Journal: EMBO Rep / Year: 2016 Title: Structural basis for receptor recognition and pore formation of a zebrafish aerolysin-like protein. Authors: 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 ...Authors: 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 / Abstract: 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.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97915 Å / Relative weight: 1
Reflection
Resolution: 1.9→50 Å / Num. obs: 63944 / % possible obs: 99.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 12
Reflection shell
Resolution: 1.9→1.97 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 3.3 / % possible all: 100
-
Processing
Software
Name
Version
Classification
REFMAC
5.7.0032
refinement
HKL-2000
datareduction
HKL-2000
datascaling
MOLREP
phasing
Refinement
Method to determine structure: SAD / Resolution: 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 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.21853
3237
5.1 %
RANDOM
Rwork
0.18074
-
-
-
obs
0.18267
60638
99.11 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK