+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-3899 | ||||||||||||
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タイトル | Polyproline-stalled ribosome in the presence of A+P site tRNA and elongation-factor P (EF-P) | ||||||||||||
マップデータ | Polyproline-stalled ribosome in the presence of A-site P-site tRNA as well as elongation factor P (EF-P) | ||||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 negative regulation of translational frameshifting / negative regulation of cytoplasmic translational initiation / translational elongation / 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 ...negative regulation of translational frameshifting / negative regulation of cytoplasmic translational initiation / translational elongation / 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 / DnaA-L2 complex / negative regulation of translational initiation / four-way junction DNA binding / translation repressor activity / translational initiation / negative regulation of DNA-templated DNA replication initiation / translation elongation factor activity / rescue of stalled ribosome / 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 / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / transcription antitermination / DNA endonuclease activity / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / : / response to radiation / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / regulation of translation / リボソーム生合成 / ribosome binding / large ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit / small ribosomal subunit / cytoplasmic translation / transferase activity / tRNA binding / negative regulation of translation / molecular adaptor activity / リボソーム / rRNA binding / 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: 3.7 Å | ||||||||||||
データ登録者 | Huter P / Wilson DN | ||||||||||||
資金援助 | ドイツ, オランダ, 3件
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引用 | ジャーナル: Mol Cell / 年: 2017 タイトル: Structural Basis for Polyproline-Mediated Ribosome Stalling and Rescue by the Translation Elongation Factor EF-P. 著者: Paul Huter / Stefan Arenz / Lars V Bock / Michael Graf / Jan Ole Frister / Andre Heuer / Lauri Peil / Agata L Starosta / Ingo Wohlgemuth / Frank Peske / Jiří Nováček / Otto Berninghausen ...著者: Paul Huter / Stefan Arenz / Lars V Bock / Michael Graf / Jan Ole Frister / Andre Heuer / Lauri Peil / Agata L Starosta / Ingo Wohlgemuth / Frank Peske / Jiří Nováček / Otto Berninghausen / Helmut Grubmüller / Tanel Tenson / Roland Beckmann / Marina V Rodnina / Andrea C Vaiana / Daniel N Wilson / 要旨: Ribosomes synthesizing proteins containing consecutive proline residues become stalled and require rescue via the action of uniquely modified translation elongation factors, EF-P in bacteria, or ...Ribosomes synthesizing proteins containing consecutive proline residues become stalled and require rescue via the action of uniquely modified translation elongation factors, EF-P in bacteria, or archaeal/eukaryotic a/eIF5A. To date, no structures exist of EF-P or eIF5A in complex with translating ribosomes stalled at polyproline stretches, and thus structural insight into how EF-P/eIF5A rescue these arrested ribosomes has been lacking. Here we present cryo-EM structures of ribosomes stalled on proline stretches, without and with modified EF-P. The structures suggest that the favored conformation of the polyproline-containing nascent chain is incompatible with the peptide exit tunnel of the ribosome and leads to destabilization of the peptidyl-tRNA. Binding of EF-P stabilizes the P-site tRNA, particularly via interactions between its modification and the CCA end, thereby enforcing an alternative conformation of the polyproline-containing nascent chain, which allows a favorable substrate geometry for peptide bond formation. | ||||||||||||
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_3899.map.gz | 20.8 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-3899-v30.xml emd-3899.xml | 63.8 KB 63.8 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_3899.png | 63.2 KB | ||
その他 | emd_3899_additional.map.gz | 22.1 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-3899 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3899 | 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_3899.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 | Polyproline-stalled ribosome in the presence of A-site P-site tRNA as well as elongation factor P (EF-P) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.084 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: Polyproline-stalled ribosome in the presence of A-site and...
ファイル | emd_3899_additional.map | ||||||||||||
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注釈 | Polyproline-stalled ribosome in the presence of A-site and P-site tRNA, but without elongation-factor P (EF-P) | ||||||||||||
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 : Polyproline-stalled ribosome in the presence of A+P site tRNA and...
+超分子 #1: Polyproline-stalled ribosome in the presence of A+P site tRNA and...
+分子 #1: 23S Ribosomal RNA
+分子 #2: 5S Ribosomal RNA
+分子 #31: 16S ribosomal RNA
+分子 #53: mRNA
+分子 #54: Proline tRNA
+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 L13
+分子 #9: 50S ribosomal protein L14
+分子 #10: 50S ribosomal protein L15
+分子 #11: 50S ribosomal protein L16
+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 L32
+分子 #26: 50S ribosomal protein L33
+分子 #27: 50S ribosomal protein L34
+分子 #28: 50S ribosomal protein L35
+分子 #29: 50S ribosomal protein L36
+分子 #30: 50S ribosomal protein L31
+分子 #32: 30S ribosomal protein S2
+分子 #33: 30S ribosomal protein S3
+分子 #34: 30S ribosomal protein S4
+分子 #35: 30S ribosomal protein S5
+分子 #36: 30S ribosomal protein S6
+分子 #37: 30S ribosomal protein S7
+分子 #38: 30S ribosomal protein S8
+分子 #39: 30S ribosomal protein S9
+分子 #40: 30S ribosomal protein S10
+分子 #41: 30S ribosomal protein S11
+分子 #42: 30S ribosomal protein S12
+分子 #43: 30S ribosomal protein S13
+分子 #44: 30S ribosomal protein S14
+分子 #45: 30S ribosomal protein S15
+分子 #46: 30S ribosomal protein S16
+分子 #47: 30S ribosomal protein S17
+分子 #48: 30S ribosomal protein S18
+分子 #49: 30S ribosomal protein S19
+分子 #50: 30S ribosomal protein S20
+分子 #51: 30S ribosomal protein S21
+分子 #52: Elongation factor P
+分子 #55: 50S ribosomal protein L1
+分子 #56: PROLINE
-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 |
-電子顕微鏡法
顕微鏡 | FEI TITAN 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: SPOT SCAN / 撮影モード: BRIGHT FIELDBright-field microscopy |
撮影 | フィルム・検出器のモデル: FEI FALCON II (4k x 4k) 平均電子線量: 28.0 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: PDB ENTRY PDBモデル - PDB ID: |
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初期 角度割当 | タイプ: PROJECTION MATCHING |
最終 角度割当 | タイプ: PROJECTION MATCHING |
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.7 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 21655 |
-原子モデル構築 1
精密化 | 空間: REAL |
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得られたモデル | PDB-6enj: |