- PDB-8j5a: Single-particle cryo-EM structure of mouse apoferritin at 1.19 An... -
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基本情報
登録情報
データベース: PDB / ID: 8j5a
タイトル
Single-particle cryo-EM structure of mouse apoferritin at 1.19 Angstrom resolution (Dataset A)
要素
Ferritin heavy chain
キーワード
STRUCTURAL PROTEIN / single-particle cryo-EM / Cold field emission / CFEG / Apoferritin / CRYO ARM
機能・相同性
機能・相同性情報
Iron uptake and transport / Golgi Associated Vesicle Biogenesis / iron ion sequestering activity / autolysosome / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / endocytic vesicle lumen / Neutrophil degranulation ...Iron uptake and transport / Golgi Associated Vesicle Biogenesis / iron ion sequestering activity / autolysosome / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / endocytic vesicle lumen / Neutrophil degranulation / ferric iron binding / ferrous iron binding / iron ion transport / iron ion binding / immune response / negative regulation of cell population proliferation / mitochondrion / extracellular region / identical protein binding / membrane / cytoplasm / cytosol 類似検索 - 分子機能
ジャーナル: Commun Chem / 年: 2023 タイトル: Measurement of charges and chemical bonding in a cryo-EM structure. 著者: Saori Maki-Yonekura / Keisuke Kawakami / Kiyofumi Takaba / Tasuku Hamaguchi / Koji Yonekura / 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.
電子線照射量: 36.47 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k)
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解析
ソフトウェア
名称: REFMAC / バージョン: 5.8.0267 / 分類: 精密化
EMソフトウェア
ID
名称
バージョン
カテゴリ
7
UCSF Chimera
1.15
モデルフィッティング
8
Coot
0.9.6
モデルフィッティング
10
REFMAC
5.8.0267
モデル精密化
14
RELION
3.1
3次元再構成
CTF補正
タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
3次元再構成
解像度: 1.19 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 2235864 / 対称性のタイプ: POINT
精密化
解像度: 1.19→126.72 Å / Cor.coef. Fo:Fc: 0.801 / SU B: 0.528 / SU ML: 0.022 / ESU R: 0.007 立体化学のターゲット値: MAXIMUM LIKELIHOOD WITH PHASES 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS