+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-4001 | ||||||||||||||||||
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タイトル | Cryo-EM structure of stringent response factor RelA bound to ErmCL-stalled ribosome complex | ||||||||||||||||||
マップデータ | None | ||||||||||||||||||
試料 |
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キーワード | Stringent Response / RelA / Ribosome (リボソーム) / Cryo-EM (低温電子顕微鏡法) | ||||||||||||||||||
機能・相同性 | 機能・相同性情報 guanosine tetraphosphate metabolic process / guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity / GTP diphosphokinase activity / guanosine tetraphosphate biosynthetic process / GTP diphosphokinase / nucleobase-containing small molecule interconversion / negative regulation of cytoplasmic translational initiation / stringent response / response to starvation / mRNA base-pairing translational repressor activity ...guanosine tetraphosphate metabolic process / guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity / GTP diphosphokinase activity / guanosine tetraphosphate biosynthetic process / GTP diphosphokinase / nucleobase-containing small molecule interconversion / negative regulation of cytoplasmic translational initiation / stringent response / response to starvation / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded 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 / translational termination / DnaA-L2 complex / four-way junction DNA binding / translation repressor activity / negative regulation of translational initiation / translational initiation / 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 / positive regulation of RNA splicing / transcription elongation factor complex / response to reactive oxygen species / 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 / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / ribosomal small 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 / cytoplasmic translation / 5S rRNA binding / kinase activity / cytosolic large ribosomal subunit / 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) / リン酸化 / response to antibiotic / mRNA binding / negative regulation of DNA-templated transcription / GTP binding / DNA binding / RNA binding / zinc ion binding / ATP 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 K-12 (大腸菌) / Escherichia coli K12 (大腸菌) / Escherichia coli (strain K12) (大腸菌) / Escherichia coli O157:H7 (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 | Arenz S / Wilson DN | ||||||||||||||||||
資金援助 | ドイツ, スウェーデン, 5件
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引用 | ジャーナル: Nucleic Acids Res / 年: 2016 タイトル: The stringent factor RelA adopts an open conformation on the ribosome to stimulate ppGpp synthesis. 著者: Stefan Arenz / Maha Abdelshahid / Daniel Sohmen / Roshani Payoe / Agata L Starosta / Otto Berninghausen / Vasili Hauryliuk / Roland Beckmann / Daniel N Wilson / 要旨: Under stress conditions, such as nutrient starvation, deacylated tRNAs bound within the ribosomal A-site are recognized by the stringent factor RelA, which converts ATP and GTP/GDP to (p)ppGpp. The ...Under stress conditions, such as nutrient starvation, deacylated tRNAs bound within the ribosomal A-site are recognized by the stringent factor RelA, which converts ATP and GTP/GDP to (p)ppGpp. The signaling molecules (p)ppGpp globally rewire the cellular transcriptional program and general metabolism, leading to stress adaptation. Despite the additional importance of the stringent response for regulation of bacterial virulence, antibiotic resistance and persistence, structural insight into how the ribosome and deacylated-tRNA stimulate RelA-mediated (p)ppGpp has been lacking. Here, we present a cryo-EM structure of RelA in complex with the Escherichia coli 70S ribosome with an average resolution of 3.7 Å and local resolution of 4 to >10 Å for RelA. The structure reveals that RelA adopts a unique 'open' conformation, where the C-terminal domain (CTD) is intertwined around an A/T-like tRNA within the intersubunit cavity of the ribosome and the N-terminal domain (NTD) extends into the solvent. We propose that the open conformation of RelA on the ribosome relieves the autoinhibitory effect of the CTD on the NTD, thus leading to stimulation of (p)ppGpp synthesis by RelA. | ||||||||||||||||||
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_4001.map.gz | 177.5 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-4001-v30.xml emd-4001.xml | 73.4 KB 73.4 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_4001.png | 33.5 KB | ||
Filedesc metadata | emd-4001.cif.gz | 14.9 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-4001 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4001 | 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_4001.map.gz / 形式: CCP4 / 大きさ: 190.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.065 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
-試料の構成要素
+全体 : Cryo-EM structure of stringent response factor RelA bound to ErmC...
+超分子 #1: Cryo-EM structure of stringent response factor RelA bound to ErmC...
+分子 #1: 23S ribosomal RNA
+分子 #2: 5S ribosomal RNA
+分子 #32: 16S ribosomal RNA
+分子 #51: mRNA
+分子 #52: P-site tRNA
+分子 #58: deacylated A/R-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 L9
+分子 #9: 50S ribosomal protein L13
+分子 #10: 50S ribosomal protein L14
+分子 #11: 50S ribosomal protein L15
+分子 #12: 50S ribosomal protein L16
+分子 #13: 50S ribosomal protein L17
+分子 #14: 50S ribosomal protein L18
+分子 #15: 50S ribosomal protein L19
+分子 #16: 50S ribosomal protein L20
+分子 #17: 50S ribosomal protein L21
+分子 #18: 50S ribosomal protein L22
+分子 #19: 50S ribosomal protein L23
+分子 #20: 50S ribosomal protein L24
+分子 #21: 50S ribosomal protein L25
+分子 #22: 50S ribosomal protein L27
+分子 #23: 50S ribosomal protein L28
+分子 #24: 50S ribosomal protein L29
+分子 #25: 50S ribosomal protein L30
+分子 #26: 50S ribosomal protein L31
+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 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 S20
+分子 #50: 30S ribosomal protein S21
+分子 #53: 50S ribosomal protein L10
+分子 #54: 50S ribosomal protein L11
+分子 #55: 30S ribosomal protein S14
+分子 #56: 30S ribosomal protein S19
+分子 #57: GTP pyrophosphokinase,GTP pyrophosphokinase,GTP pyrophosphokinase
-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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グリッド | モデル: Quantifoil R3/3 / 材質: COPPER / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY |
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 / Cs: 2.7 mm / 最大 デフォーカス(公称値): 2.2 µm 最小 デフォーカス(公称値): 0.7000000000000001 µm |
撮影 | フィルム・検出器のモデル: FEI FALCON II (4k x 4k) 検出モード: INTEGRATING / 平均電子線量: 25.0 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: INSILICO MODEL |
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初期 角度割当 | タイプ: PROJECTION MATCHING / ソフトウェア - 名称: SPIDER |
最終 角度割当 | タイプ: PROJECTION MATCHING / ソフトウェア - 名称: SPIDER |
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 / ソフトウェア - 名称: SPIDER / 使用した粒子像数: 24749 |
-原子モデル構築 1
精密化 | 空間: REAL / プロトコル: RIGID BODY FIT |
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得られたモデル | PDB-5l3p: |