2YOA | pdb_00002yoa

Synaptotagmin-1 C2B domain with phosphoserine

• PDB DOI: https://doi.org/10.2210/pdb2YOA/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-10-22 Released: 2013-03-20 
• Deposition Author(s): Honigmann, A., van den Bogaart, G., Iraheta, E., Risselada, H.J., Milovanovic, D., Mueller, V., Muellar, S., Diederichsen, U., Fasshauer, D., Grubmuller, H., Hell, S.W., Eggeling, C., Kuhnel, K., Jahn, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.204 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Phosphatidylinositol 4,5-Bisphosphate Clusters Act as Molecular Beacons for Vesicle Recruitment

Honigmann, A., Van Den Bogaart, G., Iraheta, E., Risselada, H.J., Milovanovic, D., Mueller, V., Muellar, S., Diederichsen, U., Fasshauer, D., Grubmuller, H., Hell, S.W., Eggeling, C., Kuhnel, K., Jahn, R.

(2013) Nat Struct Mol Biol 20: 679

• PubMed: 23665582 
• DOI: https://doi.org/10.1038/nsmb.2570
• Primary Citation Related Structures: 
  2YOA


• PubMed Abstract: 
  

  Synaptic-vesicle exocytosis is mediated by the vesicular Ca(2+) sensor synaptotagmin-1. Synaptotagmin-1 interacts with the SNARE protein syntaxin-1A and acidic phospholipids such as phosphatidylinositol 4,5-bisphosphate (PIP2). However, it is unclear how these interactions contribute to triggering membrane fusion. Using PC12 cells from Rattus norvegicus and artificial supported bilayers, we show that synaptotagmin-1 interacts with the polybasic linker region of syntaxin-1A independent of Ca(2+) through PIP2. This interaction allows both Ca(2+)-binding sites of synaptotagmin-1 to bind to phosphatidylserine in the vesicle membrane upon Ca(2+) triggering. We determined the crystal structure of the C2B domain of synaptotagmin-1 bound to phosphoserine, allowing development of a high-resolution model of synaptotagmin bridging two different membranes. Our results suggest that PIP2 clusters organized by syntaxin-1 act as molecular beacons for vesicle docking, with the subsequent Ca(2+) influx bringing the vesicle membrane close enough for membrane fusion.

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Organizational Affiliation: 
• Department of Nanobiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 35.65 kDa 
• Atom Count: 2,713 
• Modeled Residue Count: 298 
• Deposited Residue Count: 304 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SYNAPTOTAGMIN-1	A, B	152	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P21707 (Rattus norvegicus) Explore P21707  Go to UniProtKB:  P21707

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SEP	F [auth A], M [auth B]	PHOSPHOSERINE C3 H8 N O6 P BZQFBWGGLXLEPQ-REOHCLBHSA-N
SCN	H [auth A], I [auth A], N [auth B], O [auth B], P [auth B]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M
CA	C [auth A], D [auth A], E [auth A], G [auth A], J [auth B], K [auth B], L [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.204 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97	α = 90
b = 97	β = 90
c = 89.01	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-20 
Deposition Author(s): Honigmann, A., van den Bogaart, G., Iraheta, E., Risselada, H.J., Milovanovic, D., Mueller, V., Muellar, S., Diederichsen, U., Fasshauer, D., Grubmuller, H., Hell, S.W., Eggeling, C., Kuhnel, K., Jahn, R.

Revision History  

• Version 1.0: 2013-03-20
  Type: Initial release
  
• Version 1.1: 2013-05-15
  Changes: Database references
• Version 1.2: 2013-05-29
  Changes: Database references
• Version 1.3: 2013-06-19
  Changes: Database references
• Version 1.4: 2017-08-23
  Changes: Data collection
• Version 1.5: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description