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- PDB-9k1f: Cryo-EM structure of human taurine transporter TauT bound with GA... -

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Basic information

Entry
Database: PDB / ID: 9k1f
TitleCryo-EM structure of human taurine transporter TauT bound with GABA in an intermediate conformation in the transport cycle
Components
  • (Fragment antigen binding ...) x 2
  • Sodium- and chloride-dependent taurine transporter
KeywordsSTRUCTURAL PROTEIN/IMMUNE SYSTEM / Substrate / transport protein / STRUCTURAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


taurine transmembrane transporter activity / alanine transmembrane transporter activity / gamma-aminobutyric acid transmembrane transporter activity / taurine:sodium symporter activity / import across plasma membrane / gamma-aminobutyric acid import / gamma-aminobutyric acid:sodium:chloride symporter activity / alanine transport / amino acid:sodium symporter activity / amino acid import across plasma membrane ...taurine transmembrane transporter activity / alanine transmembrane transporter activity / gamma-aminobutyric acid transmembrane transporter activity / taurine:sodium symporter activity / import across plasma membrane / gamma-aminobutyric acid import / gamma-aminobutyric acid:sodium:chloride symporter activity / alanine transport / amino acid:sodium symporter activity / amino acid import across plasma membrane / taurine transmembrane transport / amino acid transmembrane transporter activity / Amino acid transport across the plasma membrane / SLC-mediated transport of neurotransmitters / neurotransmitter transport / microvillus membrane / amino acid transport / transport across blood-brain barrier / sodium ion transmembrane transport / cell projection / positive regulation of cell differentiation / modulation of chemical synaptic transmission / GABA-ergic synapse / basolateral plasma membrane / postsynaptic membrane / apical plasma membrane / neuronal cell body / dendrite / membrane / plasma membrane
Similarity search - Function
Sodium:neurotransmitter symporter, taurine / 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
GAMMA-AMINO-BUTANOIC ACID / Sodium- and chloride-dependent taurine transporter
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsDu, B. / Yan, K.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2025
Title: Molecular basis of human taurine transporter uptake and inhibition.
Authors: Bowen Du / Lili Cheng / Jiaying Xie / Ligong Chen / Kaige Yan /
Abstract: The taurine transporter, TauT, regulates various taurine-mediated physiological and pathological functions by facilitating taurine uptake in a sodium- and chloride-dependent manner. Dysfunction of ...The taurine transporter, TauT, regulates various taurine-mediated physiological and pathological functions by facilitating taurine uptake in a sodium- and chloride-dependent manner. Dysfunction of TauT is associated with male infertility, retinal health and cancers. Despite extensive research efforts, the intricate structure of TauT, the molecular mechanisms underlying taurine transport, and the inhibition mechanisms involved, all remain elusive. Here, we present eleven cryo-electron microscopy (cryo-EM) structures of TauT. The structures TauT bound to substrate (taurine) and substrate analogues (β-alanine, guanidinoacetate, and γ-aminobutyric acid), are captured in distinct conformations. Combining with biochemical analyses, these structures reveal that amino acids Leu134 and Glu406 play a crucial role in substrate specificity within the GABA subfamily. Five distinct inhibitors, namely, piperidine-4-sulfonic acid, imidazole-4-acetatic acid, 5-aminovaleric acid, nipecotic acid and homotaurine, stabilize TauT in an inward-open conformation. Conversely, guanidinoethyl sulphonate stabilizes TauT in the occluded state. These structural insights offer a comprehensive understanding of how these inhibitors counteract taurine transport. Collectively, these findings advance our understanding of the substrate coordination and inhibitor recognition mechanisms of TauT.
History
DepositionOct 16, 2024Deposition site: PDBJ / Processing site: PDBC
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: FSC / Data content type: FSC / 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
Revision 1.1Sep 10, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sodium- and chloride-dependent taurine transporter
H: Fragment antigen binding heavy chain
L: Fragment antigen binding light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,6676
Polymers101,5053
Non-polymers1623
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Sodium- and chloride-dependent taurine transporter / Sodium- and chloride- dependent taurine transporter TauT / Solute carrier family 6 member 6


Mass: 73446.273 Da / Num. of mol.: 1
Mutation: D486N, N487R, L488F, Y489S, D490E, G491D, E493R, Y498F, R499P, K319H, Y320N, S322V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC6A6 / Production host: Homo sapiens (human) / References: UniProt: P31641

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Antibody , 2 types, 2 molecules HL

#2: Antibody Fragment antigen binding heavy chain


Mass: 13138.654 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Fragment antigen binding light chain


Mass: 14920.076 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 3 molecules

#4: Chemical ChemComp-ABU / GAMMA-AMINO-BUTANOIC ACID / GAMMA(AMINO)-BUTYRIC ACID


Mass: 103.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION

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Details

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: Human taurine transporter complex with GABA in an intermediate state in the transport cycle
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
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: 50 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 250445 / Symmetry type: POINT

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