4IK9

High resolution structure of GCaMP3 dimer form 2 at pH 7.5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insight into enhanced calcium indicator GCaMP3 and GCaMPJ to promote further improvement.

Chen, Y.Song, X.Ye, S.Miao, L.Zhu, Y.Zhang, R.G.Ji, G.

(2013) Protein Cell 4: 299-309

  • DOI: 10.1007/s13238-013-2103-4
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Genetically encoded Ca(2+) indicators (GECI) are important for the measurement of Ca(2+) in vivo. GCaMP2, a widely-used GECI, has recently been iteratively improved. Among the improved variants, GCaMP3 exhibits significantly better fluorescent intens ...

    Genetically encoded Ca(2+) indicators (GECI) are important for the measurement of Ca(2+) in vivo. GCaMP2, a widely-used GECI, has recently been iteratively improved. Among the improved variants, GCaMP3 exhibits significantly better fluorescent intensity. In this study, we developed a new GECI called GCaMPJ and determined the crystal structures of GCaMP3 and GCaMPJ. GCaMPJ has a 1.5-fold increase in fluorescence and 1.3-fold increase in calcium affinity over GCaMP3. Upon Ca(2+) binding, GCaMP3 exhibits both monomeric and dimeric forms. The structural superposition of these two forms reveals the role of Arg-376 in improving monomer performance. However, GCaMPJ seldom forms dimers under conditions similar to GCaMP3. St ructural and mutagenesis studies on Tyr-380 confirmed its importance in blocking the cpEGFP β-barrel holes. Our study proposes an efficient tool for mapping Ca(2+) signals in intact organs to facilitate the further improvement of GCaMP sensors.


    Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RCaMP, Green fluorescent protein
A
450Aequorea victoriaEntacmaea quadricolor
This entity is chimeric
Mutation(s): 10 
Gene Names: GFP,
Find proteins for P42212 (Aequorea victoria)
Go to UniProtKB:  P42212
Find proteins for K4DIE3 (Entacmaea quadricolor)
Go to UniProtKB:  K4DIE3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-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: 1.8 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.159 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 125.617α = 90.00
b = 46.749β = 100.06
c = 68.753γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
REFMACrefinement
ADSCdata collection
HKL-2000data reduction

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: 2017-06-21
    Type: Advisory, Database references, Source and taxonomy, Structure summary