8OSI | pdb_00008osi

Genetically encoded green ratiometric calcium indicator FNCaMP in calcium-bound state

• PDB DOI: https://doi.org/10.2210/pdb8OSI/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Branchiostoma lanceolatum, Aspergillus niger
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-04-19 Released: 2023-05-24 
• Deposition Author(s): Varfolomeeva, L.A., Boyko, K.M., Nikolaeva, A.Y., Subach, O.M., Subach, F.V.
• Funding Organization(s): Russian Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free: 
  0.231 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

FNCaMP, ratiometric green calcium indicator based on mNeonGreen protein.

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

(2023) Biochem Biophys Res Commun 665: 169-177

• PubMed: 37163937 
• DOI: https://doi.org/10.1016/j.bbrc.2023.04.108
• Primary Citation of Related Structures:  
  8OSI


• PubMed Abstract: 
  

  Neurobiologists widely use green genetically encoded calcium indicators (GECIs) for visualization of neuronal activity. Among them, ratiometric GECIs allow imaging of both active and non-active neuronal populations. However, they are not popular, since their properties are inferior to intensiometric GCaMP series of GECIs. The most characterized and developed ratiometric green GECI is FGCaMP7. However, the dynamic range and sensitivity of its large Stock's shift green (LSS-Green) form is significantly lower than its Green form and its molecular design is not optimal. To address these drawbacks, we engineered a ratiometric green calcium indicator, called FNCaMP, which is based on bright mNeonGreen protein and calmodulin from A. niger and has optimal NTnC-like design. We compared the properties of the FNCaMP and FGCaMP7 indicators in vitro, in mammalian cells, and in neuronal cultures. Finally, we obtained and analyzed X-ray structure of the FNCaMP indicator.

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Organizational Affiliation: 
• Complex of NBICS Technologies, National Research Center "Kurchatov Institute", Moscow, 123182, Russia. Electronic address: [e-mail].
Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia. Electronic address: [e-mail].
Complex of NBICS Technologies, National Research Center "Kurchatov Institute", Moscow, 123182, Russia. Electronic address: [e-mail].
Complex of NBICS Technologies, National Research Center "Kurchatov Institute", Moscow, 123182, Russia. Electronic address: [e-mail].
Complex of NBICS Technologies, National Research Center "Kurchatov Institute", Moscow, 123182, Russia; Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia. Electronic address: [e-mail].
School of Life Sciences, Westlake University, Hangzhou, 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, 310024, China. Electronic address: [e-mail].
Complex of NBICS Technologies, National Research Center "Kurchatov Institute", Moscow, 123182, Russia. Electronic address: [e-mail].
Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia. Electronic address: [e-mail].
Complex of NBICS Technologies, National Research Center "Kurchatov Institute", Moscow, 123182, Russia. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 52.42 kDa 
• Atom Count: 3,251 
• Modeled Residue Count: 401 
• Deposited Residue Count: 461 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mNeonGreen,Calmodulin,Contig An16c0100, genomic contig	A	461	Branchiostoma lanceolatum, Aspergillus niger	Mutation(s): 1  Gene Names: blFP-Y3, An04g07010, An16g03050 EC: 2.7.11.17
UniProt
Find proteins for A0A100IBH9 (Aspergillus niger) Explore A0A100IBH9  Go to UniProtKB:  A0A100IBH9
Find proteins for A0A1S4NYF2 (Branchiostoma lanceolatum) Explore A0A1S4NYF2  Go to UniProtKB:  A0A1S4NYF2
Find proteins for A0A254U4M1 (Aspergillus niger) Explore A0A254U4M1  Go to UniProtKB:  A0A254U4M1
UniProt Groups	A0A1S4NYF2A0A100IBH9A0A254U4M1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA (Subject of Investigation/LOI)	B [auth A], C [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CR2	A	L-PEPTIDE LINKING	C13 H13 N3 O4		GLY, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free:  0.231 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.4	α = 90
b = 151.4	β = 90
c = 61.969	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-24 
Deposition Author(s): Varfolomeeva, L.A., Boyko, K.M., Nikolaeva, A.Y., Subach, O.M., Subach, F.V.

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Funding Organization	Location	Grant Number
Russian Science Foundation	Russian Federation	21-74-20135

Revision History  

• Version 1.0: 2023-05-24
  Type: Initial release
  
• Version 2.0: 2024-07-24
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
• Version 3.0: 2024-09-11
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
• Version 3.1: 2024-10-23
  Changes: Structure summary