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- PDB-30ut: Structure of the NaCT-Na-PF2 complex -

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Basic information

Entry
Database: PDB / ID: 30ut
TitleStructure of the NaCT-Na-PF2 complex
ComponentsNa(+)/citrate cotransporter
KeywordsMEMBRANE PROTEIN / Inhibitor / complex
Function / homology
Function and homology information


organic acid:sodium symporter activity / fumarate transport / oxaloacetate transport / SLC-mediated transport of organic anions / succinate transport / sodium:dicarboxylate symporter activity / citrate transmembrane transporter activity / citrate transport / alpha-ketoglutarate transport / succinate transmembrane transporter activity ...organic acid:sodium symporter activity / fumarate transport / oxaloacetate transport / SLC-mediated transport of organic anions / succinate transport / sodium:dicarboxylate symporter activity / citrate transmembrane transporter activity / citrate transport / alpha-ketoglutarate transport / succinate transmembrane transporter activity / cellular response to lithium ion / : / transmembrane transport / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
Sodium/sulphate symporter, conserved site / Sodium:sulfate symporter family signature. / Sodium:sulfate symporter transmembrane region / Solute carrier family 13
Similarity search - Domain/homology
Chem-X3M / Na(+)/citrate cotransporter
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.53 Å
AuthorsSauer, D.B. / Song, J. / Marden, J.J. / Wang, B. / Rice, W.J. / Wang, D.N.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM121994 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK135088 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS108151 United States
TESS Research Foundation United States
The G. Harold and Leila Y. Mathers Foundation United States
CitationJournal: bioRxiv / Year: 2026
Title: Structures of the human sodium-citrate cotransporter NaCT with and without substrates.
Authors: David B Sauer / Jinmei Song / Jennifer J Marden / Bing Wang / Kate Sowerby / Joseph C Sudar / William J Rice / Da-Neng Wang /
Abstract: The human sodium-citrate cotransporter NaCT imports various tri- and dicarboxylates into the cell as TCA cycle intermediates. This substrate uptake process is driven by an inward sodium gradient. The ...The human sodium-citrate cotransporter NaCT imports various tri- and dicarboxylates into the cell as TCA cycle intermediates. This substrate uptake process is driven by an inward sodium gradient. The protein is a member of the Divalent Anion-Sodium Symporter (DASS) family. Whereas extensive biochemical and structural studies have been carried out for NaCT, how the substrate binding and translocation is coupled to the sodium gradient remains unclear. Here using single particle cryo-electron microscopy, we determined the structures of the human NaCT protein in three states: sodium-free, in the presence of sodium, and sodium- and substrate-bound. These structures suggest a simultaneous binding mechanism for sodium-substrate coupling, distinct from the sequential binding, conformational selection mechanism previously observed for the bacterial DASS protein VcINDY.
History
DepositionMay 13, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data 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: Na(+)/citrate cotransporter
B: Na(+)/citrate cotransporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,34510
Polymers126,2222
Non-polymers1,1238
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 Na(+)/citrate cotransporter / NaCT / Sodium-coupled citrate transporter / Sodium-dependent citrate transporter / Solute carrier ...NaCT / Sodium-coupled citrate transporter / Sodium-dependent citrate transporter / Solute carrier family 13 member 5


Mass: 63110.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC13A5, NACT / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q86YT5
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-X3M / (2R)-2-[2-(4-tert-butylphenyl)ethyl]-2-hydroxybutanedioic acid


Mass: 294.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H22O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
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: NaCT-Na-PF2 complex / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
1300 mMSodium ChlorideNaCl1
225 mMTris1
30.1 %DDM1
4100 uMPF21
50.1 mMTCEP1
SpecimenConc.: 0.75 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 6900 nm / Nominal defocus min: 4000 nm
Image recordingElectron dose: 63.34 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1Warpparticle selection
2Topazparticle selection
3Leginonimage acquisition
5WarpCTF correction
10PHENIX2.0_5936model refinement
14cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2620654
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 976961 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 7JSJ

7jsj


Accession code: 7JSJ / Source name: PDB / Type: experimental model
RefinementHighest resolution: 2.53 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037578
ELECTRON MICROSCOPYf_angle_d1.04110342
ELECTRON MICROSCOPYf_dihedral_angle_d6.21998
ELECTRON MICROSCOPYf_chiral_restr0.181250
ELECTRON MICROSCOPYf_plane_restr0.0061236

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