+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-8279 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
タイトル | Structure of RelA bound to ribosome in absence of A/R tRNA (Structure I) | ||||||||||||
マップデータ | Ribosome*RelA structures reveal the mechanism of stringent response activation (Structure I) | ||||||||||||
試料 |
| ||||||||||||
機能・相同性 | 機能・相同性情報 guanosine tetraphosphate metabolic process / GTP diphosphokinase activity / guanosine tetraphosphate biosynthetic process / GTP diphosphokinase / guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity / 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 / GTP diphosphokinase activity / guanosine tetraphosphate biosynthetic process / GTP diphosphokinase / guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity / 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 / 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 / translational initiation / ribosome assembly / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / DNA endonuclease activity / regulation of DNA-templated transcription elongation / cytosolic ribosome assembly / transcription antitermination / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / ribosomal large subunit assembly / mRNA 5'-UTR binding / large ribosomal subunit / ribosome biogenesis / ribosome binding / kinase activity / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / molecular adaptor activity / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / phosphorylation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / GTP binding / DNA binding / RNA binding / zinc ion binding / ATP binding / membrane / plasma membrane / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||||||||
生物種 | Escherichia coli (strain K12) (大腸菌) / Escherichia coli K-12 (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: 3.9 Å | ||||||||||||
データ登録者 | Loveland AB / Bah E / Madireddy R / Zhang Y / Brilot AF / Grigorieff N / Korostelev AA | ||||||||||||
資金援助 | 米国, 3件
| ||||||||||||
引用 | ジャーナル: Elife / 年: 2016 タイトル: Ribosome•RelA structures reveal the mechanism of stringent response activation. 著者: Anna B Loveland / Eugene Bah / Rohini Madireddy / Ying Zhang / Axel F Brilot / Nikolaus Grigorieff / Andrei A Korostelev / 要旨: Stringent response is a conserved bacterial stress response underlying virulence and antibiotic resistance. RelA/SpoT-homolog proteins synthesize transcriptional modulators (p)ppGpp, allowing ...Stringent response is a conserved bacterial stress response underlying virulence and antibiotic resistance. RelA/SpoT-homolog proteins synthesize transcriptional modulators (p)ppGpp, allowing bacteria to adapt to stress. RelA is activated during amino-acid starvation, when cognate deacyl-tRNA binds to the ribosomal A (aminoacyl-tRNA) site. We report four cryo-EM structures of E. coli RelA bound to the 70S ribosome, in the absence and presence of deacyl-tRNA accommodating in the 30S A site. The boomerang-shaped RelA with a wingspan of more than 100 Å wraps around the A/R (30S A-site/RelA-bound) tRNA. The CCA end of the A/R tRNA pins the central TGS domain against the 30S subunit, presenting the (p)ppGpp-synthetase domain near the 30S spur. The ribosome and A/R tRNA are captured in three conformations, revealing hitherto elusive states of tRNA engagement with the ribosomal decoding center. Decoding-center rearrangements are coupled with the step-wise 30S-subunit 'closure', providing insights into the dynamics of high-fidelity tRNA decoding. | ||||||||||||
履歴 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
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_8279.map.gz | 137.6 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-8279-v30.xml emd-8279.xml | 78 KB 78 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_8279.png | 148.4 KB | ||
その他 | emd_8279_additional.map.gz emd_8279_half_map_1.map.gz emd_8279_half_map_2.map.gz | 139.7 MB 139.3 MB 139.3 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-8279 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8279 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_8279_validation.pdf.gz | 816.4 KB | 表示 | EMDB検証レポート |
---|---|---|---|---|
文書・詳細版 | emd_8279_full_validation.pdf.gz | 815.9 KB | 表示 | |
XML形式データ | emd_8279_validation.xml.gz | 18.3 KB | 表示 | |
CIF形式データ | emd_8279_validation.cif.gz | 21.6 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8279 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8279 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
---|---|
「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_8279.map.gz / 形式: CCP4 / 大きさ: 421.9 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Ribosome*RelA structures reveal the mechanism of stringent response activation (Structure I) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 0.82 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
|
-添付データ
-追加マップ: Ribosome*RelA structures reveal the mechanism of stringent response...
ファイル | emd_8279_additional.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Ribosome*RelA structures reveal the mechanism of stringent response activation (Structure I, additional map) | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-ハーフマップ: Ribosome*RelA structures reveal the mechanism of stringent response...
ファイル | emd_8279_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Ribosome*RelA structures reveal the mechanism of stringent response activation (Structure I), half map 1 | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-ハーフマップ: Ribosome*RelA structures reveal the mechanism of stringent response...
ファイル | emd_8279_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Ribosome*RelA structures reveal the mechanism of stringent response activation (Structure I), half map 2 | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-試料の構成要素
+全体 : RelA bound to 70S ribosome in the absence of A/R tRNA
+超分子 #1: RelA bound to 70S ribosome in the absence of A/R tRNA
+分子 #1: GTP pyrophosphokinase
+分子 #2: 50S ribosomal protein L2
+分子 #3: 50S ribosomal protein L3
+分子 #4: 50S ribosomal protein L4
+分子 #5: 50S ribosomal protein L5
+分子 #6: 50S ribosomal protein L6
+分子 #7: 50S ribosomal protein L9
+分子 #8: 50S ribosomal protein L10
+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 L31
+分子 #28: 50S ribosomal protein L32
+分子 #29: 50S ribosomal protein L33
+分子 #30: 50S ribosomal protein L34
+分子 #31: 50S ribosomal protein L35
+分子 #32: 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: 16S ribosomal RNA
+分子 #54: 23S ribosomal RNA
+分子 #55: 5S ribosomal RNA
+分子 #56: mRNA
+分子 #57: P site tRNAfmet
+分子 #58: E-site tRNAfMet
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
---|---|
解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
濃度 | 0.1 mg/mL |
---|---|
緩衝液 | pH: 7.4 |
グリッド | モデル: C-flat-1.2/1.3 / 材質: COPPER / メッシュ: 400 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: CONTINUOUS / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 雰囲気: AIR |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 75 % / チャンバー内温度: 295 K / 装置: GATAN CRYOPLUNGE 3 詳細: Apply 2 uL sample and blot 4 seconds before plunging into liquid ethane (GATAN CRYOPLUNGE 3).. |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
---|---|
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: 1-25 / 撮影したグリッド数: 5 / 実像数: 5763 / 平均露光時間: 0.4 sec. / 平均電子線量: 1.6 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 100.0 µm / 最大 デフォーカス(補正後): 2.2 µm / 最小 デフォーカス(補正後): 0.5 µm / 倍率(補正後): 30488 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 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): 0.5 µm / 倍率(公称値): 30488 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |