ジャーナル: EMBO Rep / 年: 2016 タイトル: Structural basis for receptor recognition and pore formation of a zebrafish aerolysin-like protein. 著者: Ning Jia / Nan Liu / Wang Cheng / Yong-Liang Jiang / Hui Sun / Lan-Lan Chen / Junhui Peng / Yonghui Zhang / Yue-He Ding / Zhi-Hui Zhang / Xuejuan Wang / Gang Cai / Junfeng Wang / Meng-Qiu ...著者: Ning Jia / Nan Liu / Wang Cheng / Yong-Liang Jiang / Hui Sun / Lan-Lan Chen / Junhui Peng / Yonghui Zhang / Yue-He Ding / Zhi-Hui Zhang / Xuejuan Wang / Gang Cai / Junfeng Wang / Meng-Qiu Dong / Zhiyong Zhang / Hui Wu / Hong-Wei Wang / Yuxing Chen / Cong-Zhao Zhou / 要旨: Various aerolysin-like pore-forming proteins have been identified from bacteria to vertebrates. However, the mechanism of receptor recognition and/or pore formation of the eukaryotic members remains ...Various aerolysin-like pore-forming proteins have been identified from bacteria to vertebrates. However, the mechanism of receptor recognition and/or pore formation of the eukaryotic members remains unknown. Here, we present the first crystal and electron microscopy structures of a vertebrate aerolysin-like protein from Danio rerio, termed Dln1, before and after pore formation. Each subunit of Dln1 dimer comprises a β-prism lectin module followed by an aerolysin module. Specific binding of the lectin module toward high-mannose glycans triggers drastic conformational changes of the aerolysin module in a pH-dependent manner, ultimately resulting in the formation of a membrane-bound octameric pore. Structural analyses combined with computational simulations and biochemical assays suggest a pore-forming process with an activation mechanism distinct from the previously characterized bacterial members. Moreover, Dln1 and its homologs are ubiquitously distributed in bony fishes and lamprey, suggesting a novel fish-specific defense molecule.
プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長
波長: 0.97915 Å / 相対比: 1
反射
解像度: 1.9→50 Å / Num. obs: 63944 / % possible obs: 99.7 % / 冗長度: 3.9 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 12
反射 シェル
解像度: 1.9→1.97 Å / 冗長度: 3.9 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 3.3 / % possible all: 100
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解析
ソフトウェア
名称
バージョン
分類
REFMAC
5.7.0032
精密化
HKL-2000
データ削減
HKL-2000
データスケーリング
MOLREP
位相決定
精密化
構造決定の手法: 単波長異常分散 / 解像度: 1.9→35.61 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.917 / SU ML: 0.087 / 交差検証法: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.129 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
反射数
%反射
Selection details
Rfree
0.21853
3237
5.1 %
RANDOM
Rwork
0.18074
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-
-
obs
0.18267
60638
99.11 %
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溶媒の処理
イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK