8J5A

Single-particle cryo-EM structure of mouse apoferritin at 1.19 Angstrom resolution (Dataset A)

8J5A の概要

• エントリーDOI: 10.2210/pdb8j5a/pdb
• EMDBエントリー: 35981 35984
• 分子名称: Ferritin heavy chain, SODIUM ION (3 entities in total)
• 機能のキーワード: single-particle cryo-em, cold field emission, cfeg, apoferritin, cryo arm, structural protein
• 由来する生物種: Mus musculus (house mouse)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 20102.58

構造登録者

Kawakami, K.,Maki-Yonekura, S.,Hamaguchi, T.,Takaba, K.,Yonekura, K. (登録日: 2023-04-21, 公開日: 2023-07-12, 最終更新日: 2024-07-03)

主引用文献

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

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: 37258702
DOI: 10.1038/s42004-023-00900-x

実験手法

ELECTRON MICROSCOPY (1.19 Å)