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- PDB-9z60: Structure of the sodium-dependent phosphate importer SLC34A2, apo -

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Basic information

Entry
Database: PDB / ID: 9z60
TitleStructure of the sodium-dependent phosphate importer SLC34A2, apo
Components
  • 12H07 heavy chain
  • 12H07 light chain
  • Solute carrier family 34 member 2a
KeywordsTRANSPORT PROTEIN / Inorganic phosphate importer
Function / homology
Function and homology information


high-affinity phosphate:sodium symporter activity / Type II Na+/Pi cotransporters / sodium:phosphate symporter activity / sodium-dependent phosphate transport / phosphate ion transport / intracellular phosphate ion homeostasis / brush border / vesicle / apical plasma membrane / plasma membrane
Similarity search - Function
Sodium-dependent phosphate transport protein / Na+/Pi-cotransporter
Similarity search - Domain/homology
CHOLESTEROL / Type II Na/Pi cotransport system protein
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.53 Å
AuthorsZhu, Q. / Diver, M.M.
Funding support United States, 1items
OrganizationGrant numberCountry
The Robertson Foundation United States
CitationJournal: bioRxiv / Year: 2026
Title: Structural and mechanistic insights into SLC34 phosphate import.
Authors: Qinyu Zhu / Omar Almakki / Melinda M Diver
Abstract: Dysregulation of inorganic phosphate (Pi) homeostasis contributes to metabolic disease, cancer, pathological calcification, and kidney disease. Systemic phosphate balance is regulated by SLC34 ...Dysregulation of inorganic phosphate (Pi) homeostasis contributes to metabolic disease, cancer, pathological calcification, and kidney disease. Systemic phosphate balance is regulated by SLC34 transporters that mediate renal Pi retention (SLC34A1/A3) and intestinal dietary Pi absorption (SLC34A2). SLC34s couple Pi uptake to the symport of sodium (Na ) down its electrochemical gradient. Mutations or altered expression of SLC34 proteins are linked to disorders such as chronic kidney disease (CKD), where hyperphosphatemia is a major complication, and the lung disease pulmonary alveolar microlithiasis (PAM), caused by inactivating SLC34A2 mutations. SLC34A2 is also overexpressed in most ovarian and uterine tumors, making it an attractive target for antibody-drug conjugates. We present cryo-EM structures of SLC34A2 when the transporter is empty, bound to Na ions only, fully loaded with Na ions and Pi, and bound to an inhibitor phosphonoformic acid (PFA), revealing its distinct architecture, substrate and ion binding sites, the role of Na , and multiple transporter states. Pi binds at a highly symmetric, membrane-embedded pocket positioned approximately mid-membrane and is coordinated by its signature QSSS repeat motifs. Na shapes the Pi-binding pocket and drives the transition from the outward-open to occluded state. Integrated with functional analyses, these structures reveal that SLC34 transporters operate through an atypical alternating access cycle defined by coordinated elevator movements of an auxiliary gate domain. This work lays a foundational framework for understanding Pi regulation and opens new avenues for therapeutic strategies targeting disorders linked to phosphate imbalance.
History
DepositionNov 13, 2025Deposition site: RCSB / Processing site: RCSB
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: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: FSC / Data content type: FSC / 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

Downloads & links

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Assembly

Deposited unit
A: Solute carrier family 34 member 2a
B: 12H07 heavy chain
C: 12H07 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,8934
Polymers118,5073
Non-polymers3871
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 34 member 2a / Type II Na/Pi cotransport system protein


Mass: 70042.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Insertion is MX35 epitope,Insertion is MX35 epitope,Insertion is MX35 epitope,Insertion is MX35 epitope
Source: (gene. exp.) Danio rerio (zebrafish)
Gene: slc34a2a, NaPi-II, NaPi-IIb1, npt2b, slc34a2, wu:fb63d07
Production host: Homo sapiens (human) / References: UniProt: Q9PTQ8
#2: Antibody 12H07 heavy chain


Mass: 24521.361 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody 12H07 light chain


Mass: 23942.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#4: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
Has ligand of interestN
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: SLC34A2 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Danio rerio (zebrafish)
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: 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: 1700 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 66 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21_5207model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 139524 / Symmetry type: POINT
RefinementHighest resolution: 3.53 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0025450
ELECTRON MICROSCOPYf_angle_d0.4347432
ELECTRON MICROSCOPYf_dihedral_angle_d3.391752
ELECTRON MICROSCOPYf_chiral_restr0.037892
ELECTRON MICROSCOPYf_plane_restr0.003910

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