3EKH

Calcium-saturated GCaMP2 T116V/K378W mutant monomer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystal Structures of the GCaMP Calcium Sensor Reveal the Mechanism of Fluorescence Signal Change and Aid Rational Design

Akerboom, J.Rivera, J.D.Guilbe, M.M.Malave, E.C.Hernandez, H.H.Tian, L.Hires, S.A.Marvin, J.S.Looger, L.L.Schreiter, E.R.

(2009) J.Biol.Chem. 284: 6455-6464

  • DOI: 10.1074/jbc.M807657200
  • Primary Citation of Related Structures:  3EK4, 3EK7, 3EK8, 3EKJ

  • PubMed Abstract: 
  • The genetically encoded calcium indicator GCaMP2 shows promise for neural network activity imaging, but is currently limited by low signal-to-noise ratio. We describe x-ray crystal structures as well as solution biophysical and spectroscopic characte ...

    The genetically encoded calcium indicator GCaMP2 shows promise for neural network activity imaging, but is currently limited by low signal-to-noise ratio. We describe x-ray crystal structures as well as solution biophysical and spectroscopic characterization of GCaMP2 in the calcium-free dark state, and in two calcium-bound bright states: a monomeric form that dominates at intracellular concentrations observed during imaging experiments and an unexpected domain-swapped dimer with decreased fluorescence. This series of structures provides insight into the mechanism of Ca2+-induced fluorescence change. Upon calcium binding, the calmodulin (CaM) domain wraps around the M13 peptide, creating a new domain interface between CaM and the circularly permuted enhanced green fluorescent protein domain. Residues from CaM alter the chemical environment of the circularly permuted enhanced green fluorescent protein chromophore and, together with flexible inter-domain linkers, block solvent access to the chromophore. Guided by the crystal structures, we engineered a series of GCaMP2 point mutants to probe the mechanism of GCaMP2 function and characterized one mutant with significantly improved signal-to-noise. The mutation is located at a domain interface and its effect on sensor function could not have been predicted in the absence of structural data.


    Related Citations: 
    • Crystallization and preliminary X-ray characterization of the genetically encoded fluorescent calcium indicator protein GCaMP2
      M Rodriguez Guilbe, M.,Alfaro Malave, E.C.,Akerboom, J.,Marvin, J.S.,Looger, L.L.,Schreiter, E.R.
      (2008) Acta Crystallogr.,Sect.F 64: 629


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Myosin light chain kinase, Green fluorescent protein, Calmodulin chimera
A
451Rattus norvegicusAequorea victoriaGallus gallus
This entity is chimeric
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
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 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.195 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 121.648α = 90.00
b = 121.648β = 90.00
c = 97.327γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-12-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2012-10-31
    Type: Database references
  • Version 1.3: 2017-06-21
    Type: Advisory, Database references, Source and taxonomy
  • Version 1.4: 2017-10-25
    Type: Refinement description