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- EMDB-73831: Structure of the sodium-dependent phosphate importer SLC34A2, Pi-... -

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Basic information

Entry
Database: EMDB / ID: EMD-73831
TitleStructure of the sodium-dependent phosphate importer SLC34A2, Pi- and Na+-bound
Map data
Sample
  • Organelle or cellular component: SLC34A2
    • Protein or peptide: Solute carrier family 34 member 2a
    • Protein or peptide: 1207 heavy chain
    • Protein or peptide: 12H07 light chain
  • Ligand: PHOSPHATE ION
  • Ligand: SODIUM ION
  • Ligand: CHOLESTEROL
KeywordsInorganic phosphate importer / TRANSPORT PROTEIN
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
Type II Na/Pi cotransport system protein
Similarity search - Component
Biological speciesDanio rerio (zebrafish) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsZhu Q / Diver MM
Funding support United States, 1 items
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, 2025-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73831.png

Downloads & links

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Map

FileDownload / File: emd_73831.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 384 pix.
= 278.4 Å		0.73 Å/pix.
x 384 pix.
= 278.4 Å		0.73 Å/pix.
x 384 pix.
= 278.4 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.725 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.5221331 - 0.7241199
Average (Standard dev.)0.000007381 (±0.0078981975)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 278.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Density modified map

Fileemd_73831_additional_1.map
AnnotationDensity modified map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_73831_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_73831_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : SLC34A2

EntireName: SLC34A2
Components
  • Organelle or cellular component: SLC34A2
    • Protein or peptide: Solute carrier family 34 member 2a
    • Protein or peptide: 1207 heavy chain
    • Protein or peptide: 12H07 light chain
  • Ligand: PHOSPHATE ION
  • Ligand: SODIUM ION
  • Ligand: CHOLESTEROL

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Supramolecule #1: SLC34A2

SupramoleculeName: SLC34A2 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Danio rerio (zebrafish)

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Macromolecule #1: Solute carrier family 34 member 2a

MacromoleculeName: Solute carrier family 34 member 2a / type: protein_or_peptide / ID: 1
Details: Insertion is MX35 epitope,Insertion is MX35 epitope
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Danio rerio (zebrafish)
Molecular weightTheoretical: 70.042875 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPEFATMAPR PKHEHESDEK QPETLDGARK KSLSMAPAVS TAALIEDDPW EMMELQDTGV KWADLDTKKK VLRVFTTAAK LIMLLGLLY MFVCSLDVLS SAFQLVGGKA AGDIFQENKV LSNPLAGLVI GMLVTLLVQS SSTSSSIVVS MVSSGMLEVA T AVPIIMGT ...String:
GPEFATMAPR PKHEHESDEK QPETLDGARK KSLSMAPAVS TAALIEDDPW EMMELQDTGV KWADLDTKKK VLRVFTTAAK LIMLLGLLY MFVCSLDVLS SAFQLVGGKA AGDIFQENKV LSNPLAGLVI GMLVTLLVQS SSTSSSIVVS MVSSGMLEVA T AVPIIMGT NIGTSVTNTL VAIAQVGDRN KFRRAFAGAT VHDFFNWLSV LVLLPLEVAS GYLEKVTSLI VRSFNIESGE KA PALLNVI TDPLTHSIIQ LDESVMSGIA VGDPEARNKS LIKVWCHTAS NTTVQNVTTT NCTSPSLCWT DGIQNWTMKN VTE IINIKK CSHIFVNTSL SDLAVGLILL AGSLLILCTC LICIVKLLNS MLKGQVAVVI KKIVNTDFPF PFAWLTGYIA ILVG AGMTF IVQSSSVFTS AITPLVGIGV ISIERAYPLS LGSNIGTTTT AILAAMASPG ETLGNSLQIA LVHFFFNLSG ILLWY PIPI TRIPIRLAKG LGETTAQYRW FAAFYIILCF FGLPLLVFGL SMAGWQVLMG VLVPIAVILI FAIIVNILQK HKPQWL PSA LRSWDFLPLW AHSLDPWDRV VTVIAARCCC CCKCCNSNEE DEKAKLENLA NGIEINDNTM TTVEIIEPKK TVDSCEI LK ATSL

UniProtKB: Type II Na/Pi cotransport system protein, Type II Na/Pi cotransport system protein

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Macromolecule #2: 1207 heavy chain

MacromoleculeName: 1207 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.521361 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: QIQLVQSGPE LKKPGETVKI SCRASGYTFT NCGMNWVKQA PGKGLKWMGW INTYTGEPTY ADDFKGRFAF SLETSANTAY LQISNLKNE DTATYFCARN YYYGSTYRGF DYWGQGTTLT VSSAKTTPPS VYPLAPGCGD TTGSSVTLGC LVKGYFPESV T VTWNSGSL ...String:
QIQLVQSGPE LKKPGETVKI SCRASGYTFT NCGMNWVKQA PGKGLKWMGW INTYTGEPTY ADDFKGRFAF SLETSANTAY LQISNLKNE DTATYFCARN YYYGSTYRGF DYWGQGTTLT VSSAKTTPPS VYPLAPGCGD TTGSSVTLGC LVKGYFPESV T VTWNSGSL SSSVHTFPAL LQSGLYTMSS SVTVPSSTWP SQTVTCSVAH PASSTTVDKK LEPSGPISTI

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Macromolecule #3: 12H07 light chain

MacromoleculeName: 12H07 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.942369 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: DIVLTQSPAS LAVSLGQRAT ISCRASESVD NFGISFMHWY HQKPGQPPKL LIYRASNLES GIPARFSGSG SGTDFTLTIN PVEADDVAT YFCQQSNEDP YTFGGGTKLE IKRADAAPTV SIFPPSSEQL TSGGASVVCF LNNFYPKDIN VKWKIDGSER Q NGVLNSWT ...String:
DIVLTQSPAS LAVSLGQRAT ISCRASESVD NFGISFMHWY HQKPGQPPKL LIYRASNLES GIPARFSGSG SGTDFTLTIN PVEADDVAT YFCQQSNEDP YTFGGGTKLE IKRADAAPTV SIFPPSSEQL TSGGASVVCF LNNFYPKDIN VKWKIDGSER Q NGVLNSWT DQDSKDSTYS MSSTLTLTKD EYERHNSYTC EATHKTSTSP IVKSFNRNEC

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Macromolecule #4: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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Macromolecule #5: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 5 / Number of copies: 4
Molecular weightTheoretical: 22.99 Da

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Macromolecule #6: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 6 / Number of copies: 1 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 556732
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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