+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-30914 | |||||||||
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タイトル | A refined cryo-EM structure of an Escherichia coli RNAP-promoter open complex (RPo) with SspA | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | bacterial RNA polymerase / Complex / TRANSCRIPTION | |||||||||
機能・相同性 | 機能・相同性情報 sigma factor antagonist complex / response to stress / submerged biofilm formation / cellular response to cell envelope stress / response to starvation / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility ...sigma factor antagonist complex / response to stress / submerged biofilm formation / cellular response to cell envelope stress / response to starvation / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription initiation / cell motility / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat / intracellular iron ion homeostasis / protein dimerization activity / response to antibiotic / negative regulation of DNA-templated transcription / DNA-templated transcription / positive regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytosol / cytoplasm 類似検索 - 分子機能 | |||||||||
生物種 | Escherichia coli (strain K12) (大腸菌) / 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: 3.68 Å | |||||||||
データ登録者 | Lin W | |||||||||
引用 | ジャーナル: Biochem Biophys Res Commun / 年: 2021 タイトル: A unique binding between SspA and RNAP βNTH across low-GC Gram-negative bacteria facilitates SspA-mediated transcription regulation. 著者: Fulin Wang / Yu Feng / Zhuo Shang / Wei Lin / 要旨: Stringent starvation protein A (SspA) involved in nucleotide metabolism, acid tolerance and virulence of bacteria has been demonstrated to function as a transcription factor to regulate σ-dependent ...Stringent starvation protein A (SspA) involved in nucleotide metabolism, acid tolerance and virulence of bacteria has been demonstrated to function as a transcription factor to regulate σ-dependent gene transcription through interacting with σ region 4 and the zinc binding domain (ZBD) of E. coli RNA polymerase (EcoRNAP) β' subunit simultaneously. Despite extensive biochemical and structural analyses were reported recently, the interactions of SspA with RNAP are not comprehensively understood. Here, we reprocessed our previous cryo-EM dataset of EcoRNAP-promoter open complex with SspA (SspA-RPo) and obtained a significantly improved density map. Unexpectedly, the new map showed that SspA interacts with both N-terminal helix of β' subunit (β'ΝΤΗ) and ω subunit, which contributes to stabilize the SspA-EcoRNAP σ holoenzyme complex. Sequence alignments and phylogenetic tree analyses of N-terminal sequences of β' subunit from different classes of bacteria revealed that β'ΝΤΗ is highly conserved and exclusively found in low-GC-content Gram-negative bacteria that harbor SspA, implying a co-evolution of β'ΝΤΗ and SspA. The transcription assays of wild-type SspA and its mutants demonstrated the interaction between SspA and β'ΝΤΗ facilitates the transcription regulation of SspA. Together, our results provide a more comprehensive insight into the interactions between SspA and RNAP and their roles in bacterial transcription regulation. | |||||||||
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_30914.map.gz | 28.5 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-30914-v30.xml emd-30914.xml | 20.8 KB 20.8 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_30914.png | 123.6 KB | ||
Filedesc metadata | emd-30914.cif.gz | 8.4 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-30914 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30914 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_30914_validation.pdf.gz | 599.3 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_30914_full_validation.pdf.gz | 598.9 KB | 表示 | |
XML形式データ | emd_30914_validation.xml.gz | 5.6 KB | 表示 | |
CIF形式データ | emd_30914_validation.cif.gz | 6.4 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30914 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30914 | 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_30914.map.gz / 形式: CCP4 / 大きさ: 30.5 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: 1.307 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 : an Escherichia coli RNAP-promoter open complex (RPo) with SspA
+超分子 #1: an Escherichia coli RNAP-promoter open complex (RPo) with SspA
+分子 #1: DNA (63-MER)
+分子 #7: DNA (63-MER)
+分子 #2: Stringent starvation protein A
+分子 #3: DNA-directed RNA polymerase subunit alpha
+分子 #4: DNA-directed RNA polymerase subunit beta
+分子 #5: DNA-directed RNA polymerase subunit beta'
+分子 #6: RNA polymerase sigma factor RpoD
+分子 #8: DNA-directed RNA polymerase subunit omega
+分子 #9: MAGNESIUM ION
+分子 #10: 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
緩衝液 | pH: 7.9 |
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グリッド | 材質: COPPER |
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI/PHILIPS CM300FEG/T |
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撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: COUNTING / 平均電子線量: 59.0 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: OTHER / 撮影モード: BRIGHT FIELD |