2YOA

Synaptotagmin-1 C2B domain with phosphoserine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

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

  • DOI: 10.1038/nsmb.2570

  • 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 ...

    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.


    Organizational Affiliation

    Department of Nanobiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SYNAPTOTAGMIN-1
A, B
152Rattus norvegicusMutation(s): 0 
Gene Names: Syt1
Find proteins for P21707 (Rattus norvegicus)
Go to UniProtKB:  P21707
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SCN
Query on SCN

Download SDF File 
Download CCD File 
A, B
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 Ligand Interaction
SEP
Query on SEP

Download SDF File 
Download CCD File 
A, B
PHOSPHOSERINE
PHOSPHONOSERINE
C3 H8 N O6 P
BZQFBWGGLXLEPQ-REOHCLBHSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.183 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 97.000α = 90.00
b = 97.000β = 90.00
c = 89.010γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
BALBESphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-20
    Type: Initial release
  • Version 1.1: 2013-05-15
    Type: Database references
  • Version 1.2: 2013-05-29
    Type: Database references
  • Version 1.3: 2013-06-19
    Type: Database references
  • Version 1.4: 2017-08-23
    Type: Data collection