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- EMDB-37330: NaS1 in IN/IN state -

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Basic information

Entry
Database: EMDB / ID: EMD-37330
TitleNaS1 in IN/IN state
Map data
Sample
  • Complex: Dimer of NaS1 in IN/IN state
    • Protein or peptide: Solute carrier family 13 member 1
  • Ligand: SODIUM ION
  • Ligand: CHOLESTEROL
KeywordsNaS1 / apo state / IN/IN state / TRANSPORT PROTEIN
Function / homology
Function and homology information


sodium:sulfate symporter activity / monoatomic anion:sodium symporter activity / Sodium-coupled sulphate, di- and tri-carboxylate transporters / : / sodium ion transport / transmembrane transport / apical plasma membrane / plasma membrane
Similarity search - Function
Sodium:sulfate symporter transmembrane region / Sodium/sulphate symporter, conserved site / Sodium:sulfate symporter family signature. / Solute carrier family 13
Similarity search - Domain/homology
Solute carrier family 13 member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsChi X / Chen Y / Li Y / Zhang Y / Shen Y / Wang Z / Yan R
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32100975 China
CitationJournal: Sci Adv / Year: 2024
Title: Cryo-EM structures of the human NaS1 and NaDC1 transporters revealed the elevator transport and allosteric regulation mechanism.
Authors: Ximin Chi / Yiming Chen / Yaning Li / Lu Dai / Yuanyuan Zhang / Yaping Shen / Yun Chen / Tianhao Shi / Haonan Yang / Zilong Wang / Renhong Yan /
Abstract: The solute carrier 13 (SLC13) family comprises electrogenic sodium ion-coupled anion cotransporters, segregating into sodium ion-sulfate cotransporters (NaSs) and sodium ion-di- and-tricarboxylate ...The solute carrier 13 (SLC13) family comprises electrogenic sodium ion-coupled anion cotransporters, segregating into sodium ion-sulfate cotransporters (NaSs) and sodium ion-di- and-tricarboxylate cotransporters (NaDCs). NaS1 and NaDC1 regulate sulfate homeostasis and oxidative metabolism, respectively. NaS1 deficiency affects murine growth and fertility, while NaDC1 affects urinary citrate and calcium nephrolithiasis. Despite their importance, the mechanisms of substrate recognition and transport remain insufficiently characterized. In this study, we determined the cryo-electron microscopy structures of human NaS1, capturing inward-facing and combined inward-facing/outward-facing conformations within a dimer both in apo and sulfate-bound states. In addition, we elucidated NaDC1's outward-facing conformation, encompassing apo, citrate-bound, and -(-amylcinnamoyl) anthranilic acid (ACA) inhibitor-bound states. Structural scrutiny illuminates a detailed elevator mechanism driving conformational changes. Notably, the ACA inhibitor unexpectedly binds primarily anchored by transmembrane 2 (TM2), Loop 10, TM11, and TM6a proximate to the cytosolic membrane. Our findings provide crucial insights into SLC13 transport mechanisms, paving the way for future drug design.
History
DepositionAug 29, 2023-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateApr 17, 2024-
Current statusApr 17, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_37330.png

Downloads & links

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Map

FileDownload / File: emd_37330.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 240 pix.
= 260.88 Å		1.09 Å/pix.
x 240 pix.
= 260.88 Å		1.09 Å/pix.
x 240 pix.
= 260.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.9
Minimum - Maximum-3.8437362 - 6.2799096
Average (Standard dev.)-0.003789736 (±0.14330892)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 260.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37330_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_37330_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Dimer of NaS1 in IN/IN state

EntireName: Dimer of NaS1 in IN/IN state
Components
  • Complex: Dimer of NaS1 in IN/IN state
    • Protein or peptide: Solute carrier family 13 member 1
  • Ligand: SODIUM ION
  • Ligand: CHOLESTEROL

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Supramolecule #1: Dimer of NaS1 in IN/IN state

SupramoleculeName: Dimer of NaS1 in IN/IN state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Solute carrier family 13 member 1

MacromoleculeName: Solute carrier family 13 member 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 67.68543 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MADYKDDDDK SGRMKFFSYI LVYRRFLFVV FTVLVLLPLP IVLHTKEAEC AYTLFVVATF WLTEALPLSV TALLPSLMLP MFGIMPSKK VASAYFKDFH LLLIGVICLA TSIEKWNLHK RIALKMVMMV GVNPAWLTLG FMSSTAFLSM WLSNTSTAAM V MPIAEAVV ...String:
MADYKDDDDK SGRMKFFSYI LVYRRFLFVV FTVLVLLPLP IVLHTKEAEC AYTLFVVATF WLTEALPLSV TALLPSLMLP MFGIMPSKK VASAYFKDFH LLLIGVICLA TSIEKWNLHK RIALKMVMMV GVNPAWLTLG FMSSTAFLSM WLSNTSTAAM V MPIAEAVV QQIINAEAEV EATQMTYFNG STNHGLEIDE SVNGHEINER KEKTKPVPGY NNDTGKISSK VELEKNSGMR TK YRTKKGH VTRKLTCLCI AYSSTIGGLT TITGTSTNLI FAEYFNTRYP DCRCLNFGSW FTFSFPAALI ILLLSWIWLQ WLF LGFNFK EMFKCGKTKT VQQKACAEVI KQEYQKLGPI RYQEIVTLVL FIIMALLWFS RDPGFVPGWS ALFSEYPGFA TDST VALLI GLLFFLIPAK TLTKTTPTGE IVAFDYSPLI TWKEFQSFMP WDIAILVGGG FALADGCEES GLSKWIGNKL SPLGS LPAW LIILISSLMV TSLTEVASNP ATITLFLPIL SPLAEAIHVN PLYILIPSTL CTSFAFLLPV ANPPNAIVFS YGHLKV IDM VKAGLGVNIV GVAVVMLGIC TWIVPMFDLY TYPSWAPAMS NETMP

UniProtKB: Solute carrier family 13 member 1

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Macromolecule #2: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 2 / Number of copies: 4
Molecular weightTheoretical: 22.99 Da

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Macromolecule #3: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 3 / Number of copies: 2 / 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: 8
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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 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: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 157920
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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