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	Structural Dynamics of RNA Polymerase II During Nucleotide Addition Cycle.
ジャーナル・号・ページ	bioRxiv, Year 2026
掲載日	2026年6月5日
著者	Gangshun Yi / Qingrong Li / Hannah Holmberg / Shisheng Li / Daniel K Clare / Dong Wang / Peijun Zhang /
PubMed 要旨	RNA polymerase II (RNAPII) drives gene expression through iterative nucleotide addition cycles (NACs) comprising translocation, substrate binding, and catalysis. The lack of pre-catalysis and post- ...RNA polymerase II (RNAPII) drives gene expression through iterative nucleotide addition cycles (NACs) comprising translocation, substrate binding, and catalysis. The lack of pre-catalysis and post-catalysis intermediates has precluded a complete mechanistic understanding of the NAC. Here we present 43 cryo-EM structures capturing distinct stages of the RNAPII elongation complex (EC) NAC, including previously intractable transition intermediates. We establish a continuous spectrum of RNAPII EC structural dynamics during the NAC, which can be divided into two coordinated phases: a substrate-induced EC tightening phase and a post-catalysis EC relaxation phase. For the substrate-induced EC tightening phase, the substrate binding initiates allosteric conformational changes across the entire RNAPII EC, including TL folding, funnel closure, clamp closure, transcription bubble ordering, and precise alignment of the RNA 3'-end with substrate to form a catalysis-competent configuration. For the post-catalysis EC relaxation phase, we captured the long-sought, short-lived post-catalysis product state and identified a series of intermediates that reveal a reverse conformational transition that facilitates rapid translocation. Together, our findings define a comprehensive structural and dynamic framework for RNAPII NAC, yielding a "molecular movie" of RNAPII in action and revealing a fundamental principle by which the enzyme balances speed and fidelity through coordinated conformational dynamics.
リンク	bioRxiv / PubMed:42282700 / PubMed Central
手法	EM (単粒子)
解像度	2.54 - 4.28 Å
構造データ	EMDB-54677: CryoEM map of Yeast RNA polymerase II elongation complex with ATP-3D class A (frame1) 手法: EM (単粒子) / 解像度: 3.63 Å EMDB-54679: CryoEM map of Yeast RNA polymerase II elongation complex with ATP-3D class E (frame9) 手法: EM (単粒子) / 解像度: 3.66 Å EMDB-54680: CryoEM map of Yeast RNA polymerase II elongation complex with ATP-3D class D (frame8) 手法: EM (単粒子) / 解像度: 3.52 Å EMDB-54681: CryoEM map of Yeast RNA polymerase II elongation complex with ATP-3D class C (frame7) 手法: EM (単粒子) / 解像度: 3.49 Å EMDB-54682: CryoEM map of Yeast RNA polymerase II elongation complex with ATP-3D class B (frame4) 手法: EM (単粒子) / 解像度: 3.54 Å EMDB-54683: CryoEM map of Yeast RNA polymerase II elongation complex with ATP-3D class F (frame 10) 手法: EM (単粒子) / 解像度: 3.95 Å EMDB-54684: CryoEM map of Yeast RNA polymerase II elongation complex with ATP-3D class G (frame 13) 手法: EM (単粒子) / 解像度: 4.08 Å EMDB-54685: CryoEM map of Yeast RNA polymerase II elongation complex with ATP-3D class H (frame 15) 手法: EM (単粒子) / 解像度: 3.29 Å EMDB-54686: CryoEM map of Yeast RNA polymerase II elongation complex with ATP-3D class I (frame 17) 手法: EM (単粒子) / 解像度: 3.28 Å EMDB-54687: CryoEM map of Yeast RNA polymerase II elongation complex with ATP-3D class J (frame 20) 手法: EM (単粒子) / 解像度: 3.21 Å 54704 9say EMDB-54704, PDB-9say: Structure of Yeast RNA polymerase II elongation complex apo-state-I 手法: EM (単粒子) / 解像度: 3.44 Å EMDB-54705: CryoEM map of Yeast RNA polymerase II elongation complex apo-state-I-A 手法: EM (単粒子) / 解像度: 3.57 Å EMDB-54706: CryoEM map of Yeast RNA polymerase II elongation complex apo-state-I-B 手法: EM (単粒子) / 解像度: 3.57 Å 54707 9saz EMDB-54707, PDB-9saz: Structure of Yeast RNA polymerase II elongation complex apo-state-II 手法: EM (単粒子) / 解像度: 3.31 Å 54708 9sb0 EMDB-54708, PDB-9sb0: Structure of Yeast RNA polymerase II elongation complex with NTP-state-VI 手法: EM (単粒子) / 解像度: 3.04 Å 54709 9sb1 EMDB-54709, PDB-9sb1: Structure of Yeast RNA polymerase II elongation complex with NTP-state-VII-A 手法: EM (単粒子) / 解像度: 2.98 Å 54710 9sb2 EMDB-54710, PDB-9sb2: Structure of Yeast RNA polymerase II elongation complex with NTP-state-VII-B 手法: EM (単粒子) / 解像度: 3.09 Å 54711 9sb3 EMDB-54711, PDB-9sb3: Structure of Yeast RNA polymerase II elongation complex with NTP-state-VII-C 手法: EM (単粒子) / 解像度: 3.05 Å 54712 9sb4 EMDB-54712, PDB-9sb4: Structure of Yeast RNA polymerase II elongation complex with NTP-state-VII-D 手法: EM (単粒子) / 解像度: 3.12 Å 54713 9sb5 EMDB-54713, PDB-9sb5: Structure of Yeast RNA polymerase II elongation complex with NTP-state-II 手法: EM (単粒子) / 解像度: 3.56 Å 54730 9sbl EMDB-54730, PDB-9sbl: Structure of Yeast RNA polymerase II elongation complex with ATP frame-1 手法: EM (単粒子) / 解像度: 4.28 Å 54731 9sbm EMDB-54731, PDB-9sbm: Structure of Yeast RNA polymerase II elongation complex with ATP frame-2 手法: EM (単粒子) / 解像度: 4.17 Å 54732 9sbn EMDB-54732, PDB-9sbn: Structure of Yeast RNA polymerase II elongation complex with ATP frame-3 手法: EM (単粒子) / 解像度: 3.95 Å 54733 9sbo EMDB-54733, PDB-9sbo: Structure of Yeast RNA polymerase II elongation complex with ATP frame-4 手法: EM (単粒子) / 解像度: 3.97 Å 54734 9sbp EMDB-54734, PDB-9sbp: Structure of Yeast RNA polymerase II elongation complex with ATP frame-5 手法: EM (単粒子) / 解像度: 3.95 Å 54735 9sbq EMDB-54735, PDB-9sbq: Structure of Yeast RNA polymerase II elongation complex with ATP frame-6 手法: EM (単粒子) / 解像度: 3.88 Å 54736 9sbr EMDB-54736, PDB-9sbr: Structure of Yeast RNA polymerase II elongation complex with ATP frame-7 手法: EM (単粒子) / 解像度: 3.96 Å 54737 9sbs EMDB-54737, PDB-9sbs: Structure of Yeast RNA polymerase II elongation complex with ATP frame-8 手法: EM (単粒子) / 解像度: 3.85 Å 54738 9sbt EMDB-54738, PDB-9sbt: Structure of Yeast RNA polymerase II elongation complex with ATP frame-9 手法: EM (単粒子) / 解像度: 3.85 Å 54739 9sbu EMDB-54739, PDB-9sbu: Structure of Yeast RNA polymerase II elongation complex with ATP frame-10 手法: EM (単粒子) / 解像度: 3.83 Å 54740 9sbv EMDB-54740, PDB-9sbv: Structure of Yeast RNA polymerase II elongation complex with ATP frame-11 手法: EM (単粒子) / 解像度: 3.73 Å 54741 9sbw EMDB-54741, PDB-9sbw: Structure of Yeast RNA polymerase II elongation complex with ATP frame-12 手法: EM (単粒子) / 解像度: 3.63 Å 54742 9sbx EMDB-54742, PDB-9sbx: Structure of Yeast RNA polymerase II elongation complex with ATP frame-13 手法: EM (単粒子) / 解像度: 3.53 Å 54743 9sby EMDB-54743, PDB-9sby: Structure of Yeast RNA polymerase II elongation complex with ATP frame-14 手法: EM (単粒子) / 解像度: 3.41 Å 54744 9sbz EMDB-54744, PDB-9sbz: Structure of Yeast RNA polymerase II elongation complex with ATP frame-15 手法: EM (単粒子) / 解像度: 3.35 Å 54745 9sc0 EMDB-54745, PDB-9sc0: Structure of Yeast RNA polymerase II elongation complex with ATP frame-16 手法: EM (単粒子) / 解像度: 3.31 Å 54746 9sc1 EMDB-54746, PDB-9sc1: Structure of Yeast RNA polymerase II elongation complex with ATP frame-17 手法: EM (単粒子) / 解像度: 3.48 Å 54747 9sc2 EMDB-54747, PDB-9sc2: Structure of Yeast RNA polymerase II elongation complex with ATP frame-18 手法: EM (単粒子) / 解像度: 3.53 Å 54748 9sc3 EMDB-54748, PDB-9sc3: Structure of Yeast RNA polymerase II elongation complex with ATP frame-19 手法: EM (単粒子) / 解像度: 3.68 Å 54749 9sc4 EMDB-54749, PDB-9sc4: Structure of Yeast RNA polymerase II elongation complex with ATP frame-20 手法: EM (単粒子) / 解像度: 3.76 Å 57322 29rf EMDB-57322, PDB-29rf: Structure of Yeast RNA polymerase II elongation complex with NTP-state-III 手法: EM (単粒子) / 解像度: 3.02 Å 57673 30ep EMDB-57673, PDB-30ep: Cryo-EM structure of the yeast RNA polymerase II elongation complex with 19-mer RNA in State III (TL-open), in the presence of substrate ATP 手法: EM (単粒子) / 解像度: 2.55 Å 57676 30es EMDB-57676, PDB-30es: Cryo-EM structure of the yeast RNA polymerase II elongation complex with 19-mer RNA in State V (TL-closed), in the presence of substrate ATP 手法: EM (単粒子) / 解像度: 2.54 Å
化合物	ChemComp-ZN: Unknown entry ChemComp-MG: Unknown entry ChemComp-GTP: GUANOSINE-5'-TRIPHOSPHATE / GTP, エネルギー貯蔵分子YM ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, エネルギー貯蔵分子YM ChemComp-PPV: PYROPHOSPHATE
由来	saccharomyces cerevisiae (パン酵母)
キーワード	TRANSCRIPTION / CryoEM / RNA Polymerase