+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22456 | ||||||||||||||||||||||||
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Title | Structure of the NaCT-PF2 complex | ||||||||||||||||||||||||
Map data | NaCT-PF2 complex | ||||||||||||||||||||||||
Sample |
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Function / homology | Function and homology information citrate transmembrane transporter activity / oxaloacetate transport / succinate transport / citrate transport / sodium:dicarboxylate symporter activity / Sodium-coupled sulphate, di- and tri-carboxylate transporters / organic acid:sodium symporter activity / fumarate transport / alpha-ketoglutarate transport / succinate transmembrane transporter activity ...citrate transmembrane transporter activity / oxaloacetate transport / succinate transport / citrate transport / sodium:dicarboxylate symporter activity / Sodium-coupled sulphate, di- and tri-carboxylate transporters / organic acid:sodium symporter activity / fumarate transport / alpha-ketoglutarate transport / succinate transmembrane transporter activity / monoatomic anion transmembrane transport / cellular response to lithium ion / membrane => GO:0016020 / nucleoplasm / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.12 Å | ||||||||||||||||||||||||
Authors | Sauer DB / Wang B / Song J / Rice WJ / Wang DN | ||||||||||||||||||||||||
Funding support | United States, 7 items
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Citation | Journal: Nature / Year: 2021 Title: Structure and inhibition mechanism of the human citrate transporter NaCT. Authors: David B Sauer / Jinmei Song / Bing Wang / Jacob K Hilton / Nathan K Karpowich / Joseph A Mindell / William J Rice / Da-Neng Wang / Abstract: Citrate is best known as an intermediate in the tricarboxylic acid cycle of the cell. In addition to this essential role in energy metabolism, the tricarboxylate anion also acts as both a precursor ...Citrate is best known as an intermediate in the tricarboxylic acid cycle of the cell. In addition to this essential role in energy metabolism, the tricarboxylate anion also acts as both a precursor and a regulator of fatty acid synthesis. Thus, the rate of fatty acid synthesis correlates directly with the cytosolic concentration of citrate. Liver cells import citrate through the sodium-dependent citrate transporter NaCT (encoded by SLC13A5) and, as a consequence, this protein is a potential target for anti-obesity drugs. Here, to understand the structural basis of its inhibition mechanism, we determined cryo-electron microscopy structures of human NaCT in complexes with citrate or a small-molecule inhibitor. These structures reveal how the inhibitor-which binds to the same site as citrate-arrests the transport cycle of NaCT. The NaCT-inhibitor structure also explains why the compound selectively inhibits NaCT over two homologous human dicarboxylate transporters, and suggests ways to further improve the affinity and selectivity. Finally, the NaCT structures provide a framework for understanding how various mutations abolish the transport activity of NaCT in the brain and thereby cause epilepsy associated with mutations in SLC13A5 in newborns (which is known as SLC13A5-epilepsy). | ||||||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22456.map.gz | 93 MB | EMDB map data format | |
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Header (meta data) | emd-22456-v30.xml emd-22456.xml | 13.9 KB 13.9 KB | Display Display | EMDB header |
Images | emd_22456.png | 94.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22456 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22456 | HTTPS FTP |
-Related structure data
Related structure data | 7jsjMC 7jskC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_22456.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | NaCT-PF2 complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.073 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Dimer of NaCT in complex with PF2
Entire | Name: Dimer of NaCT in complex with PF2 |
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Components |
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-Supramolecule #1: Dimer of NaCT in complex with PF2
Supramolecule | Name: Dimer of NaCT in complex with PF2 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Experimental: 125 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
-Macromolecule #1: Solute carrier family 13 member 5
Macromolecule | Name: Solute carrier family 13 member 5 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 63.110812 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MASALSYVSK FKSFVILFVT PLLLLPLVIL MPAKFVRCAY VIILMAIYWC TEVIPLAVTS LMPVLLFPLF QILDSRQVCV QYMKDTNML FLGGLIVAVA VERWNLHKRI ALRTLLWVGA KPARLMLGFM GVTALLSMWI SNTATTAMMV PIVEAILQQM E ATSAATEA ...String: MASALSYVSK FKSFVILFVT PLLLLPLVIL MPAKFVRCAY VIILMAIYWC TEVIPLAVTS LMPVLLFPLF QILDSRQVCV QYMKDTNML FLGGLIVAVA VERWNLHKRI ALRTLLWVGA KPARLMLGFM GVTALLSMWI SNTATTAMMV PIVEAILQQM E ATSAATEA GLELVDKGKA KELPGSQVIF EGPTLGQQED QERKRLCKAM TLCICYAASI GGTATLTGTG PNVVLLGQMN EL FPDSKDL VNFASWFAFA FPNMLVMLLF AWLWLQFVYM RFNFKKSWGC GLESKKNEKA ALKVLQEEYR KLGPLSFAEI NVL ICFFLL VILWFSRDPG FMPGWLTVAW VEGETKYVSD ATVAIFVATL LFIVPSQKPK FNFRSQTEEE RKTPFYPPPL LDWK VTQEK VPWGIVLLLG GGFALAKGSE ASGLSVWMGK QMEPLHAVPP AAITLILSLL VAVFTECTSN VATTTLFLPI FASMS RSIG LNPLYIMLPC TLSASFAFML PVATPPNAIV FTYGHLKVAD MVKTGVIMNI IGVFCVFLAV NTWGRAIFDL DHFPDW ANV THIET |
-Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 2 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Macromolecule #3: (2R)-2-[2-(4-tert-butylphenyl)ethyl]-2-hydroxybutanedioic acid
Macromolecule | Name: (2R)-2-[2-(4-tert-butylphenyl)ethyl]-2-hydroxybutanedioic acid type: ligand / ID: 3 / Number of copies: 2 / Formula: X3M |
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Molecular weight | Theoretical: 294.343 Da |
Chemical component information | ChemComp-X3M: |
-Macromolecule #4: SODIUM ION
Macromolecule | Name: SODIUM ION / type: ligand / ID: 4 / Number of copies: 4 |
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Molecular weight | Theoretical: 22.99 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 22500 |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average exposure time: 10.0 sec. / Average electron dose: 69.42 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: Warp |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 600496 |