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- PDB-9rwt: high-affinity choline transporter in DDM with Na+ -

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Basic information

Entry
Database: PDB / ID: 9rwt
Titlehigh-affinity choline transporter in DDM with Na+
ComponentsSolute carrier family 5 (High affinity choline transporter), member 7
KeywordsMEMBRANE PROTEIN / Choline transporter
Function / homologycholine:sodium symporter activity / : / acetylcholine biosynthetic process / Sodium/solute symporter / Sodium/glucose symporter superfamily / Sodium:solute symporter family / Sodium:solute symporter family profile. / plasma membrane / Solute carrier family 5 (High affinity choline transporter), member 7
Function and homology information
Biological speciesSalimicrobium flavidum (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsVilchez-Garcia, J. / Lopez-Alonso, J.P. / Jiang, H. / Ubarretxena-Belandia, I. / Tascon, I.
Funding support Spain, 1items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI)PID2023-146771NA-I00 Spain
CitationJournal: Sci Adv / Year: 2026
Title: Structural insights into a conserved mechanism of choline translocation through CHT.
Authors: Jesus Vilchez-Garcia / Adrián Martínez-Jiménez / Hanxing Jiang / Miguel Luengo / Borja Ochoa-Lizarralde / Jorge Pedro López-Alonso / Jerónimo Pérez-Lorente / Paola Bartoccioni / Raúl ...Authors: Jesus Vilchez-Garcia / Adrián Martínez-Jiménez / Hanxing Jiang / Miguel Luengo / Borja Ochoa-Lizarralde / Jorge Pedro López-Alonso / Jerónimo Pérez-Lorente / Paola Bartoccioni / Raúl Estévez / Victor Guallar / Ekaitz Errasti-Murugarren / Iban Ubarretxena-Belandia / Igor Tascón /
Abstract: Choline is an essential nutrient critical for cellular homeostasis across all domains of life. In humans, choline uptake in cholinergic neurons for its recycling into acetylcholine is mediated by the ...Choline is an essential nutrient critical for cellular homeostasis across all domains of life. In humans, choline uptake in cholinergic neurons for its recycling into acetylcholine is mediated by the high-affinity Na-dependent transporter SLC5A7 (CHT1). Prokaryotes also depend on choline as an osmo-protectant and as metabolite, raising the possibility that bacteria also have choline transporters akin to CHT1. Here, we identify and characterize a bacterial Na-dependent choline transporter (sfCHT) with high sequence identity to CHT1. Cryo-EM structures of Na- and choline-bound sfCHT reveal a LeuT-fold architecture with Na coordination geometry similar to CHT1. Captured in an inward-facing conformation, in sfCHT choline is found at a site near the cytoplasmic side. Computational analysis and transport assays of sfCHT and CHT1 variants reveal local conformational rearrangements in conserved residues along a defined pathway to the cytosolic site. These findings provide structural and mechanistic insights into intracellular choline transition, suggesting an evolutionarily conserved mechanism between the bacterial and human choline transporters.
History
DepositionJul 10, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Solute carrier family 5 (High affinity choline transporter), member 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7302
Polymers59,7071
Non-polymers231
Water00
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

#1: Protein Solute carrier family 5 (High affinity choline transporter), member 7


Mass: 59706.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salimicrobium flavidum (bacteria) / Gene: SAMN05421687_10333 / Plasmid: pB24 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A1N7IZC0
#2: Chemical ChemComp-NA / SODIUM ION


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

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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: high-affinity choline transporter in DDM with Na+ / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Salimicrobium flavidum (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21 / Plasmid: pB24
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
10.02 %dodecyl-b-D-maltoside (DDM)C24H46O111
220 mMTrisC4H11NO31
3100 mMsodium chlorideNaCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R0./1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: LAB6 / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60.6 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Num. of grids imaged: 1
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.4particle selection
2Topazparticle selection
3EPU3.8.0.7600image acquisition
5cryoSPARCv4.4CTF correction
8UCSF ChimeraX1.6rc202304202331model fitting
10cryoSPARCv4.4initial Euler assignment
11cryoSPARCv4.4final Euler assignment
12cryoSPARCv4.4classification
13cryoSPARCv4.43D reconstruction
14PHENIX1.21.1_5286model refinement
15Coot0.9.4.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 285470 / Symmetry type: POINT
Atomic model buildingB value: 77.74 / Protocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingDetails: Model generated with Model Angelo / Source name: Other / Type: in silico model
RefinementHighest resolution: 2.83 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0034002
ELECTRON MICROSCOPYf_angle_d0.5985469
ELECTRON MICROSCOPYf_dihedral_angle_d3.803548
ELECTRON MICROSCOPYf_chiral_restr0.039638
ELECTRON MICROSCOPYf_plane_restr0.005661

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