ジャーナル: Proc Natl Acad Sci U S A / 年: 2017 タイトル: Detection of isolated protein-bound metal ions by single-particle cryo-STEM. 著者: Nadav Elad / Giuliano Bellapadrona / Lothar Houben / Irit Sagi / Michael Elbaum / 要旨: Metal ions play essential roles in many aspects of biological chemistry. Detecting their presence and location in proteins and cells is important for understanding biological function. Conventional ...Metal ions play essential roles in many aspects of biological chemistry. Detecting their presence and location in proteins and cells is important for understanding biological function. Conventional structural methods such as X-ray crystallography and cryo-transmission electron microscopy can identify metal atoms on protein only if the protein structure is solved to atomic resolution. We demonstrate here the detection of isolated atoms of Zn and Fe on ferritin, using cryogenic annular dark-field scanning transmission electron microscopy (cryo-STEM) coupled with single-particle 3D reconstructions. Zn atoms are found in a pattern that matches precisely their location at the ferroxidase sites determined earlier by X-ray crystallography. By contrast, the Fe distribution is smeared along an arc corresponding to the proposed path from the ferroxidase sites to the mineral nucleation sites along the twofold axes. In this case the single-particle reconstruction is interpreted as a probability distribution function based on the average of individual locations. These results establish conditions for detection of isolated metal atoms in the broader context of electron cryo-microscopy and tomography.
ダウンロード / ファイル: emd_3849.map.gz / 形式: CCP4 / 大きさ: 2 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈
Ferritin with 100 Fe atoms from single particle cryo-STEM data
ボクセルのサイズ
X=Y=Z: 3.3 Å
密度
表面レベル
登録者による: 0.04 / ムービー #1: 0.04
最小 - 最大
-0.026305879 - 0.04511763
平均 (標準偏差)
0.0006757258 (±0.0042300415)
対称性
空間群: 1
詳細
EMDB XML:
マップ形状
Axis order
X
Y
Z
Origin
0
0
0
サイズ
80
80
80
Spacing
80
80
80
セル
A=B=C: 264.0 Å α=β=γ: 90.0 °
CCP4マップ ヘッダ情報:
mode
Image stored as Reals
Å/pix. X/Y/Z
3.3
3.3
3.3
M x/y/z
80
80
80
origin x/y/z
0.000
0.000
0.000
length x/y/z
264.000
264.000
264.000
α/β/γ
90.000
90.000
90.000
MAP C/R/S
1
2
3
start NC/NR/NS
0
0
0
NC/NR/NS
80
80
80
D min/max/mean
-0.026
0.045
0.001
-
添付データ
-
試料の構成要素
-
全体 : Human heavy chain ferritin with Fe at low stoichiometry
全体
名称: Human heavy chain ferritin with Fe at low stoichiometry
要素
複合体: Human heavy chain ferritin with Fe at low stoichiometry
-
超分子 #1: Human heavy chain ferritin with Fe at low stoichiometry
超分子
名称: Human heavy chain ferritin with Fe at low stoichiometry タイプ: complex / ID: 1 / 親要素: 0 詳細: Bacterially expressed and purified human heavy chain ferritin mixed with a 100 fold molar excess of Fe(II)SO4
詳細: The initial model was prepared from the of the human ferritin heavy chain crystal structure from which all heavy atoms were removed. The protein PDB coordinates were converted to structure ...詳細: The initial model was prepared from the of the human ferritin heavy chain crystal structure from which all heavy atoms were removed. The protein PDB coordinates were converted to structure factors and low pass filtered to 4 nm.
最終 再構成
想定した対称性 - 点群: O (正8面体型対称) / 解像度のタイプ: BY AUTHOR / 解像度: 21.0 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: RELION (ver. 1.4) / 使用した粒子像数: 1484