8J5A
Single-particle cryo-EM structure of mouse apoferritin at 1.19 Angstrom resolution (Dataset A)
Summary for 8J5A
| Entry DOI | 10.2210/pdb8j5a/pdb |
| EMDB information | 35981 35984 |
| Descriptor | Ferritin heavy chain, SODIUM ION (3 entities in total) |
| Functional Keywords | single-particle cryo-em, cold field emission, cfeg, apoferritin, cryo arm, structural protein |
| Biological source | Mus musculus (house mouse) |
| Total number of polymer chains | 1 |
| Total formula weight | 20102.58 |
| Authors | Kawakami, K.,Maki-Yonekura, S.,Hamaguchi, T.,Takaba, K.,Yonekura, K. (deposition date: 2023-04-21, release date: 2023-07-12, Last modification date: 2024-07-03) |
| Primary citation | Maki-Yonekura, S.,Kawakami, K.,Takaba, K.,Hamaguchi, T.,Yonekura, K. Measurement of charges and chemical bonding in a cryo-EM structure. Commun Chem, 6:98-98, 2023 Cited by PubMed Abstract: Hydrogen bonding, bond polarity, and charges in protein molecules play critical roles in the stabilization of protein structures, as well as affecting their functions such as enzymatic catalysis, electron transfer, and ligand binding. These effects can potentially be measured in Coulomb potentials using cryogenic electron microscopy (cryo-EM). We here present charges and bond properties of hydrogen in a sub-1.2 Å resolution structure of a protein complex, apoferritin, by single-particle cryo-EM. A weighted difference map reveals positive densities for most hydrogen atoms in the core region of the complex, while negative densities around acidic amino-acid side chains are likely related to negative charges. The former positive densities identify the amino- and oxo-termini of asparagine and glutamine side chains. The latter observations were verified by spatial-resolution selection and a dose-dependent frame series. The average position of the hydrogen densities depends on the parent bonded-atom type, and this is validated by the estimated level of the standard uncertainties in the bond lengths. PubMed: 37258702DOI: 10.1038/s42004-023-00900-x PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (1.19 Å) |
Structure validation
Download full validation report
