EMDB/PDB/SASBDBから引用されている文献のデータベース

キーワード
構造解析手法	All X線回折 NMR 電子顕微鏡小角散乱中性子線回折線維回折粉末回折赤外分光 EPR FRET 理論モデルハイブリッド
著者・登録者
ジャーナル
IF	>30 >20 >10 >5 all

タイトル	Molecular basis for noncanonical transcription initiation from NpA alarmones.
ジャーナル・号・ページ	Nat Chem Biol, Year 2025
掲載日	2025年10月15日
著者	Wenqian Duan / Abhishek Kaushik / Ilona C Unarta / Yue Wu / Mengjie M J Liu / Jacob W Weaver / Bing Wang / William J Rice / Daniel J Luciano / Joel G Belasco / Xuhui Huang / Evgeny Nudler / Alexander Serganov /
PubMed 要旨	Stress-induced dinucleoside tetraphosphates (NpNs, where N is adenosine, guanosine, cytosine or uridine) are ubiquitous in living organisms, yet their function has been largely elusive for over 50 ...Stress-induced dinucleoside tetraphosphates (NpNs, where N is adenosine, guanosine, cytosine or uridine) are ubiquitous in living organisms, yet their function has been largely elusive for over 50 years. Recent studies have revealed that RNA polymerase can influence the cellular lifetime of transcripts by incorporating these alarmones into RNA as 5'-terminal caps. Here we present structural and biochemical data that reveal the molecular basis of noncanonical transcription initiation from NpAs by Escherichia coli and Thermus thermophilus RNA polymerases. Our results show the influence of the first two nucleotide incorporation steps on capping efficiency and the different interactions of NpAs with transcription initiation complexes. These data provide critical insights into the substrate selectivity that dictates levels of Np capping in bacterial cells.
リンク	Nat Chem Biol / PubMed:41094128 / PubMed Central
手法	EM (単粒子) / X線回折
解像度	2.33 - 3.16 Å
構造データ	64215 9ujk EMDB-64215, PDB-9ujk: CryoEM structure of the T.thermophilus transcription initiation complex in the presence of ATP 手法: EM (単粒子) / 解像度: 2.49 Å 64216 9ujl EMDB-64216, PDB-9ujl: CryoEM structure of the T.thermophilus transcription initiation complex in the presence of Ap4A 手法: EM (単粒子) / 解像度: 2.61 Å 64218 9ujn EMDB-64218, PDB-9ujn: CryoEM structure of the T.thermophilus transcription initiation complex bound to ATP-C, -1 dC in the template DNA strand 手法: EM (単粒子) / 解像度: 2.8 Å 64219 9ujp EMDB-64219, PDB-9ujp: CryoEM structure of the T.thermophilus transcription initiation complex in the presence of Up4A 手法: EM (単粒子) / 解像度: 2.53 Å 64250 9ukn EMDB-64250, PDB-9ukn: CryoEM structure of the T.thermophilus transcription initiation complex 手法: EM (単粒子) / 解像度: 2.97 Å 64251 9uko EMDB-64251, PDB-9uko: CryoEM structure of the T.thermophilus transcription initiation complex bound to Ap4A-C, -1 dA in the template DNA strand 手法: EM (単粒子) / 解像度: 2.89 Å 64252 9ukp EMDB-64252, PDB-9ukp: CryoEM structure of the T.thermophilus transcription initiation complex bound to Ap4A-C, -1 dC in the template DNA strand 手法: EM (単粒子) / 解像度: 2.73 Å 64253 9uks EMDB-64253, PDB-9uks: CryoEM structure of the T.thermophilus transcription initiation complex in the presence of Gp4A, -1 dA in the template DNA strand 手法: EM (単粒子) / 解像度: 2.33 Å 64254 9ukt EMDB-64254, PDB-9ukt: CryoEM structure of the T.thermophilus transcription initiation complex bound to Gp4A-C-U and CTP, -1 dC in the template DNA strand 手法: EM (単粒子) / 解像度: 2.77 Å 64255 9uku EMDB-64255, PDB-9uku: CryoEM structure of the T.thermophilus transcription initiation complex bound to Gp4A-C, -1 dC in the template DNA strand 手法: EM (単粒子) / 解像度: 2.73 Å 64266 9uls EMDB-64266, PDB-9uls: CryoEM structure of the T.thermophilus transcription initiation complex bound to Up4A-C and Up4A, -1 dA in the template DNA strand 手法: EM (単粒子) / 解像度: 2.5 Å 64267 9ult EMDB-64267, PDB-9ult: CryoEM structure of the T.thermophilus transcription initiation complex bound to Up4A-C and UTP, -1 dA in the template DNA strand 手法: EM (単粒子) / 解像度: 2.48 Å 64271 9uma EMDB-64271, PDB-9uma: CryoEM structure of T.thermophilus transcription initiation complex bound to Gp4A-C, -1 dA in the template DNA strand 手法: EM (単粒子) / 解像度: 2.77 Å 64404 9upw EMDB-64404, PDB-9upw: CryoEM structure of the T.thermophilus transcription initiation complex in the presence of Gp4A, -1 dC in the template DNA strand 手法: EM (単粒子) / 解像度: 3.16 Å PDB-9v4m: Crystal structure of the T.thermophilus transcription initiation complex bound to Ap4G 手法: X-RAY DIFFRACTION / 解像度: 3 Å
化合物	ChemComp-MG: Unknown entry ChemComp-ZN: Unknown entry ChemComp-1N7: CHAPSO / 可溶化剤YM ChemComp-HOH: WATER ChemComp-C5P: CYTIDINE-5'-MONOPHOSPHATE ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, エネルギー貯蔵分子YM ChemComp-B4P: BIS(ADENOSINE)-5'-TETRAPHOSPHATE ChemComp-CTP: CYTIDINE-5'-TRIPHOSPHATE PDB-1if9: Carbonic Anhydrase II Complexed With N-[2-(1H-Indol-5-yl)-butyl]-4-sulfamoyl-benzamide PDB-1l89: SIMILAR HYDROPHOBIC REPLACEMENTS OF LEU 99 AND PHE 153 WITHIN THE CORE OF T4 LYSOZYME HAVE DIFFERENT STRUCTURAL AND THERMODYNAMIC CONSEQUENCES ChemComp-UTP: URIDINE 5'-TRIPHOSPHATE / UTPYM PDB-1l9g: CRYSTAL STRUCTURE OF URACIL-DNA GLYCOSYLASE FROM T. MARITIMA ChemComp-TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / pH緩衝剤YM
由来	thermus thermophilus hb8 (バクテリア) dna molecule (その他) synthetic construct (人工物)
キーワード	TRANSCRIPTION / Complex