6DGV | pdb_00006dgv

iGABASnFR Fluorescent GABA Sensor precursor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.228 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6DGV

This is version 2.0 of the entry. See complete history

Literature

A genetically encoded fluorescent sensor for in vivo imaging of GABA.

Marvin, J.S.Shimoda, Y.Magloire, V.Leite, M.Kawashima, T.Jensen, T.P.Kolb, I.Knott, E.L.Novak, O.Podgorski, K.Leidenheimer, N.J.Rusakov, D.A.Ahrens, M.B.Kullmann, D.M.Looger, L.L.

(2019) Nat Methods 16: 763-770

  • DOI: https://doi.org/10.1038/s41592-019-0471-2
  • Primary Citation Related Structures: 
    6DGV

  • PubMed Abstract: 

    Current techniques for monitoring GABA (γ-aminobutyric acid), the primary inhibitory neurotransmitter in vertebrates, cannot follow transients in intact neural circuits. To develop a GABA sensor, we applied the design principles used to create the fluorescent glutamate receptor iGluSnFR. We used a protein derived from a previously unsequenced Pseudomonas fluorescens strain and performed structure-guided mutagenesis and library screening to obtain intensity-based GABA sensing fluorescence reporter (iGABASnFR) variants. iGABASnFR is genetically encoded, detects GABA release evoked by electric stimulation of afferent fibers in acute brain slices and produces readily detectable fluorescence increases in vivo in mice and zebrafish. We applied iGABASnFR to track mitochondrial GABA content and its modulation by an anticonvulsant, swimming-evoked, GABA-mediated transmission in zebrafish cerebellum, GABA release events during interictal spikes and seizures in awake mice, and found that GABA-mediated tone decreases during isoflurane anesthesia.


  • Organizational Affiliation
    • Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.

Macromolecule Content 

  • Total Structure Weight: 62.63 kDa 
  • Atom Count: 4,321 
  • Modeled Residue Count: 554 
  • Deposited Residue Count: 566 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fluorescent GABA Sensor precursor566Pseudomonas fluorescensMutation(s): 0 
UniProt
Find proteins for A0A1B3D787 (Pseudomonas fluorescens)
Explore A0A1B3D787 
Go to UniProtKB:  A0A1B3D787
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1B3D787
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CRO
Query on CRO
A
L-PEPTIDE LINKINGC15 H17 N3 O5THR, TYR, GLY

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.228 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 160.97α = 90
b = 160.97β = 90
c = 50.071γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-03
    Type: Initial release
  • Version 1.1: 2019-07-31
    Changes: Data collection, Database references
  • Version 1.2: 2019-08-14
    Changes: Data collection, Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2023-11-15
    Changes: Data collection
  • Version 1.5: 2024-10-30
    Changes: Structure summary
  • Version 2.0: 2026-03-18
    Changes: Polymer sequence