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TitleMeasurement of charges and chemical bonding in a cryo-EM structure.
Journal, issue, pagesCommun Chem, Vol. 6, Issue 1, Page 98, Year 2023
Publish dateMay 31, 2023
AuthorsSaori Maki-Yonekura / Keisuke Kawakami / Kiyofumi Takaba / Tasuku Hamaguchi / Koji Yonekura /
PubMed AbstractHydrogen 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, ...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.
External linksCommun Chem / PubMed:37258702 / PubMed Central
MethodsEM (single particle)
Resolution1.19 - 1.49 Å
Structure data

EMDB-35981: Single-particle cryo-EM structure of mouse apoferritin at 1.49 Angstrom resolution (Dataset B)
Method: EM (single particle) / Resolution: 1.49 Å

35984

8j5a

EMDB-35984, PDB-8j5a:
Single-particle cryo-EM structure of mouse apoferritin at 1.19 Angstrom resolution (Dataset A)
Method: EM (single particle) / Resolution: 1.19 Å

Chemicals

ChemComp-NA:
Unknown entry

ChemComp-HOH:
WATER / Water

Source
  • mus musculus (house mouse)
KeywordsSTRUCTURAL PROTEIN / single-particle cryo-EM / Cold field emission / CFEG / Apoferritin / CRYO ARM

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