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-Structure paper
タイトル | Measurement of charges and chemical bonding in a cryo-EM structure. |
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ジャーナル・号・ページ | Commun Chem, Vol. 6, Issue 1, Page 98, Year 2023 |
掲載日 | 2023年5月31日 |
![]() | Saori Maki-Yonekura / Keisuke Kawakami / Kiyofumi Takaba / Tasuku Hamaguchi / Koji Yonekura / ![]() |
PubMed 要旨 | 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, ...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. |
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手法 | EM (単粒子) |
解像度 | 1.19 - 1.49 Å |
構造データ | ![]() EMDB-35981: Single-particle cryo-EM structure of mouse apoferritin at 1.49 Angstrom resolution (Dataset B) EMDB-35984, PDB-8j5a: |
化合物 | ![]() ChemComp-NA: ![]() ChemComp-HOH: |
由来 |
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![]() | STRUCTURAL PROTEIN / single-particle cryo-EM / Cold field emission / CFEG / Apoferritin / CRYO ARM |