8YT4
Structure of Aquifex aeolicus Lumazine Synthase by Cryo-Electron Microscopy to 1.42 Angstrom Resolution
Summary for 8YT4
| Entry DOI | 10.2210/pdb8yt4/pdb |
| EMDB information | 39478 |
| Descriptor | 6,7-dimethyl-8-ribityllumazine synthase, PHOSPHATE ION (3 entities in total) |
| Functional Keywords | enzyme involved in riboflavin biosynthesis, biosynthetic protein |
| Biological source | Aquifex aeolicus |
| Total number of polymer chains | 1 |
| Total formula weight | 17864.32 |
| Authors | Savva, C.G.,Sobhy, M.A.,De Biasio, A.,Hamdan, S.M. (deposition date: 2024-03-24, release date: 2024-04-10, Last modification date: 2024-09-11) |
| Primary citation | Savva, C.G.,Sobhy, M.A.,De Biasio, A.,Hamdan, S.M. Structure of Aquifex aeolicus lumazine synthase by cryo-electron microscopy to 1.42 angstrom resolution. Iucrj, 11:723-729, 2024 Cited by PubMed Abstract: Single-particle cryo-electron microscopy (cryo-EM) has become an essential structural determination technique with recent hardware developments making it possible to reach atomic resolution, at which individual atoms, including hydrogen atoms, can be resolved. In this study, we used the enzyme involved in the penultimate step of riboflavin biosynthesis as a test specimen to benchmark a recently installed microscope and determine if other protein complexes could reach a resolution of 1.5 Å or better, which so far has only been achieved for the iron carrier ferritin. Using state-of-the-art microscope and detector hardware as well as the latest software techniques to overcome microscope and sample limitations, a 1.42 Å map of Aquifex aeolicus lumazine synthase (AaLS) was obtained from a 48 h microscope session. In addition to water molecules and ligands involved in the function of AaLS, we can observe positive density for ∼50% of the hydrogen atoms. A small improvement in the resolution was achieved by Ewald sphere correction which was expected to limit the resolution to ∼1.5 Å for a molecule of this diameter. Our study confirms that other protein complexes can be solved to near-atomic resolution. Future improvements in specimen preparation and protein complex stabilization may allow more flexible macromolecules to reach this level of resolution and should become a priority of study in the field. PubMed: 38965901DOI: 10.1107/S2052252524005530 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (1.42 Å) |
Structure validation
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