9BZO
Class 50 model for combined refinement of Bacillus subtilis ribonucleotide reductase complex
Summary for 9BZO
| Entry DOI | 10.2210/pdb9bzo/pdb |
| EMDB information | 45072 |
| Descriptor | Ribonucleoside-diphosphate reductase subunit alpha, Ribonucleoside-diphosphate reductase subunit beta, ADENOSINE-5'-TRIPHOSPHATE, ... (7 entities in total) |
| Functional Keywords | ribonucleotide reductase, oxidoreductase |
| Biological source | Bacillus subtilis More |
| Total number of polymer chains | 4 |
| Total formula weight | 246158.38 |
| Authors | Xu, D.,Thomas, W.C.,Burnim, A.A.,Ando, N. (deposition date: 2024-05-24, release date: 2025-03-19, Last modification date: 2025-03-26) |
| Primary citation | Xu, D.,Thomas, W.C.,Burnim, A.A.,Ando, N. Conformational landscapes of a class I ribonucleotide reductase complex during turnover reveal intrinsic dynamics and asymmetry. Nat Commun, 16:2458-2458, 2025 Cited by 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 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. PubMed: 40075098DOI: 10.1038/s41467-025-57735-4 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (4.48 Å) |
Structure validation
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