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Open data
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Basic information
Entry | Database: PDB / ID: 8gnk | |||||||||
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Title | CryoEM structure of cytosol-facing, substrate-bound ratGAT1 | |||||||||
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![]() | MEMBRANE PROTEIN / Neurotransmitter sodium symporter / GABA transporter / solute carrier 6 / secondary active transport | |||||||||
Function / homology | ![]() Na+/Cl- dependent neurotransmitter transporters / Reuptake of GABA / neurotransmitter reuptake / gamma-aminobutyric acid:sodium:chloride symporter activity / sodium:chloride symporter activity / gamma-aminobutyric acid transmembrane transporter activity / gamma-aminobutyric acid import / inorganic anion import across plasma membrane / amino acid:sodium symporter activity / negative regulation of synaptic transmission, GABAergic ...Na+/Cl- dependent neurotransmitter transporters / Reuptake of GABA / neurotransmitter reuptake / gamma-aminobutyric acid:sodium:chloride symporter activity / sodium:chloride symporter activity / gamma-aminobutyric acid transmembrane transporter activity / gamma-aminobutyric acid import / inorganic anion import across plasma membrane / amino acid:sodium symporter activity / negative regulation of synaptic transmission, GABAergic / positive regulation of gamma-aminobutyric acid secretion / response to sucrose / response to purine-containing compound / sodium ion import across plasma membrane / associative learning / sodium ion transmembrane transport / : / GABA-ergic synapse / chloride transmembrane transport / response to organonitrogen compound / : / response to cocaine / learning / response to lead ion / synapse organization / response to organic cyclic compound / response to toxic substance / memory / response to calcium ion / presynapse / response to estradiol / presynaptic membrane / postsynaptic membrane / neuron projection / axon / neuronal cell body / cell surface / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
![]() | Nayak, S.R. / Joseph, D. / Penmatsa, A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of GABA transporter 1 reveals substrate recognition and transport mechanism. Authors: Smruti Ranjan Nayak / Deepthi Joseph / Georg Höfner / Archishman Dakua / Arunabh Athreya / Klaus T Wanner / Baruch I Kanner / Aravind Penmatsa / ![]() ![]() ![]() ![]() Abstract: The inhibitory neurotransmitter γ-aminobutyric acid (GABA) is cleared from the synaptic cleft by the sodium- and chloride-coupled GABA transporter GAT1. Inhibition of GAT1 prolongs the GABAergic ...The inhibitory neurotransmitter γ-aminobutyric acid (GABA) is cleared from the synaptic cleft by the sodium- and chloride-coupled GABA transporter GAT1. Inhibition of GAT1 prolongs the GABAergic signaling at the synapse and is a strategy to treat certain forms of epilepsy. In this study, we present the cryo-electron microscopy structure of Rattus norvegicus GABA transporter 1 (rGAT1) at a resolution of 3.1 Å. The structure elucidation was facilitated by epitope transfer of a fragment-antigen binding (Fab) interaction site from the Drosophila dopamine transporter (dDAT) to rGAT1. The structure reveals rGAT1 in a cytosol-facing conformation, with a linear density in the primary binding site that accommodates a molecule of GABA, a displaced ion density proximal to Na site 1 and a bound chloride ion. A unique insertion in TM10 aids the formation of a compact, closed extracellular gate. Besides yielding mechanistic insights into ion and substrate recognition, our study will enable the rational design of specific antiepileptics. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 174 KB | Display | ![]() |
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PDB format | ![]() | 130.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 40.9 KB | Display | |
Data in CIF | ![]() | 58.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 34167MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Antibody , 2 types, 2 molecules LH
#2: Antibody | Mass: 23306.586 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#3: Antibody | Mass: 23619.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Protein / Sugars , 2 types, 3 molecules A![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 63200.676 Da / Num. of mol.: 1 Mutation: F312Y, Y481S, D482E, N483D, Q485R, E486D, V488I, S490F, R491P Source method: isolated from a genetically manipulated source Details: ratGAT1 construct / Source: (gene. exp.) ![]() ![]() ![]() |
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#4: Sugar |
-Non-polymers , 6 types, 16 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ABU.gif)
![](data/chem/img/CLR.gif)
![](data/chem/img/PTY.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ABU.gif)
![](data/chem/img/CLR.gif)
![](data/chem/img/PTY.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-CL / | ||||
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#6: Chemical | ChemComp-NA / | ||||
#7: Chemical | ChemComp-ABU / | ||||
#8: Chemical | ChemComp-CLR / #9: Chemical | ChemComp-PTY / | #10: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
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Molecular weight | Value: 111 kDa/nm / Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 8 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: The sample was a one to one complex of ratGAT1 with an antibody fragment and was homogenous. | ||||||||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1 | ||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Calibrated magnification: 105000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: BASIC |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 K / Temperature (min): 100 K |
Image recording | Average exposure time: 2.7 sec. / Electron dose: 50.09 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 18152 Details: Images were collected in movie mode at 50 frames per image |
EM imaging optics | Energyfilter name: GIF Bioquantum / Chromatic aberration corrector: No applicable / Energyfilter slit width: 20 eV / Phase plate: OTHER / Spherical aberration corrector: Not applicable |
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Processing
Software | Name: PHENIX / Version: 1.20rc4_4425: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 5838634 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 872611 / Num. of class averages: 3 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 165 / Protocol: OTHER / Space: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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