3WLC

Crystal structure of dimeric GCaMP6m


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structural basis of the ultrasensitive calcium indicator GCaMP6.

Ding, J.Luo, A.F.Hu, L.Wang, D.Shao, F.

(2014) Sci China Life Sci 57: 269-274

  • DOI: https://doi.org/10.1007/s11427-013-4599-5
  • Primary Citation of Related Structures:  
    3WLC, 3WLD

  • PubMed Abstract: 

    GCaMP is one of the most widely used calcium indicators in neuronal imaging and calcium cell biology. The newly developed GCaMP6 shows superior brightness and ultrasensitivity to calcium concentration change. In this study, we determined crystal structures of Ca(2+)-bound GCaMP6 monomer and dimer and presented detailed structural analyses in comparison with its parent version GCaMP5G. Our analyses reveal the structural basis for the outperformance of this newly developed Ca(2+) indicator. Three substitution mutations and the resulting changes of local structure and interaction explain the ultrasensitivity and increased fluorescence intensity common to all three versions of GCaMP6. Each particular substitution in the three GCaMP6 is also structurally consistent with their differential sensitivity and intensity, maximizing the potential of using GCaMP6 in solving diverse problems in neuronal research and calcium signaling. Our studies shall also be beneficial to further structure-guided optimization of GCaMP and facilitate the design of novel calcium indicators.


  • 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
Myosin light chain kinase, Green fluorescent protein, Calmodulin448Gallus gallusAequorea victoriaRattus norvegicusMutation(s): 18 
UniProt
Find proteins for P42212 (Aequorea victoria)
Explore P42212 
Go to UniProtKB:  P42212
Find proteins for P11799 (Gallus gallus)
Explore P11799 
Go to UniProtKB:  P11799
Find proteins for P0DP29 (Rattus norvegicus)
Explore P0DP29 
Go to UniProtKB:  P0DP29
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP42212P0DP29P11799
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.44α = 90
b = 46.86β = 99.36
c = 68.34γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-22
    Type: Initial release
  • Version 1.1: 2017-06-21
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2018-11-21
    Changes: Data collection
  • Version 1.3: 2022-08-24
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-11-08
    Changes: Data collection, Refinement description
  • Version 1.5: 2023-12-06
    Changes: Data collection