Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Conformational landscapes of a class I ribonucleotide reductase complex during turnover reveal intrinsic dynamics and asymmetry.
Journal, issue, pages	Nat Commun, Vol. 16, Issue 1, Page 2458, Year 2025
Publish date	Mar 12, 2025
Authors	Da Xu / William C Thomas / Audrey A Burnim / Nozomi Ando /
PubMed Abstract	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.
External links	Nat Commun / PubMed:40075098 / PubMed Central
Methods	EM (single particle)
Resolution	2.42 - 8.11 Å
Structure data	44947 9bw3 EMDB-44947, PDB-9bw3: Consensus model for preturnover condition of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 2.42 Å 44985 9bwx EMDB-44985, PDB-9bwx: Consensus full-complex model for preturnover condition of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 2.91 Å 44991 9bx2 EMDB-44991, PDB-9bx2: Class 2 model for preturnover condition of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 3.79 Å 44992 9bx3 EMDB-44992, PDB-9bx3: Class 5 model for preturnover condition of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 3.9 Å 44995 9bx6 EMDB-44995, PDB-9bx6: Class 9 model for preturnover condition of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 3.44 Å 44999 9bx8 EMDB-44999, PDB-9bx8: Class 12 model for preturnover condition of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 3.59 Å 45000 9bx9 EMDB-45000, PDB-9bx9: Class 15 model for preturnover condition of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 3.79 Å 45004 9bxc EMDB-45004, PDB-9bxc: Consensus model for pre-reduction condition of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 2.76 Å 45010 9bxs EMDB-45010, PDB-9bxs: Consensus full-complex model for pre-reduction condition of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 3.37 Å 45011 9bxt EMDB-45011, PDB-9bxt: TrxA focus-classified model for pre-reduction condition of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 2.88 Å 45014 9bxx EMDB-45014, PDB-9bxx: Class 11 model for pre-reduction condition of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 4.26 Å 45015 9bxz EMDB-45015, PDB-9bxz: Class 15 model for pre-reduction condition of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 8.11 Å 45016 9by0 EMDB-45016, PDB-9by0: Class 16 model for pre-reduction condition of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 4.19 Å 45017 9by1 EMDB-45017, PDB-9by1: Consensus model for product condition of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 2.55 Å 45018 9by2 EMDB-45018, PDB-9by2: Consensus full-complex model for product condition of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 3.1 Å 45019 9by3 EMDB-45019, PDB-9by3: Class 3 model for product condition of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 3.57 Å 45020 9by7 EMDB-45020, PDB-9by7: Class 8 model for product condition of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 3.67 Å 45021 9by8 EMDB-45021, PDB-9by8: Class 9 model for product condition of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 3.88 Å 45023 9by9 EMDB-45023, PDB-9by9: Class 10 model for product condition of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 4.14 Å 45024 9bya EMDB-45024, PDB-9bya: Class 11 model for product condition of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 4.01 Å 45026 9byc EMDB-45026, PDB-9byc: Class 12 model for product condition of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 3.94 Å 45029 9byd EMDB-45029, PDB-9byd: Class 16 model for product condition of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 4.2 Å 45030 9byg EMDB-45030, PDB-9byg: Class 19 model for product condition of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 3.77 Å 45031 9byh EMDB-45031, PDB-9byh: Consensus model for turnover condition of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 2.53 Å 45037 9byl EMDB-45037, PDB-9byl: Consensus full-complex model for turnover condition of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 2.99 Å 45044 9byt EMDB-45044, PDB-9byt: Class 1 model for turnover condition of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 3.52 Å 45045 9byv EMDB-45045, PDB-9byv: Class 4 model for turnover condition of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 3.83 Å 45046 9byw EMDB-45046, PDB-9byw: Class 5 model for turnover condition of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 4.64 Å 45047 9byx EMDB-45047, PDB-9byx: Class 8 model for turnover condition of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 3.94 Å 45048 9byy EMDB-45048, PDB-9byy: Class 9 model for turnover condition of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 4.07 Å 45049 9byz EMDB-45049, PDB-9byz: Class 12 model for turnover condition of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 3.94 Å 45051 9bz2 EMDB-45051, PDB-9bz2: Class 14 model for turnover condition of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 3.83 Å 45052 9bz3 EMDB-45052, PDB-9bz3: Class 17 model for turnover condition of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 4.01 Å 45053 9bz5 EMDB-45053, PDB-9bz5: Class 6 model for combined refinement of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 3.93 Å 45054 9bz6 EMDB-45054, PDB-9bz6: Class 7 model for combined refinement of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 3.87 Å 45057 9bz9 EMDB-45057, PDB-9bz9: Class 15 model for combined refinement of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 4.64 Å 45061 9bza EMDB-45061, PDB-9bza: Class 18 model for combined refinement of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 3.93 Å 45064 9bzd EMDB-45064, PDB-9bzd: Class 23 model for combined refinement of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 3.82 Å 45065 9bze EMDB-45065, PDB-9bze: Class 26 model for combined refinement of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 4.19 Å 45066 9bzf EMDB-45066, PDB-9bzf: Class 28 model for combined refinement of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 4.4 Å 45067 9bzh EMDB-45067, PDB-9bzh: Class 29 model for combined refinement of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 5.9 Å 45068 9bzi EMDB-45068, PDB-9bzi: Class 31 model for combined refinement of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 3.99 Å 45069 9bzj EMDB-45069, PDB-9bzj: Class 40 model for combined refinement of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 4.12 Å 45070 9bzk EMDB-45070, PDB-9bzk: Class 43 model for combined refinement of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 4.19 Å 45071 9bzm EMDB-45071, PDB-9bzm: Class 45 model for combined refinement of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 4.19 Å 45072 9bzo EMDB-45072, PDB-9bzo: Class 50 model for combined refinement of Bacillus subtilis ribonucleotide reductase complex Method: EM (single particle) / Resolution: 4.48 Å
Chemicals	ChemComp-TTP: THYMIDINE-5'-TRIPHOSPHATE ChemComp-MG: Unknown entry ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying moleculeYM ChemComp-MN: Unknown entry ChemComp-GDP: GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying moleculeYM ChemComp-DGI: 2'-DEOXYGUANOSINE-5'-DIPHOSPHATE
Source	bacillus subtilis (bacteria)
Keywords	OXIDOREDUCTASE / ribonucleotide reductase preturnover condition / Ribonucleotide Reductase