5UKG

Crystal Structure of the genetically encoded calcium indicator K-GECO

• PDB DOI: https://doi.org/10.2210/pdb5UKG/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Entacmaea quadricolor
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-01-22 Released: 2018-02-07 
• Deposition Author(s): Schreiter, E.R.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free: 0.275 
• R-Value Work: 0.206 
• R-Value Observed: 0.210 

Literature

A genetically encoded Ca2+indicator based on circularly permutated sea anemone red fluorescent protein eqFP578.

Shen, Y., Dana, H., Abdelfattah, A.S., Patel, R., Shea, J., Molina, R.S., Rawal, B., Rancic, V., Chang, Y.F., Wu, L., Chen, Y., Qian, Y., Wiens, M.D., Hambleton, N., Ballanyi, K., Hughes, T.E., Drobizhev, M., Kim, D.S., Koyama, M., Schreiter, E.R., Campbell, R.E.

(2018) BMC Biol 16: 9-9

• PubMed: 29338710 
• DOI: https://doi.org/10.1186/s12915-018-0480-0
• Primary Citation of Related Structures:  
  5UKG


• PubMed Abstract: 
  

  Genetically encoded calcium ion (Ca ²⁺ ) indicators (GECIs) are indispensable tools for measuring Ca ²⁺ dynamics and neuronal activities in vitro and in vivo. Red fluorescent protein (RFP)-based GECIs have inherent advantages relative to green fluorescent protein-based GECIs due to the longer wavelength light used for excitation. Longer wavelength light is associated with decreased phototoxicity and deeper penetration through tissue. Red GECI can also enable multicolor visualization with blue- or cyan-excitable fluorophores.

---

Organizational Affiliation: 

Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 93.65 kDa 
• Atom Count: 6,275 
• Modelled Residue Count: 784 
• Deposited Residue Count: 834 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
K-GECO	A, B	417	Entacmaea quadricolor	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth A], E [auth A], F [auth A], G [auth B], H [auth B], I [auth B], J [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NRQ	A, B	L-PEPTIDE LINKING	C16 H17 N3 O4 S		MET, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free: 0.275 
• R-Value Work: 0.206 
• R-Value Observed: 0.210 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.284	α = 90
b = 129.249	β = 106.27
c = 78.715	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-02-07 
Deposition Author(s): Schreiter, E.R.

Revision History  

• Version 1.0: 2018-02-07
  Type: Initial release
  
• Version 1.1: 2019-02-20
  Changes: Data collection, Database references