4NPJ

Extended-Synaptotagmin 2, C2A- and C2B-domains


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1016/j.str.2013.11.011
  • Primary Citation of Related Structures:  
    4NPJ, 4NPK

  • 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 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.


  • 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Extended synaptotagmin-2
A, B
299Homo sapiensMutation(s): 0 
Gene Names: ESYT2extended-synaptotagmin 2FAM62BKIAA1228
UniProt & NIH Common Fund Data Resources
Find proteins for A0FGR8 (Homo sapiens)
Explore A0FGR8 
Go to UniProtKB:  A0FGR8
PHAROS:  A0FGR8
GTEx:  ENSG00000117868 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0FGR8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.3α = 90
b = 62.3β = 90
c = 226.395γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
MLPHAREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-29
    Type: Initial release
  • Version 1.1: 2014-03-19
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations