30UT | pdb_000030ut

Structure of the NaCT-Na-PF2 complex

PDB DOI: https://doi.org/10.2210/pdb30UT/pdb
EM Map EMD-58071: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2026-05-13 Released: 2026-07-29
Deposition Author(s): Sauer, D.B., Song, J., Marden, J.J., Wang, B., Rice, W.J., Wang, D.N.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), TESS Research Foundation, The G. Harold and Leila Y. Mathers Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.53 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structures of the human sodium-citrate cotransporter NaCT with and without substrates.

Sauer, D.B., Song, J., Marden, J.J., Wang, B., Sowerby, K., Sudar, J.C., Rice, W.J., Wang, D.N.

(2026) bioRxiv

PubMed: 42465234 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.64898/2026.07.08.737274
Primary Citation Related Structures:
30UT, 30UU, 30UV

PubMed 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 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.

Organizational Affiliation

Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA.

Macromolecule Content

Total Structure Weight: 127.34 kDa
Atom Count: 7,388
Modeled Residue Count: 936
Deposited Residue Count: 1,136
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Na(+)/citrate cotransporter	A, B	568	Homo sapiens	Mutation(s): 0 Gene Names: SLC13A5, NACT
UniProt & NIH Common Fund Data Resources
Find proteins for Q86YT5 (Homo sapiens) Explore Q86YT5 Go to UniProtKB: Q86YT5
GTEx: ENSG00000141485
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q86YT5
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B	Go to GlyGen: Q86YT5-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
X3M (Subject of Investigation/LOI) Query on X3M Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	(2R)-2-[2-(4-tert-butylphenyl)ethyl]-2-hydroxybutanedioic acid C₁₆ H₂₂ O₅ QNFWRHKLBLSSPB-MRXNPFEDSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
NA (Subject of Investigation/LOI) Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A]	E [auth A], F [auth A], I [auth B], J [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.53 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	2.0_5936
RECONSTRUCTION	cryoSPARC

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-07-29

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM121994
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	R01DK135088
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R01NS108151
TESS Research Foundation	United States	--
The G. Harold and Leila Y. Mathers Foundation	United States	--