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- PDB-9kyo: GES bound mTAUT -

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Basic information

Entry
Database: PDB / ID: 9kyo
TitleGES bound mTAUT
Components
  • Heavy chain of 9D5 fab
  • Light chain of 9D5 fab
  • Sodium- and chloride-dependent taurine transporter
KeywordsMEMBRANE PROTEIN/IMMUNE SYSTEM / Taurine / transporter / SLC6A6 / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Na+/Cl- dependent neurotransmitter transporters / Amino acid transport across the plasma membrane / alanine transmembrane transporter activity / taurine:sodium symporter activity / gamma-aminobutyric acid:sodium:chloride symporter activity / amino acid:sodium symporter activity / amino acid import across plasma membrane / taurine transmembrane transport / neurotransmitter transport / microvillus membrane ...Na+/Cl- dependent neurotransmitter transporters / Amino acid transport across the plasma membrane / alanine transmembrane transporter activity / taurine:sodium symporter activity / gamma-aminobutyric acid:sodium:chloride symporter activity / amino acid:sodium symporter activity / amino acid import across plasma membrane / taurine transmembrane transport / neurotransmitter transport / microvillus membrane / GABA-ergic synapse / positive regulation of cell differentiation / modulation of chemical synaptic transmission / basolateral plasma membrane / postsynaptic membrane / apical plasma 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
Taurocyamine / Sodium- and chloride-dependent taurine transporter
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsShe, J. / Wang, M.X. / He, J.
Funding support China, 4items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFF0600801 China
National Natural Science Foundation of China (NSFC)32071201 China
National Natural Science Foundation of China (NSFC)32100967 China
The Center for Advanced Interdisciplinary Science and Biomedicine of IHMQYPY20220009 China
CitationJournal: To Be Published
Title: Molecular basis for substrate recognition and transport of mammalian taurine transporters
Authors: She, J. / Wang, M.X. / He, J.
History
DepositionDec 9, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 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
H: Heavy chain of 9D5 fab
A: Sodium- and chloride-dependent taurine transporter
L: Light chain of 9D5 fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,9207
Polymers94,6713
Non-polymers2494
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 70051.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Slc6a6, Taut / Production host: Homo sapiens (human) / References: UniProt: O35316

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Antibody , 2 types, 2 molecules HL

#1: Antibody Heavy chain of 9D5 fab


Mass: 13138.654 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm)
#3: Antibody Light chain of 9D5 fab


Mass: 11480.681 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm)

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Non-polymers , 4 types, 5 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / 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-3S5 / Taurocyamine / 2-carbamimidamidoethanesulfonic acid


Mass: 167.187 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9N3O3S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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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: GES bound mTAUT / Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2700 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 54 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.18.2_3874 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 266435 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0066206
ELECTRON MICROSCOPYf_angle_d0.9088436
ELECTRON MICROSCOPYf_dihedral_angle_d8.626841
ELECTRON MICROSCOPYf_chiral_restr0.056921
ELECTRON MICROSCOPYf_plane_restr0.0071040

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