9JTI | pdb_00009jti

X-ray structure of NeIle indicator complexed with isoleucine

• PDB DOI: https://doi.org/10.2210/pdb9JTI/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Escherichia coli, Escherichia coli O157:H7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-10-04 Released: 2024-12-25 
• Deposition Author(s): Samygina, V.R., Subach, O.M., Vlaskina, A.V., Dronova, E.A., Subach, F.V.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 
  0.184 (Depositor) 
• R-Value Work: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

NeIle, a Genetically Encoded Indicator for Branched-Chain Amino Acids Based on mNeonGreen Fluorescent Protein and LIVBP Protein.

Asanova, A.N., Subach, O.M., Myachina, S.A., Evteeva, M.A., Gunitseva, N.M., Borisova, A.A., Patrushev, M.V., Vlaskina, A.V., Nikolaeva, A.Y., Yang, L., Gabdulkhakov, A., Dronova, E., Samygina, V.R., Xiao, X., Zhao, H., Piatkevich, K.D., Subach, F.V.

(2024) ACS Sens 9: 5135-5147

• PubMed: 39400357 
• DOI: https://doi.org/10.1021/acssensors.4c01055
• Primary Citation of Related Structures:  
  8Z0G, 9JTI


• PubMed Abstract: 
  

  Branched-chain amino acids (BCAAs) play an important role in the functioning of mammalian cells and the central nervous system. However, available genetically encoded indicators for BCAAs are based on Förster resonance energy transfer and have a limited dynamic range. We developed a single fluorescent protein-based sensor for BCAAs, called NeIle, which is composed of circularly permutated mNeonGreen protein inserted into the leucine-isoleucine-valine binding protein (LIVBP) from Escherichia coli bacteria. In solution, the NeIle indicator displayed a positive fluorescence response to adding isoleucine, leucine, and valin amino acids with high Δ F / F dynamic ranges of 27-, 19-, and 11-fold and the corresponding affinity values of 5.0, 2.9, and 75 mM, respectively. The spectral and biochemical properties of the NeIle indicator were characterized in solution. We characterized the brightness of the NeIle indicator in living mammalian cells, including cultured neurons. Using the NeIle indicator, we successfully visualized the dynamics of isoleucine transients in different organelles of mammalian cells. We obtained and analyzed the X-ray crystal structure of the NeIle indicator in an isoleucine-bound state. Structure-guided directed mutagenesis of the NeIle indicator revealed the basis of its fluorescence response and selectivity to isoleucine.

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Organizational Affiliation: 

Complex of NBICS Technologies, National Research Center "Kurchatov Institute", Moscow 123182, Russia.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 64.96 kDa 
• Atom Count: 5,074 
• Modelled Residue Count: 571 
• Deposited Residue Count: 593 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NeIle,Leu/Ile/Val-binding protein	A	593	Escherichia coli, Escherichia coli O157:H7 This entity is chimeric	Mutation(s): 0
UniProt
Find proteins for P0AD96 (Escherichia coli (strain K12)) Explore P0AD96  Go to UniProtKB:  P0AD96

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ILE (Subject of Investigation/LOI)	B [auth A]	ISOLEUCINE C6 H13 N O2 AGPKZVBTJJNPAG-WHFBIAKZSA-N
GOL (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CR2	A	L-PEPTIDE LINKING	C13 H13 N3 O4		GLY, TYR, GLY
CSX	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free:  0.184 (Depositor) 
• R-Value Work:  0.158 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.1	α = 90
b = 69.2	β = 111.11
c = 80.5	γ = 90

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: 2024-12-25 
Deposition Author(s): Samygina, V.R., Subach, O.M., Vlaskina, A.V., Dronova, E.A., Subach, F.V.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-12-25
  Type: Initial release
  
• Version 1.1: 2025-01-01
  Changes: Structure summary