Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Substrate translocation and inhibition in human dicarboxylate transporter NaDC3.
Journal, issue, pages	Nat Struct Mol Biol, Year 2024
Publish date	Dec 2, 2024
Authors	Yan Li / Jinmei Song / Vedrana Mikusevic / Jennifer J Marden / Alissa Becerril / Huihui Kuang / Bing Wang / William J Rice / Joseph A Mindell / Da-Neng Wang /
PubMed Abstract	The human high-affinity sodium-dicarboxylate cotransporter (NaDC3) imports various substrates into the cell as tricarboxylate acid cycle intermediates, lipid biosynthesis precursors and signaling ...The human high-affinity sodium-dicarboxylate cotransporter (NaDC3) imports various substrates into the cell as tricarboxylate acid cycle intermediates, lipid biosynthesis precursors and signaling molecules. Understanding the cellular signaling process and developing inhibitors require knowledge of the structural basis of the dicarboxylate specificity and inhibition mechanism of NaDC3. To this end, we determined the cryo-electron microscopy structures of NaDC3 in various dimers, revealing the protomer in three conformations: outward-open C, outward-occluded C and inward-open C. A dicarboxylate is first bound and recognized in C and how the substrate interacts with NaDC3 in C likely helps to further determine the substrate specificity. A phenylalanine from the scaffold domain interacts with the bound dicarboxylate in the C state and modulates the kinetic barrier to the transport domain movement. Structural comparison of an inhibitor-bound structure of NaDC3 to that of the sodium-dependent citrate transporter suggests ways for making an inhibitor that is specific for NaDC3.
External links	Nat Struct Mol Biol / PubMed:39622972
Methods	EM (single particle)
Resolution	2.09 - 2.92 Å
Structure data	42614 8uvb EMDB-42614, PDB-8uvb: Structure of NaCT-PF4a complex Method: EM (single particle) / Resolution: 2.13 Å 42615 8uvc EMDB-42615, PDB-8uvc: Structure of NaDC3-aKG complex Method: EM (single particle) / Resolution: 2.09 Å 42616 8uvd EMDB-42616, PDB-8uvd: Structure of NaDC3-PF4a complex Method: EM (single particle) / Resolution: 2.16 Å 42617 8uve EMDB-42617, PDB-8uve: Structure of NaDC3-Succinate complex in Coo-Ci conformation Method: EM (single particle) / Resolution: 2.6 Å 42618 8uvf EMDB-42618, PDB-8uvf: Structure of NaDC3-DMS complex in Ci-Ci conformation Method: EM (single particle) / Resolution: 2.17 Å 42619 8uvg EMDB-42619, PDB-8uvg: Structure of NaDC3-DMS complex in Co-Ci conformation Method: EM (single particle) / Resolution: 2.92 Å 42620 8uvh EMDB-42620, PDB-8uvh: Structure of NaCT-succ complex Method: EM (single particle) / Resolution: 2.33 Å 42621 8uvi EMDB-42621, PDB-8uvi: Structure of NaDC3-Succinate complex in Coo-Coo conformation Method: EM (single particle) / Resolution: 2.53 Å
Chemicals	ChemComp-NA: Unknown entry ChemComp, No image ChemComp-XKC: Unknown entry ChemComp-AKG: 2-OXOGLUTARIC ACID ChemComp-C14: TETRADECANE ChemComp-3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipidYM ChemComp-CLR: CHOLESTEROL ChemComp-SIN: SUCCINIC ACID ChemComp, No image ChemComp-XKH*: Unknown entry
Source	homo sapiens (human)
Keywords	TRANSPORT PROTEIN / Na(+)/citrate cotransporter(NaCT) / Solute carries / Elevator type alternating access / membrane protein / Na(+)/dicarboxylate cotransporter(NaDC3)