3SG4

Crystal Structure of GCaMP3-D380Y, LP(linker 2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Optimization of a GCaMP calcium indicator for neural activity imaging.

Akerboom, J.Chen, T.W.Wardill, T.J.Tian, L.Marvin, J.S.Mutlu, S.Calderon, N.C.Esposti, F.Borghuis, B.G.Sun, X.R.Gordus, A.Orger, M.B.Portugues, R.Engert, F.Macklin, J.J.Filosa, A.Aggarwal, A.Kerr, R.A.Takagi, R.Kracun, S.Shigetomi, E.Khakh, B.S.Baier, H.Lagnado, L.Wang, S.S.Bargmann, C.I.Kimmel, B.E.Jayaraman, V.Svoboda, K.Kim, D.S.Schreiter, E.R.Looger, L.L.

(2012) J.Neurosci. 32: 13819-13840

  • DOI: 10.1523/JNEUROSCI.2601-12.2012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Genetically encoded calcium indicators (GECIs) are powerful tools for systems neuroscience. Recent efforts in protein engineering have significantly increased the performance of GECIs. The state-of-the art single-wavelength GECI, GCaMP3, has been dep ...

    Genetically encoded calcium indicators (GECIs) are powerful tools for systems neuroscience. Recent efforts in protein engineering have significantly increased the performance of GECIs. The state-of-the art single-wavelength GECI, GCaMP3, has been deployed in a number of model organisms and can reliably detect three or more action potentials in short bursts in several systems in vivo. Through protein structure determination, targeted mutagenesis, high-throughput screening, and a battery of in vitro assays, we have increased the dynamic range of GCaMP3 by severalfold, creating a family of "GCaMP5" sensors. We tested GCaMP5s in several systems: cultured neurons and astrocytes, mouse retina, and in vivo in Caenorhabditis chemosensory neurons, Drosophila larval neuromuscular junction and adult antennal lobe, zebrafish retina and tectum, and mouse visual cortex. Signal-to-noise ratio was improved by at least 2- to 3-fold. In the visual cortex, two GCaMP5 variants detected twice as many visual stimulus-responsive cells as GCaMP3. By combining in vivo imaging with electrophysiology we show that GCaMP5 fluorescence provides a more reliable measure of neuronal activity than its predecessor GCaMP3. GCaMP5 allows more sensitive detection of neural activity in vivo and may find widespread applications for cellular imaging in general.


    Organizational Affiliation

    Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia 20147, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Myosin light chain kinase, Green fluorescent protein, Calmodulin-1 chimera
A
450Rattus norvegicusAequorea victoriaGallus gallus
This entity is chimeric
Mutation(s): 12 
Gene Names: Calm1 (Calm, Cam, Cam1, CaMI), GFP, Mylk
EC: 2.7.11.18
Find proteins for P0DP29 (Rattus norvegicus)
Go to UniProtKB:  P0DP29
Find proteins for P42212 (Aequorea victoria)
Go to UniProtKB:  P42212
Find proteins for P11799 (Gallus gallus)
Go to UniProtKB:  P11799
Small Molecules
Ligands 1 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
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: 2.4 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.172 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 120.184α = 90.00
b = 120.184β = 90.00
c = 97.352γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
SPECdata collection
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-06-20
    Type: Initial release
  • Version 1.1: 2014-01-08
    Type: Database references
  • Version 1.2: 2017-06-28
    Type: Database references, Source and taxonomy, Structure summary