Crystal structure of the engineered fluorescent protein mRuby, crystal form 1, pH 8.5

Experimental Data Snapshot

  • Resolution: 1.65 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


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: https://doi.org/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. 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
mRuby230Entacmaea quadricolorMutation(s): 2 
Find proteins for Q8ISF8 (Entacmaea quadricolor)
Explore Q8ISF8 
Go to UniProtKB:  Q8ISF8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8ISF8
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on NRQ
Experimental Data & Validation

Experimental Data

  • Resolution: 1.65 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.706α = 90
b = 67.081β = 90
c = 95.001γ = 90
Software Package:
Software NamePurpose
SPECdata collection
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
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-12-06
    Changes: Data collection