The structure and flexibility analysis of the Arabidopsis synaptotagmin 1 reveal the basis of its regulation at membrane contact sites

Benavente J, Siliqi D, Infantes L, Lagartera L, Mills A, Gago F, Ruiz-López N, Botella M, Sánchez-Barrena M, Albert A, Life Science Alliance 4(10):e202101152 (2021) DOI

SASDKK9 – C2AB construct of synaptotagmin-1 (SYT1) in presence of Ca cations

MWexperimental 33 kDa
MWexpected 33 kDa
VPorod 54 nm3
log I(s) 1.64×10-2 1.64×10-3 1.64×10-4 1.64×10-5
Synaptotagmin-1 small angle scattering data  s, nm-1
ln I(s)
Synaptotagmin-1 Guinier plot ln 1.65×10-2 Rg: 2.9 nm 0 (2.9 nm)-2 s2
Synaptotagmin-1 Kratky plot 1.104 0 3 sRg
Synaptotagmin-1 pair distance distribution function Rg: 3.1 nm 0 Dmax: 13.8 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Synaptotagmin-1 MULTIFOXS model
Synaptotagmin-1 MULTIFOXS model
Synaptotagmin-1 MULTIFOXS model

log I(s)
 s, nm-1
Synaptotagmin-1 DAMFILT model

SAXS data were collected in the bioSAXS beamline B21, at Diamond Light Source, Harwell, United Kingdom. For the SYT1C2AB, 45 μl of sample with a concentration of 10 mg/ml, were injected onto a Superdex 200 increase 3.2/300 column at 20°C using 50 mM Tris, pH8, 50 mM NaCl as the running buffer. The output flow from the Agilent HPLC was directed through a 1.6 mm diameter quartz capillary cell held in vacuum. The flow rate was set to 0.08 mL min-1 and 1162 frames (with an exposure time of 3 s) were collected using a PILATUS 2M (Dectris, Switzerland) detector at the distance of 3.7 m from the sample. The collected two-dimensional images were corrected for variations in beam current, normalized for exposure time and processed into one- dimensional scattering curves using GDA and the DAWN software (Diamond Light Source, UK). The background was manually subtracted using the program ScÅtter and CHROMIXS (ATSAS).

The final concentration of Ca2+ cations is 1 mM.

Synaptotagmin-1 (SYS1C2AB)
Mol. type   Protein
Organism   Arabidopsis thaliana
Olig. state   Monomer
Mon. MW   33.2 kDa
UniProt   Q9SKR2 (253-541)
Sequence   FASTA