8P6G

Crystal structure of the improved version of the Genetically Encoded Green Calcium Indicator YTnC2-5

• PDB DOI: https://doi.org/10.2210/pdb8P6G/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-05-26 Released: 2024-04-03 
• Deposition Author(s): Boyko, K.M., Nikolaeva, A.Y., Subach, O.M., Vlaskina, A.V., Agapova, Y.K., Popov, V.O., Subach, F.V.
• Funding Organization(s): Ministry of Science and Higher Education of the Russian Federation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.229 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 

Literature

YTnC2, an improved genetically encoded green calcium indicator based on toadfish troponin C.

Subach, O.M., Vlaskina, A.V., Agapova, Y.K., Nikolaeva, A.Y., Varizhuk, A.M., Podgorny, O.V., Piatkevich, K.D., Patrushev, M.V., Boyko, K.M., Subach, F.V.

(2023) FEBS Open Bio 13: 2047-2060

• PubMed: 37650870 
• DOI: https://doi.org/10.1002/2211-5463.13702
• Primary Citation of Related Structures:  
  8P6G


• PubMed Abstract: 
  

  Genetically encoded calcium indicators based on truncated troponin C are attractive probes for calcium imaging due to their relatively small molecular size and twofold reduced calcium ion buffering. However, the best-suited members of this family, YTnC and cNTnC, suffer from low molecular brightness, limited dynamic range, and/or poor sensitivity to calcium transients in neurons. To overcome these limitations, we developed an enhanced version of YTnC, named YTnC2. Compared with YTnC, YTnC2 had 5.7-fold higher molecular brightness and 6.4-fold increased dynamic range in vitro. YTnC2 was successfully used to reveal calcium transients in the cytosol and in the lumen of mitochondria of both mammalian cells and cultured neurons. Finally, we obtained and analyzed the crystal structure of the fluorescent domain of the YTnC2 mutant.

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Organizational Affiliation: 

Complex of NBICS Technologies, National Research Center "Kurchatov Institute", Moscow, Russia.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 71.86 kDa 
• Atom Count: 4,137 
• Modelled Residue Count: 490 
• Deposited Residue Count: 628 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Genetically Encoded Green Calcium Indicator YTnC2-5 based on Troponin C from toadfish	A [auth B], B [auth D]	314	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	C [auth B], D	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CRO	A [auth B], B [auth D]	L-PEPTIDE LINKING	C15 H17 N3 O5		THR, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.229 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.736	α = 90
b = 65.736	β = 90
c = 315.036	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-03 
Deposition Author(s): Boyko, K.M., Nikolaeva, A.Y., Subach, O.M., Vlaskina, A.V., Agapova, Y.K., Popov, V.O., Subach, F.V.

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Funding Organization	Location	Grant Number
Ministry of Science and Higher Education of the Russian Federation	Russian Federation	075-15-2021-1354

Revision History  

• Version 1.0: 2024-04-03
  Type: Initial release