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	DNA topoisomerase I acts as supercoiling sensor for bacterial transcription elongation.
ジャーナル・号・ページ	Nat Struct Mol Biol, Year 2025
掲載日	2025年12月1日
著者	Vita Vidmar / Céline Borde / Lisa Bruno / Nataliya Miropolskaya / Maria Takacs / Claire Batisse / Charlotte Saint-André / Chengjin Zhu / Olivier Espéli / Valérie Lamour / Albert Weixlbaumer /
PubMed 要旨	During transcription, RNA polymerase (RNAP) continuously unwinds and rewinds DNA, generating negative and positive supercoils upstream and downstream, respectively. Using single-particle cryo-EM, we ...During transcription, RNA polymerase (RNAP) continuously unwinds and rewinds DNA, generating negative and positive supercoils upstream and downstream, respectively. Using single-particle cryo-EM, we elucidated how bacterial RNAP and DNA topoisomerase I (TopoI), which relaxes negative supercoils, operate in close spatial proximity. TopoI binds to relaxed DNA upstream of RNAP, and this involves a conformational switch in the TopoI functional domains. This suggests that TopoI exerts a sensing role before the formation of negative supercoils. On DNA substrates mimicking negatively supercoiled DNA, TopoI threads one strand into the active site for cleavage and binds the complementary strand with an auxiliary domain. Transcriptomic and phenotypic analyses suggest that mutations affecting conformational changes in TopoI impact gene expression and operon polarity in bacteria. In summary, we propose a comprehensive model for DNA relaxation in the proximity of active bacterial transcription.
リンク	Nat Struct Mol Biol / PubMed:41326756
手法	EM (単粒子)
解像度	2.6 - 5.6 Å
構造データ	EMDB-51252: RNAP-TopoI complex on duplex scaffold - consensus map 手法: EM (単粒子) / 解像度: 2.7 Å EMDB-51253: RNAP-TopoI complex on duplex scaffold - focused map (TopoI) 手法: EM (単粒子) / 解像度: 3.3 Å EMDB-51254: RNAP-TopoI complex on duplex scaffold - focused map (TopoI D2/D3) 手法: EM (単粒子) / 解像度: 3.4 Å EMDB-51255: RNAP-TopoI complex on duplex scaffold - focused map (RNAP core) 手法: EM (単粒子) / 解像度: 2.6 Å EMDB-51256: RNAP-TopoI complex on duplex scaffold - focused map (RNAP swivel module 1) 手法: EM (単粒子) / 解像度: 2.7 Å EMDB-51257: RNAP-TopoI complex on duplex scaffold - focused map (RNAP swivel module 2) 手法: EM (単粒子) / 解像度: 2.7 Å EMDB-51258: RNAP-TopoI complex on duplex scaffold - focused map (RNAP beta protrusion and lobe) 手法: EM (単粒子) / 解像度: 2.8 Å 51259 9gda EMDB-51259, PDB-9gda: RNAP-TopoI complex on duplex scaffold 手法: EM (単粒子) / 解像度: 2.7 Å 51260 9gdb EMDB-51260, PDB-9gdb: RNAP-TopoI complex on bubble scaffold - consensus reconstruction 手法: EM (単粒子) / 解像度: 3.8 Å 51261 9gdc EMDB-51261, PDB-9gdc: RNAP-TopoI complex on bubble scaffold - single-bubble configuration 手法: EM (単粒子) / 解像度: 4.3 Å 51262 9gdd EMDB-51262, PDB-9gdd: RNAP-TopoI complex on bubble scaffold - two-bubble configuration 手法: EM (単粒子) / 解像度: 4.3 Å 51263 9gde EMDB-51263, PDB-9gde: RNAP-TopoI complex on long-overhang scaffold - orientation 1 手法: EM (単粒子) / 解像度: 4.0 Å 51264 9gdh EMDB-51264, PDB-9gdh: RNAP-TopoI complex on long-overhang scaffold - orientation 2 手法: EM (単粒子) / 解像度: 3.9 Å EMDB-51265: RNAP-TopoI complex on duplex scaffold with visible TOPRIM loop - consensus map 手法: EM (単粒子) / 解像度: 2.8 Å EMDB-51266: RNAP-TopoI complex on duplex scaffold with visible TOPRIM loop - focused map (TopoI) 手法: EM (単粒子) / 解像度: 3.8 Å EMDB-51267: RNAP-TopoI complex on duplex scaffold with visible TOPRIM loop 手法: EM (単粒子) / 解像度: 3.8 Å EMDB-51268: RNAP-TopoI complex on long-overhang scaffold - orientation 3 手法: EM (単粒子) / 解像度: 5.6 Å EMDB-51269: RNAP-TopoI complex on long-overhang scaffold - TopoI gate opening (orientation 2) 手法: EM (単粒子) / 解像度: 4.3 Å EMDB-51270: RNAP-TopoI complex on short-overhang scaffold - orientation 1 手法: EM (単粒子) / 解像度: 3.8 Å EMDB-51271: RNAP-TopoI complex on short-overhang scaffold - orientation 2 手法: EM (単粒子) / 解像度: 4.4 Å
化合物	ChemComp-MG: Unknown entry ChemComp-ZN: Unknown entry
由来	escherichia coli (大腸菌) synthetic construct (人工物)
キーワード	TRANSCRIPTION / RNA polymerase / topoisomerase / DNA topology