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- PDB-9lk9: Cryo-EM structure of GAT3 -

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Basic information

Entry
Database: PDB / ID: 9lk9
TitleCryo-EM structure of GAT3
ComponentsSodium- and chloride-dependent GABA transporter 3
KeywordsSTRUCTURAL PROTEIN / protein structure / STRUCTUAL PROTEIN
Function / homology
Function and homology information


gamma-aminobutyric acid reuptake / Reuptake of GABA / monocarboxylic acid transmembrane transporter activity / monocarboxylic acid transport / Creatine metabolism / taurine:sodium symporter activity / gamma-aminobutyric acid:sodium:chloride symporter activity / SLC-mediated transport of neurotransmitters / amino acid binding / amino acid transport ...gamma-aminobutyric acid reuptake / Reuptake of GABA / monocarboxylic acid transmembrane transporter activity / monocarboxylic acid transport / Creatine metabolism / taurine:sodium symporter activity / gamma-aminobutyric acid:sodium:chloride symporter activity / SLC-mediated transport of neurotransmitters / amino acid binding / amino acid transport / sodium ion transmembrane transport / cell projection / GABA-ergic synapse / presynaptic membrane / postsynaptic membrane / response to xenobiotic stimulus / membrane / plasma membrane
Similarity search - Function
Sodium:neurotransmitter symporter, GABA, GAT-3 / Sodium:neurotransmitter symporter family signature 2. / Sodium:neurotransmitter symporter family signature 1. / Sodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile.
Similarity search - Domain/homology
: / Sodium- and chloride-dependent GABA transporter 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / Resolution: 3.58 Å
AuthorsZhao, Y. / Xu, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Transport mechanisms of GAT3
Authors: Zhao, Y. / Xu, H.
History
DepositionJan 16, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sodium- and chloride-dependent GABA transporter 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1693
Polymers70,6281
Non-polymers5412
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Sodium- and chloride-dependent GABA transporter 3 / GAT-3 / Solute carrier family 6 member 11


Mass: 70628.312 Da / Num. of mol.: 1 / Mutation: C28S,C612S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC6A11, GABT3, GAT3 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P48066
#2: Chemical ChemComp-A1AZJ / (3S)-1-{2-[tris(4-methoxyphenyl)methoxy]ethyl}piperidine-3-carboxylic acid


Mass: 505.602 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H35NO6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: structure of GAT3 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18209 / Symmetry type: POINT
RefinementHighest resolution: 3.58 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0044179
ELECTRON MICROSCOPYf_angle_d0.7585697
ELECTRON MICROSCOPYf_dihedral_angle_d6.762551
ELECTRON MICROSCOPYf_chiral_restr0.039633
ELECTRON MICROSCOPYf_plane_restr0.009689

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