3U0K

Crystal Structure of the genetically encoded calcium indicator RCaMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Genetically encoded calcium indicators for multi-color neural activity imaging and combination with optogenetics.

Akerboom, J.Carreras Calderon, N.Tian, L.Wabnig, S.Prigge, M.Tolo, J.Gordus, A.Orger, M.B.Severi, K.E.Macklin, J.J.Patel, R.Pulver, S.R.Wardill, T.J.Fischer, E.Schuler, C.Chen, T.W.Sarkisyan, K.S.Marvin, J.S.Bargmann, C.I.Kim, D.S.Kugler, S.Lagnado, L.Hegemann, P.Gottschalk, A.Schreiter, E.R.Looger, L.L.

(2013) Front Mol Neurosci 6: 2-2

  • DOI: 10.3389/fnmol.2013.00002
  • Primary Citation of Related Structures:  
    3U0K, 3U0L, 3U0M, 3U0N, 4I2Y

  • PubMed Abstract: 
  • Genetically encoded calcium indicators (GECIs) are powerful tools for systems neuroscience. Here we describe red, single-wavelength GECIs, "RCaMPs," engineered from circular permutation of the thermostable red fluorescent protein mRuby. High-resolution crystal structures of mRuby, the red sensor RCaMP, and the recently published red GECI R-GECO1 give insight into the chromophore environments of the Ca(2+)-bound state of the sensors and the engineered protein domain interfaces of the different indicators ...

    Genetically encoded calcium indicators (GECIs) are powerful tools for systems neuroscience. Here we describe red, single-wavelength GECIs, "RCaMPs," engineered from circular permutation of the thermostable red fluorescent protein mRuby. High-resolution crystal structures of mRuby, the red sensor RCaMP, and the recently published red GECI R-GECO1 give insight into the chromophore environments of the Ca(2+)-bound state of the sensors and the engineered protein domain interfaces of the different indicators. We characterized the biophysical properties and performance of RCaMP sensors in vitro and in vivo in Caenorhabditis elegans, Drosophila larvae, and larval zebrafish. Further, we demonstrate 2-color calcium imaging both within the same cell (registering mitochondrial and somatic [Ca(2+)]) and between two populations of cells: neurons and astrocytes. Finally, we perform integrated optogenetics experiments, wherein neural activation via channelrhodopsin-2 (ChR2) or a red-shifted variant, and activity imaging via RCaMP or GCaMP, are conducted simultaneously, with the ChR2/RCaMP pair providing independently addressable spectral channels. Using this paradigm, we measure calcium responses of naturalistic and ChR2-evoked muscle contractions in vivo in crawling C. elegans. We systematically compare the RCaMP sensors to R-GECO1, in terms of action potential-evoked fluorescence increases in neurons, photobleaching, and photoswitching. R-GECO1 displays higher Ca(2+) affinity and larger dynamic range than RCaMP, but exhibits significant photoactivation with blue and green light, suggesting that integrated channelrhodopsin-based optogenetics using R-GECO1 may be subject to artifact. Finally, we create and test blue, cyan, and yellow variants engineered from GCaMP by rational design. This engineered set of chromatic variants facilitates new experiments in functional imaging and optogenetics.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RCaMP A440Entacmaea quadricolorMutation(s): 0 
Find proteins for K4DIE3 (Entacmaea quadricolor)
Explore K4DIE3 
Go to UniProtKB:  K4DIE3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CRK
Query on CRK
AL-PEPTIDE LINKINGC16 H15 N2 O4 SMET, TYR, GLY
NFA
Query on NFA
AL-PEPTIDE LINKINGC9 H12 N2 OPHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.918α = 90
b = 75.918β = 90
c = 123.161γ = 120
Software Package:
Software NamePurpose
SPECdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-03
    Type: Initial release
  • Version 1.1: 2014-01-29
    Changes: Database references