5DI0

Crystal structure of Dln1

Summary for 5DI0

• Entry DOI: 10.2210/pdb5di0/pdb
• Related: 4ZNO
• Descriptor: Natterin-like protein, 1,2-ETHANEDIOL, DI(HYDROXYETHYL)ETHER, ... (7 entities in total)
• Functional Keywords: pore-forming protein, aeolysin-like protein, vetebrate, high-mannose glycans, complex, sugar binding protein
• Biological source: Danio rerio (Zebrafish)
• Total number of polymer chains: 2
• Total formula weight: 76839.01

Authors

Jia, N.,Jiang, Y.L.,Cheng, W.,Wang, H.W.,Zhou, C.Z.,Chen, Y. (deposition date: 2015-08-31, release date: 2016-02-03, Last modification date: 2023-11-08)

Primary citation

Jia, N.,Liu, N.,Cheng, W.,Jiang, Y.L.,Sun, H.,Chen, L.L.,Peng, J.,Zhang, Y.,Ding, Y.H.,Zhang, Z.H.,Wang, X.,Cai, G.,Wang, J.,Dong, M.Q.,Zhang, Z.,Wu, H.,Wang, H.W.,Chen, Y.,Zhou, C.Z.
Structural basis for receptor recognition and pore formation of a zebrafish aerolysin-like protein.
Embo Rep., 17:235-248, 2016

PubMed 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 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.

PubMed: 26711430
DOI: 10.15252/embr.201540851

Experimental method

X-RAY DIFFRACTION (1.7 Å)