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	Conformational landscapes of a class I ribonucleotide reductase complex during turnover reveal intrinsic dynamics and asymmetry.
ジャーナル・号・ページ	Nat Commun, Vol. 16, Issue 1, Page 2458, Year 2025
掲載日	2025年3月12日
著者	Da Xu / William C Thomas / Audrey A Burnim / Nozomi Ando /
PubMed 要旨	Understanding the structural dynamics associated with enzymatic catalysis has been a long-standing goal of biochemistry. With the advent of modern cryo-electron microscopy (cryo-EM), it has become ...Understanding the structural dynamics associated with enzymatic catalysis has been a long-standing goal of biochemistry. With the advent of modern cryo-electron microscopy (cryo-EM), it has become conceivable to redefine a protein's structure as the continuum of all conformations and their distributions. However, capturing and interpreting this information remains challenging. Here, we use classification and deep-learning-based analyses to characterize the conformational heterogeneity of a class I ribonucleotide reductase (RNR) during turnover. By converting the resulting information into physically interpretable 2D conformational landscapes, we demonstrate that RNR continuously samples a wide range of motions while maintaining surprising asymmetry to regulate the two halves of its turnover cycle. Remarkably, we directly observe the appearance of highly transient conformations needed for catalysis, as well as the interaction of RNR with its endogenous reductant thioredoxin also contributing to the asymmetry and dynamics of the enzyme complex. Overall, this work highlights the role of conformational dynamics in regulating key steps in enzyme mechanisms.
リンク	Nat Commun / PubMed:40075098 / PubMed Central
手法	EM (単粒子)
解像度	2.42 - 8.11 Å
構造データ	44947 9bw3 EMDB-44947, PDB-9bw3: Consensus model for preturnover condition of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 2.42 Å 44985 9bwx EMDB-44985, PDB-9bwx: Consensus full-complex model for preturnover condition of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 2.91 Å 44991 9bx2 EMDB-44991, PDB-9bx2: Class 2 model for preturnover condition of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 3.79 Å 44992 9bx3 EMDB-44992, PDB-9bx3: Class 5 model for preturnover condition of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 3.9 Å 44995 9bx6 EMDB-44995, PDB-9bx6: Class 9 model for preturnover condition of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 3.44 Å 44999 9bx8 EMDB-44999, PDB-9bx8: Class 12 model for preturnover condition of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 3.59 Å 45000 9bx9 EMDB-45000, PDB-9bx9: Class 15 model for preturnover condition of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 3.79 Å 45004 9bxc EMDB-45004, PDB-9bxc: Consensus model for pre-reduction condition of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 2.76 Å 45010 9bxs EMDB-45010, PDB-9bxs: Consensus full-complex model for pre-reduction condition of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 3.37 Å 45011 9bxt EMDB-45011, PDB-9bxt: TrxA focus-classified model for pre-reduction condition of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 2.88 Å 45014 9bxx EMDB-45014, PDB-9bxx: Class 11 model for pre-reduction condition of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 4.26 Å 45015 9bxz EMDB-45015, PDB-9bxz: Class 15 model for pre-reduction condition of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 8.11 Å 45016 9by0 EMDB-45016, PDB-9by0: Class 16 model for pre-reduction condition of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 4.19 Å 45017 9by1 EMDB-45017, PDB-9by1: Consensus model for product condition of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 2.55 Å 45018 9by2 EMDB-45018, PDB-9by2: Consensus full-complex model for product condition of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 3.1 Å 45019 9by3 EMDB-45019, PDB-9by3: Class 3 model for product condition of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 3.57 Å 45020 9by7 EMDB-45020, PDB-9by7: Class 8 model for product condition of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 3.67 Å 45021 9by8 EMDB-45021, PDB-9by8: Class 9 model for product condition of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 3.88 Å 45023 9by9 EMDB-45023, PDB-9by9: Class 10 model for product condition of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 4.14 Å 45024 9bya EMDB-45024, PDB-9bya: Class 11 model for product condition of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 4.01 Å 45026 9byc EMDB-45026, PDB-9byc: Class 12 model for product condition of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 3.94 Å 45029 9byd EMDB-45029, PDB-9byd: Class 16 model for product condition of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 4.2 Å 45030 9byg EMDB-45030, PDB-9byg: Class 19 model for product condition of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 3.77 Å 45031 9byh EMDB-45031, PDB-9byh: Consensus model for turnover condition of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 2.53 Å 45037 9byl EMDB-45037, PDB-9byl: Consensus full-complex model for turnover condition of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 2.99 Å 45044 9byt EMDB-45044, PDB-9byt: Class 1 model for turnover condition of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 3.52 Å 45045 9byv EMDB-45045, PDB-9byv: Class 4 model for turnover condition of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 3.83 Å 45046 9byw EMDB-45046, PDB-9byw: Class 5 model for turnover condition of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 4.64 Å 45047 9byx EMDB-45047, PDB-9byx: Class 8 model for turnover condition of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 3.94 Å 45048 9byy EMDB-45048, PDB-9byy: Class 9 model for turnover condition of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 4.07 Å 45049 9byz EMDB-45049, PDB-9byz: Class 12 model for turnover condition of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 3.94 Å 45051 9bz2 EMDB-45051, PDB-9bz2: Class 14 model for turnover condition of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 3.83 Å 45052 9bz3 EMDB-45052, PDB-9bz3: Class 17 model for turnover condition of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 4.01 Å 45053 9bz5 EMDB-45053, PDB-9bz5: Class 6 model for combined refinement of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 3.93 Å 45054 9bz6 EMDB-45054, PDB-9bz6: Class 7 model for combined refinement of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 3.87 Å 45057 9bz9 EMDB-45057, PDB-9bz9: Class 15 model for combined refinement of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 4.64 Å 45061 9bza EMDB-45061, PDB-9bza: Class 18 model for combined refinement of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 3.93 Å 45064 9bzd EMDB-45064, PDB-9bzd: Class 23 model for combined refinement of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 3.82 Å 45065 9bze EMDB-45065, PDB-9bze: Class 26 model for combined refinement of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 4.19 Å 45066 9bzf EMDB-45066, PDB-9bzf: Class 28 model for combined refinement of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 4.4 Å 45067 9bzh EMDB-45067, PDB-9bzh: Class 29 model for combined refinement of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 5.9 Å 45068 9bzi EMDB-45068, PDB-9bzi: Class 31 model for combined refinement of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 3.99 Å 45069 9bzj EMDB-45069, PDB-9bzj: Class 40 model for combined refinement of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 4.12 Å 45070 9bzk EMDB-45070, PDB-9bzk: Class 43 model for combined refinement of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 4.19 Å 45071 9bzm EMDB-45071, PDB-9bzm: Class 45 model for combined refinement of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 4.19 Å 45072 9bzo EMDB-45072, PDB-9bzo: Class 50 model for combined refinement of Bacillus subtilis ribonucleotide reductase complex 手法: EM (単粒子) / 解像度: 4.48 Å
化合物	ChemComp-TTP: THYMIDINE-5'-TRIPHOSPHATE / dTTP ChemComp-MG: Unknown entry / マグネシウムジカチオン ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP / ATP, エネルギー貯蔵分子YM ChemComp-MN: Unknown entry ChemComp-GDP: GUANOSINE-5'-DIPHOSPHATE / GDP / GDP, エネルギー貯蔵分子YM ChemComp-DGI: 2'-DEOXYGUANOSINE-5'-DIPHOSPHATE / dGDP
由来	bacillus subtilis (枯草菌)
キーワード	OXIDOREDUCTASE / ribonucleotide reductase preturnover condition / Ribonucleotide Reductase