Structure of NaDC3-DMS complex in Ci-Ci conformation

2025-04-02 REL RCSB INITIAL_RELEASE REPOSITORY DATA_PROCESSING em_admin em_particle_selection _em_admin.last_update _em_particle_selection.num_particles_selected DATABASE_REFERENCES citation citation_author em_admin _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation_author.identifier_ORCID _em_admin.last_update RCSB RCSB 2023-11-02 2024-12-25 2024-12-25 2025-04-02 National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) R01NS108151 United States National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) R01DK135088 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) R01AI165782 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01GM121994 United States Structure of NaDC3-DMS complex in Ci-Ci conformation Li Y Wang DN Mindell JA Rice WJ Song J Mikusevic V Marden JJ Becerril A Kuang H Wang B Na(+)/dicarboxylate cotransporter(NaDC3), Solute carries, Elevator type alternating access, membrane protein, TRANSPORT PROTEIN Li Y Song J Mikusevic V Marden JJ Becerril A Kuang H Wang B Rice WJ Mindell JA Wang DN Substrate translocation and inhibition in human dicarboxylate transporter NaDC3. Nat.Struct.Mol.Biol. US 32 502 512 2025 39622972 doi:10.1038/s41594-024-01433-0 1545-9985 EMD-42615 other EM volume

Structure of NaDC3-aKG

EMD-42616 other EM volume

Structure of NaDC3-PF4a

EMD-42617 other EM volume

Structure of NaDC3-Succ in Coo-Ci conformation

EMD-42621 other EM volume

Structure of NaDC3-Succ in Coo-Coo conformation

EMD-42619 other EM volume

Structure of NaDC3-DMS in Co-Ci conformation

8uvf FULLOVERLAP Dimer of NaDC3 in complex with 2,3-DMS Dimer of NaDC3 in complex with 2,3-DMS 0 1 Homo sapiens 0.063062 Na(+)/dicarboxylate cotransporter 3 Homo sapiens 0.06723602299999999

Solute carrier family 13 member 3

2 Trichoplusia ni LEVO MAALAAAAKKVWSARRLLVLLFTPLALLPVVFALPPKEGRCLFVILLMAVYWCTEALPLSVTALLPIVLFPFMGILPSNK VCPQYFLDTNFLFLSGLIMASAIEEWNLHRRIALKILMLVGVQPARLILGMMVTTSFLSMWLSNTASTAMMLPIANAILK SLFGQKEVRKDPSQESEENTAAVRRNGLHTVPTEMQFLASTEAKDHPGETEVPLDLPADSRKEDEYRRNIWKGFLISIPY SASIGGTATLTGTAPNLILLGQLKSFFPQCDVVNFGSWFIFAFPLMLLFLLAGWLWISFLYGGLSFRGWRKNKSEIRTNA EDRARAVIREEYQNLGPIKFAEQAVFILFCMFAILLFTRDPKFIPGWASLFNPGFLSDAVTGVAIVTILFFFPSQRPSLK WWFDFKAPNTETEPLLTWKKAQETVPWNIILLLGGGFAMAKGCEESGLSVWIGGQLHPLENVPPALAVLLITVVIAFFTE FASNTATIIIFLPVLAELAIRLRVHPLYLMIPGTVGCSFAFMLPVSTPPNSIAFASGHLLVKDMVRTGLLMNLMGVLLLS LAMNTWAQTIFQLGTFPDWADMYSVNVTALPPTLANDTFRTLSGAGA Q8WWT9 SODIUM ION 2.299e-05 4 NA TETRADECANE 0.000198388 6 C14 1,2-Distearoyl-sn-glycerophosphoethanolamine 0.000748065 4 3PE CHOLESTEROL 0.000386654 8 CLR singleParticle particle 6 7.5 25.0 Tris-HCl Tris (Hydroxymethyl) Aminomethane Hydrochloride 100.0 NaCl sodium chloride 20.0 2,3-DMS 2,3-Dimethylsuccinate 0.02 GDN glyco-diosgenin UltrAuFoil R1.2/1.3 GOLD 300 GOLD HOLEY 50.0 GLOW DISCHARGE 25 AIR 0.026000000000000002

Hold 10s before glow discharge

ETHANE 100 281.15 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 1.2 0.8 1.6 3.0 105000.0 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 80.0 80.0 0.05 GIF Bioquantum 20 GATAN K3 BIOQUANTUM (6k x 4k) 5760 4092 1 19524 1.8 52.58

5416 untilted images were collected in super resolution mode at 40 frames per micrograph, 569 untilted images and 13540 tilted images were collected in super resolution mode at 60 frames per micrograph

The micrographs with an overall resolution worse than 5 angstrom were excluded

689596

Particles were selected form 5850 untilted images and 13540 40 degree tilted images

Ab-initio reconstruction in cryoSPARC

1 C2 FOURIER SPACE 2.17 FSC 0.143 CUT-OFF cryoSPARC 3.3.1 397856 MAXIMUM LIKELIHOOD cryoSPARC 3.3.1

branch-and-bound maximum likelihood

MAXIMUM LIKELIHOOD cryoSPARC 3.3.1

branch-and-bound maximum likelihood

3 cryoSPARC 3.3.1

Number of particles for 3 classes are 397856, 139897, 3132. The reported resolutions are 3.36, 3.76, 10.4 angstom, respectively.

emd_42618.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 264.0 264.0 264.0 90.0 90.0 90.0 X Y Z -1.536532 2.5799177 0.0011674077 0.041762702 0.825 0.825 0.825 0.213 AUTHOR ::::EMDATABANK.org::::EMD-42618:::: Sharpened map of NaDC3-DMS in Ci-Ci conformation AB 1-602 AlphaFold in silico model

The whole model was used as an initial model

OTHER

Initial local fitting was done using Chimera and then coot was used for ajustment.

cross-correlation coefficient REAL 43.719999999999999 emd_42618_msk_1.map emd_42618_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 264.0 264.0 264.0 90.0 90.0 90.0 X Y Z -0.24383491 0.6345479 0.0011680379 0.01955634 0.825 0.825 0.825 AUTHOR ::::EMDATABANK.org::::EMD-42618:::: Unsharpened map of NaDC3-DMS in Ci-Ci conformation emd_42618_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 264.0 264.0 264.0 90.0 90.0 90.0 X Y Z -0.26502505 0.6779374 0.001251024 0.020789715 0.825 0.825 0.825 AUTHOR ::::EMDATABANK.org::::EMD-42618:::: Half map B of NaDC3-DMS in Ci-Ci conformation emd_42618_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 264.0 264.0 264.0 90.0 90.0 90.0 X Y Z -0.2894396 0.6841434 0.0012611793 0.020782415 0.825 0.825 0.825 AUTHOR ::::EMDATABANK.org::::EMD-42618:::: Half map A of NaDC3-DMS in Ci-Ci conformation