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 Molecular and Cellular Physiology, Stanford University Medical School, 265 Campus Drive, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University Medical School, 265 Campus Drive, Stanford, CA 94305, USA.,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. Electronic address: jose@arnie.swmed.edu.,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 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