4L12

Crystal structure of EGFP-based Calcium Sensor CatchER complexed with Gd


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for a hand-like site in the calcium sensor CatchER with fast kinetics.

Zhang, Y.Reddish, F.Tang, S.Zhuo, Y.Wang, Y.F.Yang, J.J.Weber, I.T.

(2013) Acta Crystallogr.,Sect.D 69: 2309-2319

  • DOI: 10.1107/S0907444913021306
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Calcium ions, which are important signaling molecules, can be detected in the endoplasmic reticulum by an engineered mutant of green fluorescent protein (GFP) designated CatchER with a fast off-rate. High resolution (1.78-1.20 Å) crystal structures w ...

    Calcium ions, which are important signaling molecules, can be detected in the endoplasmic reticulum by an engineered mutant of green fluorescent protein (GFP) designated CatchER with a fast off-rate. High resolution (1.78-1.20 Å) crystal structures were analyzed for CatchER in the apo form and in complexes with calcium or gadolinium to probe the binding site for metal ions. While CatchER exhibits a 1:1 binding stoichiometry in solution, two positions were observed for each of the metal ions bound within the hand-like site formed by the carboxylate side chains of the mutated residues S147E, S202D, Q204E, F223E and T225E that may be responsible for its fast kinetic properties. Comparison of the structures of CatchER, wild-type GFP and enhanced GFP confirmed that different conformations of Thr203 and Glu222 are associated with the two forms of Tyr66 of the chromophore which are responsible for the absorbance wavelengths of the different proteins. Calcium binding to CatchER may shift the equilibrium for conformational population of the Glu222 side chain and lead to further changes in its optical properties.


    Organizational Affiliation

    Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EGFP-based Calcium Sensor CatchER
A
232Aequorea victoriaMutation(s): 8 
Gene Names: GFP
Find proteins for P42212 (Aequorea victoria)
Go to UniProtKB:  P42212
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GD
Query on GD

Download SDF File 
Download CCD File 
A
GADOLINIUM ATOM
Gd
UIWYJDYFSGRHKR-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CRO
Query on CRO
A
L-PEPTIDE LINKINGC15 H17 N3 O5THR, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.196 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 61.062α = 90.00
b = 88.334β = 90.00
c = 118.167γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
HKL-2000data reduction
SERGUIdata collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-06-01 
  • Released Date: 2013-12-11 
  • Deposition Author(s): Zhang, Y., Weber, I.T.

Revision History 

  • Version 1.0: 2013-12-11
    Type: Initial release
  • Version 1.1: 2014-01-08
    Type: Database references