1TJX

Crystallographic Identification of Ca2+ Coordination Sites in Synaptotagmin I C2B Domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.04 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystallographic identification of Ca2+ and Sr2+ coordination sites in synaptotagmin I C2B domain.

Cheng, Y.Sequeira, S.M.Malinina, L.Tereshko, V.Sollner, T.H.Patel, D.J.

(2004) Protein Sci. 13: 2665-2672

  • DOI: 10.1110/ps.04832604
  • Primary Citation of Related Structures:  1TJM, 1UOV, 1UOW

  • PubMed Abstract: 
  • Synaptotagmin I has two tandem Ca(2+)-binding C(2) domains, which are essential for fast synchronous synaptic transmission in the central nervous system. We have solved four crystal structures of the C(2)B domain, one of them in the cation-free form ...

    Synaptotagmin I has two tandem Ca(2+)-binding C(2) domains, which are essential for fast synchronous synaptic transmission in the central nervous system. We have solved four crystal structures of the C(2)B domain, one of them in the cation-free form at 1.50 A resolution, two in the Ca(2+)-bound form at 1.04 A (two bound Ca(2+) ions) and 1.65 A (three bound Ca(2+) ions) resolution and one in the Sr(2+)-bound form at 1.18 A (one bound Sr(2+) ion) resolution. The side chains of four highly conserved aspartic acids (D303, D309, D363, and D365) and two main chain oxygens (M302:O and Y364:O), together with water molecules, are in direct contact with two bound Ca(2+) ions (sites 1 and 2). At higher Ca(2+) concentrations, the side chain of N333 rotates and cooperates with D309 to generate a third Ca(2+) coordination site (site 3). Divalent cation binding sites 1 and 2 in the C(2)B domain were previously identified from NMR NOE patterns and titration studies, supplemented by site-directed mutation analysis. One difference between the crystal and NMR studies involves D371, which is not involved in coordination with any of the identified Ca(2+) sites in the crystal structures, while it is coordinated to Ca(2+) in site 2 in the NMR structure. In the presence of Sr(2+), which is also capable of triggering exocytosis, but with lower efficiency, only one cation binding site (site 1) was occupied in the crystallographic structure.


    Organizational Affiliation

    Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA. chengy@mskcc.org




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
similar to synaptotagminI/p65
A
159Rattus norvegicusGene Names: Syt1
Find proteins for P21707 (Rattus norvegicus)
Go to UniProtKB:  P21707
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

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

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.04 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.166 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 54.550α = 90.00
b = 54.550β = 90.00
c = 103.590γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
AMoREphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-11-23
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2012-04-11
    Type: Structure summary