+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-3903 | |||||||||
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タイトル | Polyproline-stalled ribosome in the presence of elongation-factor P (EF-P) | |||||||||
マップデータ | Polyproline stalled ribosome in presence of EF-P with a truncated mRNA in the A-site. | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 peptide biosynthetic process / negative regulation of translational frameshifting / negative regulation of cytoplasmic translational initiation / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / translational elongation / transcriptional attenuation ...peptide biosynthetic process / negative regulation of translational frameshifting / negative regulation of cytoplasmic translational initiation / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / translational elongation / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translation elongation factor activity / four-way junction DNA binding / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / rescue of stalled ribosome / ribosome assembly / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / regulation of DNA-templated transcription elongation / cytosolic ribosome assembly / DNA endonuclease activity / transcription antitermination / response to reactive oxygen species / translational initiation / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / large ribosomal subunit / ribosome biogenesis / small ribosomal subunit rRNA binding / ribosome binding / ribosomal large subunit assembly / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / large ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / molecular adaptor activity / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm 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: 3.1 Å | |||||||||
データ登録者 | Huter P / Arenz S / Wilson DN | |||||||||
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_3903.map.gz | 14.1 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-3903-v30.xml emd-3903.xml | 64 KB 64 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_3903.png | 63.9 KB | ||
その他 | emd_3903_additional.map.gz | 21.1 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-3903 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3903 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_3903_validation.pdf.gz | 258.2 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_3903_full_validation.pdf.gz | 257.3 KB | 表示 | |
XML形式データ | emd_3903_validation.xml.gz | 6.8 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3903 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3903 | 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_3903.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 presence of EF-P with a truncated mRNA in the A-site. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.084 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 with a truncated mRNA in the A-site.
ファイル | emd_3903_additional.map | ||||||||||||
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注釈 | Polyproline stalled ribosome with a truncated mRNA in the A-site. | ||||||||||||
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 absence of elongation factor P
+超分子 #1: Polyproline stalled ribosome in the absence of elongation factor P
+分子 #1: 16S ribosomal RNA
+分子 #22: mRNA
+分子 #23: 23S Ribosomal RNA
+分子 #24: 5S Ribosomal RNA
+分子 #54: Proline tRNA
+分子 #2: 30S ribosomal protein S2
+分子 #3: 30S ribosomal protein S3
+分子 #4: 30S ribosomal protein S4
+分子 #5: 30S ribosomal protein S5
+分子 #6: 30S ribosomal protein S6
+分子 #7: 30S ribosomal protein S7
+分子 #8: 30S ribosomal protein S8
+分子 #9: 30S ribosomal protein S9
+分子 #10: 30S ribosomal protein S10
+分子 #11: 30S ribosomal protein S11
+分子 #12: 30S ribosomal protein S12
+分子 #13: 30S ribosomal protein S13
+分子 #14: 30S ribosomal protein S14
+分子 #15: 30S ribosomal protein S15
+分子 #16: 30S ribosomal protein S16
+分子 #17: 30S ribosomal protein S17
+分子 #18: 30S ribosomal protein S18
+分子 #19: 30S ribosomal protein S19
+分子 #20: 30S ribosomal protein S20
+分子 #21: 30S ribosomal protein S21
+分子 #25: 50S ribosomal protein L2
+分子 #26: 50S ribosomal protein L3
+分子 #27: 50S ribosomal protein L4
+分子 #28: 50S ribosomal protein L5
+分子 #29: 50S ribosomal protein L6
+分子 #30: 50S ribosomal protein L9
+分子 #31: 50S ribosomal protein L13
+分子 #32: 50S ribosomal protein L14
+分子 #33: 50S ribosomal protein L15
+分子 #34: 50S ribosomal protein L16
+分子 #35: 50S ribosomal protein L17
+分子 #36: 50S ribosomal protein L18
+分子 #37: 50S ribosomal protein L19
+分子 #38: 50S ribosomal protein L20
+分子 #39: 50S ribosomal protein L21
+分子 #40: 50S ribosomal protein L22
+分子 #41: 50S ribosomal protein L23
+分子 #42: 50S ribosomal protein L24
+分子 #43: 50S ribosomal protein L25
+分子 #44: 50S ribosomal protein L27
+分子 #45: 50S ribosomal protein L28
+分子 #46: 50S ribosomal protein L29
+分子 #47: 50S ribosomal protein L30
+分子 #48: 50S ribosomal protein L32
+分子 #49: 50S ribosomal protein L33
+分子 #50: 50S ribosomal protein L34
+分子 #51: 50S ribosomal protein L35
+分子 #52: 50S ribosomal protein L36
+分子 #53: 50S ribosomal protein L31
+分子 #55: 50S ribosomal protein L1
+分子 #56: Elongation factor P
+分子 #57: 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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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 |
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 FIELD |
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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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.1 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 63665 |
初期 角度割当 | タイプ: PROJECTION MATCHING |
最終 角度割当 | タイプ: PROJECTION MATCHING |
-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-6enu: |