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- EMDB-37320: CryoEM structure of NaDC1 with Citrate -

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Basic information

Entry
Database: EMDB / ID: EMD-37320
TitleCryoEM structure of NaDC1 with Citrate
Map data
Sample
  • Complex: Structure of NaDC1 in complex with citrate
    • Protein or peptide: Solute carrier family 13 member 2
  • Ligand: SODIUM IONSodium
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: CITRIC ACID
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: water
KeywordsCitrate / transporter / TRANSPORT PROTEIN
Function / homology
Function and homology information


low-affinity sodium:dicarboxylate symporter activity / sodium:dicarboxylate symporter activity / fumarate transmembrane transporter activity / fumarate transport / Sodium-coupled sulphate, di- and tri-carboxylate transporters / alpha-ketoglutarate transmembrane transporter activity / alpha-ketoglutarate transport / succinate transmembrane transport / succinate transmembrane transporter activity / cellular response to lithium ion ...low-affinity sodium:dicarboxylate symporter activity / sodium:dicarboxylate symporter activity / fumarate transmembrane transporter activity / fumarate transport / Sodium-coupled sulphate, di- and tri-carboxylate transporters / alpha-ketoglutarate transmembrane transporter activity / alpha-ketoglutarate transport / succinate transmembrane transport / succinate transmembrane transporter activity / cellular response to lithium ion / apical plasma membrane / extracellular exosome / 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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsChi X / Chen Y / Li Y / Dai L / Zhang Y / Shen Y / Shi T / Yang H / 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 28, 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_37320.png

Downloads & links

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Map

FileDownload / File: emd_37320.map.gz / Format: CCP4 / Size: 64 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 256 pix.
= 278.272 Å		1.09 Å/pix.
x 256 pix.
= 278.272 Å		1.09 Å/pix.
x 256 pix.
= 278.272 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.22114892 - 0.31906354
Average (Standard dev.)0.000082024504 (±0.008027582)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 278.272 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37320_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_37320_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 : Structure of NaDC1 in complex with citrate

EntireName: Structure of NaDC1 in complex with citrate
Components
  • Complex: Structure of NaDC1 in complex with citrate
    • Protein or peptide: Solute carrier family 13 member 2
  • Ligand: SODIUM IONSodium
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: CITRIC ACID
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: water

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Supramolecule #1: Structure of NaDC1 in complex with citrate

SupramoleculeName: Structure of NaDC1 in complex with citrate / 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 2

MacromoleculeName: Solute carrier family 13 member 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 65.93425 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MADYKDDDDK SGRMATCWQA LWAYRSYLIV FFVPILLLPL PILVPSKEAY CAYAIILMAL FWCTEALPLA VTALFPLILF PMMGIVDAS EVAVEYLKDS NLLFFGGLLV AIAVEHWNLH KRIALRVLLI VGVRPAPLIL GFMLVTAFLS MWISNTATSA M MVPIAHAV ...String:
MADYKDDDDK SGRMATCWQA LWAYRSYLIV FFVPILLLPL PILVPSKEAY CAYAIILMAL FWCTEALPLA VTALFPLILF PMMGIVDAS EVAVEYLKDS NLLFFGGLLV AIAVEHWNLH KRIALRVLLI VGVRPAPLIL GFMLVTAFLS MWISNTATSA M MVPIAHAV LDQLHSSQAS SNVEEGSNNP TFELQEPSPQ KEVTKLDNGQ ALPVTSASSE GRAHLSQKHL HLTQCMSLCV CY SASIGGI ATLTGTAPNL VLQGQINSLF PQNGNVVNFA SWFSFAFPTM VILLLLAWLW LQILFLGFNF RKNFGIGEKM QEQ QQAAYC VIQTEHRLLG PMTFAEKAIS ILFVILVLLW FTREPGFFLG WGNLAFPNAK GESMVSDGTV AIFIGIIMFI IPSK FPGLT QDPENPGKLK APLGLLDWKT VNQKMPWNIV LLLGGGYALA KGSERSGLSE WLGNKLTPLQ SVPAPAIAII LSLLV ATFT ECTSNVATTT IFLPILASMA QAICLHPLYV MLPCTLATSL AFMLPVATPP NAIVFSFGDL KVLDMARAGF LLNIIG VLV IALAINSWGI PLFSLHSFPS WAQSNTTAQC LPSLANTTTP SP

UniProtKB: Solute carrier family 13 member 2

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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 HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #4: CITRIC ACID

MacromoleculeName: CITRIC ACID / type: ligand / ID: 4 / Number of copies: 2 / Formula: CIT
Molecular weightTheoretical: 192.124 Da
Chemical component information

ChemComp-CIT:
CITRIC ACID / Citric acid

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Macromolecule #5: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

MacromoleculeName: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: 3PH
Molecular weightTheoretical: 704.998 Da
Chemical component information

ChemComp-3PH:
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / Phosphatidic acid

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1369087

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