PDB ID or protein name

1byn » Synaptotagmin-1, C2A domain (Calcium bound)

1byn » Synaptotagmin-1, C2A domain (Calcium bound)
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Topology in Eukaryotic plasma membrane
Topologyextracellular side
cytoplasmic side
1byn » Synaptotagmin-1, C2A domain (Calcium bound)
Depth 3.8 ± 1.6 Å
Tilt Angle 32 ± 19°
ΔGtransfer -4.7 kcal/mol
Links to 1byn PDB Sum, PDB, SCOP, MSD, OCA, MMDB
Topology cytoplasmic
Resolution NMR
Other PDB entries representing this structure none
Number of subunits 1
Experimental Verification for 1byn » Synaptotagmin-1, C2A domain (Calcium bound)
Side-chains of residues in positions M173, G174, and F234 penetrate into the hydrophobic core of the membrane in the calculated orientation. Experimental membrane depth parameters are positive in positions 174 and 234 (only) but negative in position 173 (Frazier et al. 2003). However, residue M173 has been identified as most important for membrane binding by Gerber et al. (2002). Three calcium ions are located at the distances of 6.1, 6.3 and 3.3 A beyond the hydrophobic boundary, i.e. 1.1, 1.3 and -1.7 A, respectively, from the level of bulk lipid phosphates. This is consistent with EPR studies (Malmberg and Falke 2005). Maximal membrane binding affinity: -6.5 kcal/mol (Nalefski et al. 2001).
4 references
Frazier AA, Roller CR, Havelka JJ, Hinderliter A, and Cafiso DS (2003) Membrane-bound orientation and position of the synaptotagmin IC2A domain by site-directed spin labeling Biochemistry 42: 96-105. PubMed
Gerber SH, Rizo J, Sudhof TC. 2002. Role of electrostatic and hydrophobic interactions in Ca(2+)-dependent phospholipid binding by the C(2)A-domain from synaptotagmin I. Diabetes. 51 Suppl 1:S12-S18. PubMed
Malmberg NJ, Falke JJ. 2005. Use of EPR power saturation to analyze the membrane-docking geometries of peripheral proteins: applications to C2 domains. Annu Rev Biophys Biomol Struct. 34: 71-90. PubMed
Nalefski EA, Wisner MA, Chen JZ, Sprang SR, Fukuda M, Mikoshiba K, Falke JJ. 2001. C2 domains from different Ca2+ signaling pathways display functional and mechanistic diversity. Biochemistry. 40:3089-100. PubMed