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- EMDB-41428: Substrate Binding Plasticity Revealed by Cryo-EM Structures of SLC26A2 -

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Basic information

Entry
Database: EMDB / ID: EMD-41428
TitleSubstrate Binding Plasticity Revealed by Cryo-EM Structures of SLC26A2
Map data
Sample
  • Complex: SLC26A2 with oxalate
    • Protein or peptide: Sulfate transporter
  • Ligand: OXALATE ION
KeywordsSLC26A2 / sulfate transporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


Defective SLC26A2 causes chondrodysplasias / Transport and metabolism of PAPS / Inorganic anion exchange by SLC26 transporters / sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / chondrocyte proliferation / sulfate transmembrane transport / secondary active sulfate transmembrane transporter activity / solute:inorganic anion antiporter activity / bicarbonate transmembrane transporter activity ...Defective SLC26A2 causes chondrodysplasias / Transport and metabolism of PAPS / Inorganic anion exchange by SLC26 transporters / sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / chondrocyte proliferation / sulfate transmembrane transport / secondary active sulfate transmembrane transporter activity / solute:inorganic anion antiporter activity / bicarbonate transmembrane transporter activity / chloride transmembrane transporter activity / microvillus membrane / chondrocyte differentiation / chloride transmembrane transport / apical plasma membrane / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Sulphate anion transporter, conserved site / SLC26A transporters signature. / SLC26A/SulP transporter / SLC26A/SulP transporter domain / Sulfate permease family / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsHu W / Song A
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM126626 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)AG064572 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI175646 United States
CitationJournal: Nat Commun / Year: 2024
Title: Substrate binding plasticity revealed by Cryo-EM structures of SLC26A2.
Authors: Wenxin Hu / Alex Song / Hongjin Zheng
Abstract: SLC26A2 is a vital solute carrier responsible for transporting essential nutritional ions, including sulfate, within the human body. Pathogenic mutations within SLC26A2 give rise to a spectrum of ...SLC26A2 is a vital solute carrier responsible for transporting essential nutritional ions, including sulfate, within the human body. Pathogenic mutations within SLC26A2 give rise to a spectrum of human diseases, ranging from lethal to mild symptoms. The molecular details regarding the versatile substrate-transporter interactions and the impact of pathogenic mutations on SLC26A2 transporter function remain unclear. Here, using cryo-electron microscopy, we determine three high-resolution structures of SLC26A2 in complexes with different substrates. These structures unveil valuable insights, including the distinct features of the homodimer assembly, the dynamic nature of substrate binding, and the potential ramifications of pathogenic mutations. This structural-functional information regarding SLC26A2 will advance our understanding of cellular sulfate transport mechanisms and provide foundations for future therapeutic development against various human diseases.
History
DepositionAug 2, 2023-
Header (metadata) releaseMay 22, 2024-
Map releaseMay 22, 2024-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41428.png

Downloads & links

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Map

FileDownload / File: emd_41428.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 264.32 Å		0.83 Å/pix.
x 320 pix.
= 264.32 Å		0.83 Å/pix.
x 320 pix.
= 264.32 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.033
Minimum - Maximum-0.7250564 - 0.8950218
Average (Standard dev.)0.000531025 (±0.01573436)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 264.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_41428_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_41428_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : SLC26A2 with oxalate

EntireName: SLC26A2 with oxalate
Components
  • Complex: SLC26A2 with oxalate
    • Protein or peptide: Sulfate transporter
  • Ligand: OXALATE ION

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Supramolecule #1: SLC26A2 with oxalate

SupramoleculeName: SLC26A2 with oxalate / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Sulfate transporter

MacromoleculeName: Sulfate transporter / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 74.410359 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: HRILIERQEK SDTNFKEFVI KKLQKNCQCS PAKAKNMILG FLPVLQWLPK YDLKKNILGD VMSGLIVGIL LVPQSIAYSL LAGQEPVYG LYTSFFASII YFLLGTSRHI SVGIFGVLCL MIGETVDREL QKAGYDNAHS APSLGMVSNG STLLNHTSDR I CDKSCYAI ...String:
HRILIERQEK SDTNFKEFVI KKLQKNCQCS PAKAKNMILG FLPVLQWLPK YDLKKNILGD VMSGLIVGIL LVPQSIAYSL LAGQEPVYG LYTSFFASII YFLLGTSRHI SVGIFGVLCL MIGETVDREL QKAGYDNAHS APSLGMVSNG STLLNHTSDR I CDKSCYAI MVGSTVTFIA GVYQVAMGFF QVGFVSVYLS DALLSGFVTG ASFTILTSQA KYLLGLNLPR TNGVGSLITT WI HVFRNIH KTNLCDLITS LLCLLVLLPT KELNEHFKSK LKAPIPIELV VVVAATLASH FGKLHENYNS SIAGHIPTGF MPP KVPEWN LIPSVAVDAI AISIIGFAIT VSLSEMFAKK HGYTVKANQE MYAIGFCNII PSFFHCFTTS AALAKTLVKE STGC HTQLS GVVTALVLLL VLLVIAPLFY SLQKSVLGVI TIVNLRGALR KFRDLPKMWS ISRMDTVIWF VTMLSSALLS TEIGL LVGV CFSIFCVILR TQKPKSSLLG LVEESEVFES VSAYKNLQIK PGIKIFRFVA PLYYINKECF KSALYKQTVN PILIKV AWK KAAKRKIKEK VVTLGGIQDE MSVQLSHDPL ELHTIVIDCS AIQFLDTAGI HTLKEVRRDY EAIGIQVLLA QCNPTVR DS LTNGEYCKKE EENLLFYSVY EAMAFAEVSK N

UniProtKB: Sulfate transporter

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Macromolecule #2: OXALATE ION

MacromoleculeName: OXALATE ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: OXL
Molecular weightTheoretical: 88.019 Da
Chemical component information

ChemComp-OXL:
OXALATE ION

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k 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: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 137202
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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