9D57 | pdb_00009d57

iGABASnFR2 fluorescent GABA sensor in complex with GABA

PDB DOI: https://doi.org/10.2210/pdb9D57/pdb

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

Deposited: 2024-08-13 Released: 2025-08-20
Deposition Author(s): Zhang, Y., Looger, L.L.
Funding Organization(s): Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.249 (Depositor), 0.244 (DCC)
R-Value Work:
0.206 (Depositor), 0.202 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

iGABASnFR2 is an improved genetically encoded protein sensor of GABA.

Kolb, I., Hasseman, J.P., Matsumoto, A., Jensen, T.P., Kopach, O., Arthur, B.J., Zhang, Y., Tsang, A., Reep, D., Tsegaye, G., Zheng, J., Patel, R.H., Looger, L.L., Marvin, J.S., Korff, W.L., Rusakov, D.A., Yonehara, K., Turner, G.C.

(2026) Elife 14

PubMed: 41848771 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.7554/eLife.108319
Primary Citation Related Structures:
9D57

PubMed Abstract:
Monitoring GABAergic inhibition in the nervous system has been enabled by the development of an intensiometric molecular sensor that directly detects GABA. However, the first generation iGABASnFR exhibits low signal-to-noise and suboptimal kinetics, making in vivo experiments challenging. To improve sensor performance, we targeted several sites in the protein for near-saturation mutagenesis and evaluated the resulting sensor variants in a high-throughput screening system using evoked synaptic release in primary cultured neurons. This identified a sensor variant, iGABASnFR2, with 4.1-fold improved sensitivity and 30% faster rise time, and binding affinity that remained in a range sensitive to changes in GABA concentration at synapses. We also identified sensors with an inverted response, decreasing fluorescence intensity upon GABA binding. We termed the best such negative-going sensor iGABASnFR2n, which can be used to corroborate observations with the positive-going sensor. These improvements yielded a qualitative enhancement of in vivo performance when compared directly to the original sensor. iGABASnFR2 enabled the first measurements of direction-selective GABA release in the retina. In vivo imaging in somatosensory cortex revealed that iGABASnFR2 can report volume-transmitted GABA release following whisker stimulation. Overall, the improved sensitivity and kinetics of iGABASnFR2 make it a more effective tool for imaging GABAergic transmission in intact neural circuits.

Organizational Affiliation

Janelia GENIE Project Team, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.

Macromolecule Content

Total Structure Weight: 375.5 kDa
Atom Count: 24,592
Modeled Residue Count: 3,232
Deposited Residue Count: 3,384
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter substrate-binding protein, Circular permuted superfolder GFP fusion	A B C [auth D] D [auth F] E [auth C] A, B, C [auth D], D [auth F], E [auth C], F [auth E]	564	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ABU (Subject of Investigation/LOI) Query on ABU Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth D] SDF format, chain J [auth F] SDF format, chain K [auth C] SDF format, chain L [auth E] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth D] MOL2 format, chain J [auth F] MOL2 format, chain K [auth C] MOL2 format, chain L [auth E] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth D] mmCIF format, chain J [auth F] mmCIF format, chain K [auth C] mmCIF format, chain L [auth E]	G [auth A] H [auth B] I [auth D] J [auth F] K [auth C] G [auth A], H [auth B], I [auth D], J [auth F], K [auth C], L [auth E]	GAMMA-AMINO-BUTANOIC ACID C₄ H₉ N O₂ BTCSSZJGUNDROE-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth D] Focus chain J [auth F] Focus chain K [auth C] Focus chain L [auth E] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth D] Focus chain J [auth F] Focus chain K [auth C] Focus chain L [auth E]

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