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 insight into 5' RNA capping with NpNs by bacterial RNA polymerase.
ジャーナル・号・ページ	Nat Chem Biol, Year 2026
掲載日	2026年1月9日
著者	Valentina M Serianni / Jana Škerlová / Anna Knopp Dubánková / Anton Škríba / Hana Šváchová / Tereza Vučková / Anatolij Filimoněnko / Milan Fábry / Pavlína Řezáčová / Tomáš Kouba / Hana Cahova
PubMed 要旨	RNA capped with dinucleoside polyphosphates has been discovered in bacteria and eukaryotes only recently. The likely mechanism of this specific capping involves direct incorporation of dinucleoside ...RNA capped with dinucleoside polyphosphates has been discovered in bacteria and eukaryotes only recently. The likely mechanism of this specific capping involves direct incorporation of dinucleoside polyphosphates by RNA polymerase as noncanonical initiating nucleotides. However, how these compounds bind into the active site of RNA polymerase during transcription initiation is unknown. Here, we explored transcription initiation in vitro, using a series of DNA templates in combination with dinucleoside polyphosphates and model RNA polymerase from Thermus thermophilus. We observed that the transcription start site can vary on the basis of the compatibility of the specific template and dinucleoside polyphosphate. Cryo-electron microscopy structures of transcription initiation complexes with dinucleoside polyphosphates revealed that both nucleobase moieties can pair with the DNA template. The first encoded nucleotide pairs in a canonical Watson-Crick manner, whereas the second nucleobase pairs noncanonically in a reverse Watson-Crick manner. Our work provides a structural explanation of how dinucleoside polyphosphates initiate RNA transcription.
リンク	Nat Chem Biol / PubMed:41513851
手法	EM (単粒子)
解像度	2.42 - 3.8 Å
構造データ	50618 9fo6 EMDB-50618, PDB-9fo6: GTP bound in de novo transcription initiation T. thermophilus RNA polymerase complex with TC DNA template 手法: EM (単粒子) / 解像度: 2.76 Å 50622 9fog EMDB-50622, PDB-9fog: Ap3G bound in de novo transcription initiation T. thermophilus RNA polymerase complex with TC DNA template 手法: EM (単粒子) / 解像度: 2.51 Å 50625 9fok EMDB-50625, PDB-9fok: Ap4G bound in de novo transcription initiation T. thermophilus RNA polymerase complex with TC DNA template 手法: EM (単粒子) / 解像度: 3.0 Å 50634 9fp3 EMDB-50634, PDB-9fp3: Ap4A bound in de novo transcription initiation T. thermophilus RNA polymerase complex with TC DNA template 手法: EM (単粒子) / 解像度: 2.42 Å 50715 9frj EMDB-50715, PDB-9frj: Ap4A bound in de novo transcription initiation T. thermophilus RNA polymerase complex with aTT DNA template 手法: EM (単粒子) / 解像度: 2.66 Å 53711 9r75 EMDB-53711, PDB-9r75: Transcription initiation T. thermophilus RNA polymerase complex with anti-scrunched TC DNA template 手法: EM (単粒子) / 解像度: 3.8 Å
化合物	ChemComp-MG: Unknown entry / マグネシウムジカチオン ChemComp-ZN: Unknown entry ChemComp-GTP: GUANOSINE-5'-TRIPHOSPHATE / GTP / GTP, エネルギー貯蔵分子YM ChemComp-2TM: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine / 5′-シチジルオキシホスホニルメチルホスホニルオキシホスホン酸 ChemComp-G3A: GUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE / Ap₃G PDB-1if9: Carbonic Anhydrase II Complexed With N-[2-(1H-Indol-5-yl)-butyl]-4-sulfamoyl-benzamide ChemComp-B4P: BIS(ADENOSINE)-5'-TETRAPHOSPHATE / ジアデノシン四りん酸 ChemComp-G2P: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMPCPP / GMP-CPP, エネルギー貯蔵分子類似体YM
由来	thermus thermophilus hb8 (バクテリア) synthetic construct (人工物)
キーワード	TRANSCRIPTION / TRANSCRIPTION-DNA complex / non-canonical cap