+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-3561 | |||||||||
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タイトル | map of the RNA polymerase lambda-based antitermination complex solved by cryo-EM | |||||||||
マップデータ | ||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 bacterial-type RNA polymerase core enzyme binding / RNA stem-loop binding / RNA polymerase binding / transcription elongation-coupled chromatin remodeling / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly ...bacterial-type RNA polymerase core enzyme binding / RNA stem-loop binding / RNA polymerase binding / transcription elongation-coupled chromatin remodeling / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / transcription antitermination factor activity, RNA binding / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / 運動性 / DNA-templated transcription termination / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / ポリメラーゼ / cytosolic small ribosomal subunit / リボソーム生合成 / protein complex oligomerization / cytoplasmic translation / small ribosomal subunit / response to heat / protein-containing complex assembly / intracellular iron ion homeostasis / tRNA binding / single-stranded RNA binding / protein dimerization activity / structural constituent of ribosome / DNA-binding transcription factor activity / protein domain specific binding / nucleotide binding / response to antibiotic / regulation of transcription by RNA polymerase II / magnesium ion binding / 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) / Escherichia phage lambda (λファージ) / 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: 9.8 Å | |||||||||
データ登録者 | Said N / Krupp F | |||||||||
引用 | ジャーナル: Nat Microbiol / 年: 2017 タイトル: Structural basis for λN-dependent processive transcription antitermination. 著者: Nelly Said / Ferdinand Krupp / Ekaterina Anedchenko / Karine F Santos / Olexandr Dybkov / Yong-Heng Huang / Chung-Tien Lee / Bernhard Loll / Elmar Behrmann / Jörg Bürger / Thorsten Mielke / ...著者: Nelly Said / Ferdinand Krupp / Ekaterina Anedchenko / Karine F Santos / Olexandr Dybkov / Yong-Heng Huang / Chung-Tien Lee / Bernhard Loll / Elmar Behrmann / Jörg Bürger / Thorsten Mielke / Justus Loerke / Henning Urlaub / Christian M T Spahn / Gert Weber / Markus C Wahl / 要旨: λN-mediated processive antitermination constitutes a paradigmatic transcription regulatory event, during which phage protein λN, host factors NusA, NusB, NusE and NusG, and an RNA nut site render ...λN-mediated processive antitermination constitutes a paradigmatic transcription regulatory event, during which phage protein λN, host factors NusA, NusB, NusE and NusG, and an RNA nut site render elongating RNA polymerase termination-resistant. The structural basis of the process has so far remained elusive. Here we describe a crystal structure of a λN-NusA-NusB-NusE-nut site complex and an electron cryo-microscopic structure of a complete transcription antitermination complex, comprising RNA polymerase, DNA, nut site RNA, all Nus factors and λN, validated by crosslinking/mass spectrometry. Due to intrinsic disorder, λN can act as a multiprotein/RNA interaction hub, which, together with nut site RNA, arranges NusA, NusB and NusE into a triangular complex. This complex docks via the NusA N-terminal domain and the λN C-terminus next to the RNA exit channel on RNA polymerase. Based on the structures, comparative crosslinking analyses and structure-guided mutagenesis, we hypothesize that λN mounts a multipronged strategy to reprogram the transcriptional machinery, which may include (1) the λN C terminus clamping the RNA exit channel, thus stabilizing the DNA:RNA hybrid; (2) repositioning of NusA and RNAP elements, thus redirecting nascent RNA and sequestering the upstream branch of a terminator hairpin; and (3) hindering RNA engagement of termination factor ρ and/or obstructing ρ translocation on the transcript. | |||||||||
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_3561.map.gz | 48.4 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-3561-v30.xml emd-3561.xml | 25.4 KB 25.4 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_3561.png | 137.3 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-3561 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3561 | 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_3561.map.gz / 形式: CCP4 / 大きさ: 52.7 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 1.28 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 : lambdaN-dependent antitermination complex
+超分子 #1: lambdaN-dependent antitermination complex
+分子 #1: Antitermination protein N
+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: 30S ribosomal protein S10
+分子 #7: Transcription termination/antitermination protein NusG
+分子 #11: Transcription antitermination protein NusB
+分子 #12: Transcription termination/antitermination protein NusA
+分子 #13: DNA-directed RNA polymerase subunit omega
+分子 #2: nascent RNA
+分子 #8: RNA transcription bubble
+分子 #9: DNAI
+分子 #10: DNAII
+分子 #14: MAGNESIUM ION
+分子 #15: 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: 7.5 |
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凍結 | 凍結剤: ETHANE |
詳細 | 10 mM HEPES-NaOH, pH 7.5, 50 mM NaCl, 1 mM DTT |
-電子顕微鏡法
顕微鏡 | FEI POLARA 300 |
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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: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy |
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 / 平均電子線量: 1.0 e/Å2 |
実験機器 | モデル: Tecnai Polara / 画像提供: FEI Company |
-画像解析
初期モデル | モデルのタイプ: INSILICO MODEL 詳細: Generate from class averages using the VIPER algorithm. |
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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 | 想定した対称性 - 点群: C1 (非対称) / 解像度のタイプ: BY AUTHOR / 解像度: 9.8 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 23983 |