-25 / 平均露光時間: 6.0 sec. / 平均電子線量: 20.0 e/Å2 |
-画像解析
-原子モデル構築 1
精密化 | 空間: RECIPROCAL / プロトコル: FLEXIBLE FIT / 当てはまり具合の基準: Average FSC |
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得られたモデル | PDB-5u4i: |