4WEE

High-resolution structure of Synaptotagmin 1 C2A

Summary for 4WEE

• Entry DOI: 10.2210/pdb4wee/pdb
• Descriptor: Synaptotagmin-1, SODIUM ION, SULFATE ION, ... (4 entities in total)
• Functional Keywords: synaptotagmin, c2 domain, ca2+, beta-sandwich, metal binding protein
• Biological source: Rattus norvegicus (Rat)
• Cellular location: Cytoplasmic vesicle, secretory vesicle, synaptic vesicle membrane; Single-pass membrane protein: P21707
• Total number of polymer chains: 1
• Total formula weight: 16450.36

Authors

Sutton, R.B.,Fuson, K.L. (deposition date: 2014-09-09, release date: 2014-10-01, Last modification date: 2025-01-15)

Primary citation

Dominguez, M.J.,Bui, A.A.,Villarreal, J.,Snow, A.,Karmakar, S.,Harsini, F.M.,Rock, P.J.,Rice, A.M.,Fuson, K.L.,Sutton, R.B.
The AD3 locus of synaptotagmin-1 C2 domains modulates domain stability.
Biophys.J., 2024

PubMed Abstract: Synaptotagmin-1 (syt1) functions as the Ca-dependent sensor that triggers the rapid and synchronous release of neurotransmitters from neurotransmitter-containing vesicles during neuronal exocytosis. The syt1 protein has two homologous tandem C2 domains that interact with phospholipids in a Ca-dependent manner. Despite the crucial role of syt1 in exocytosis, the precise interactions between Ca, syt1, and phospholipids are not fully understood. In a study involving recessive lethal mutations in the syt1 gene, a specific mutation named AD3 was generated in Drosophila syt1, resulting in a significant reduction in Ca-dependent exocytosis. Further investigation revealed that the AD3 mutation was a missense mutation located in a conserved consensus sequence within the C2B domain of Drosophila syt1. However, the biophysical impact of the AD3 mutation had not been analyzed. Our study uses x-ray crystallography, isothermal titration calorimetry, thermodynamic analysis, and molecular dynamics simulation to show that the primary defect caused by the AD3 mutation in the syt1 protein is reduced thermodynamic stability. This instability alters the population of Ca-receptive states, leading to two major consequences: decreased affinity for calcium ions and compromised stabilization of the domain normally enhanced by Ca. We conclude that this conserved residue acts as a structural constraint, delimiting the movement of loop 3 within the pocket and ultimately influencing the affinity of the calcium ion binding with the C2 domain.

PubMed: 39578407
DOI: 10.1016/j.bpj.2024.11.009

Experimental method

X-RAY DIFFRACTION (0.891 Å)