4NPJ

Extended-Synaptotagmin 2, C2A- and C2B-domains


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.101 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and ca(2+)-binding properties of the tandem c2 domains of e-syt2.

Xu, J.Bacaj, T.Zhou, A.Tomchick, D.R.Sudhof, T.C.Rizo, J.

(2014) Structure 22: 269-280

  • DOI: 10.1016/j.str.2013.11.011
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Contacts between the endoplasmic reticulum and the plasma membrane involve extended synaptotagmins (E-Syts) in mammals or tricalbins in yeast, proteins with multiple C₂ domains. One of the tandem C₂ domains of E-Syt2 is predicted to bind Ca²⁺, but no ...

    Contacts between the endoplasmic reticulum and the plasma membrane involve extended synaptotagmins (E-Syts) in mammals or tricalbins in yeast, proteins with multiple C₂ domains. One of the tandem C₂ domains of E-Syt2 is predicted to bind Ca²⁺, but no Ca²⁺-dependent function has been attributed to this protein. We have determined the crystal structures of the tandem C₂ domains of E-Syt2 in the absence and presence of Ca²⁺ and analyzed their Ca²⁺-binding properties by nuclear magnetic resonance spectroscopy. Our data reveal an unexpected V-shaped structure with a rigid orientation between the two C₂ domains that is not substantially altered by Ca²⁺. The E-Syt2 C2A domain binds up to four Ca²⁺ ions, whereas the C₂B domain does not bind Ca²⁺. These results suggest that E-Syt2 performs an as yet unidentified Ca²⁺-dependent function through its C₂A domain and uncover fundamental differences between the properties of the tandem C₂ domains of E-Syts and synaptotagmins.


    Related Citations: 
    • E-Syts, a family of membranous Ca2+-sensor proteins with multiple C2 domains.
      Min, S.W.,Chang, W.P.,Sudhof, T.C.
      (2007) Proc.Natl.Acad.Sci.USA 104: 3823


    Organizational Affiliation

    Department of Biophysics, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA; Department of Pharmacology, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Extended synaptotagmin-2
A, B
299Homo sapiensMutation(s): 0 
Gene Names: ESYT2 (FAM62B, KIAA1228)
Find proteins for A0FGR8 (Homo sapiens)
Go to Gene View: ESYT2
Go to UniProtKB:  A0FGR8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.101 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.200 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 62.300α = 90.00
b = 62.300β = 90.00
c = 226.395γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data reduction
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
HKL-3000data scaling
MLPHAREphasing
DENZOdata reduction
HKL-3000data collection
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-29
    Type: Initial release
  • Version 1.1: 2014-03-19
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Refinement description