4IK4

High resolution structure of GCaMP3 at pH 5.0


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.1007/s13238-013-2103-4
  • Primary Citation of Related Structures:  
    4IK1, 4IK3, 4IK4, 4IK5, 4IK8, 4IK9

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RCaMP, Green fluorescent protein448Entacmaea quadricolorAequorea victoriaMutation(s): 11 
UniProt
Find proteins for P42212 (Aequorea victoria)
Explore P42212 
Go to UniProtKB:  P42212
Find proteins for K4DIE3 (Entacmaea quadricolor)
Explore K4DIE3 
Go to UniProtKB:  K4DIE3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsK4DIE3P42212
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.486α = 90
b = 46.917β = 100.53
c = 66.775γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-05
    Type: Initial release
  • Version 1.1: 2017-06-21
    Changes: Advisory, Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2024-10-30
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary