3U0N

Crystal structure of the engineered fluorescent protein mRuby, crystal form 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.154 

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, 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-resoluti ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
mRuby
A
232Entacmaea quadricolorN/A
Find proteins for Q8ISF8 (Entacmaea quadricolor)
Go to UniProtKB:  Q8ISF8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
NRQ
Query on NRQ
A
L-PEPTIDE LINKINGC16 H17 N3 O4 SMET,TYR,GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.154 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 67.269α = 90.00
b = 82.523β = 90.00
c = 88.910γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHASERphasing
SPECdata collection
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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