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Open data
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Basic information
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Title | Cryo-EM structure of human sodium-chloride cotransporter | |||||||||
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Function / homology | ![]() Defective SLC12A3 causes Gitelman syndrome (GS) / sodium:chloride symporter activity / sodium:potassium:chloride symporter activity / : / Cation-coupled Chloride cotransporters / sodium ion homeostasis / renal sodium ion absorption / chloride ion homeostasis / potassium ion homeostasis / cell volume homeostasis ...Defective SLC12A3 causes Gitelman syndrome (GS) / sodium:chloride symporter activity / sodium:potassium:chloride symporter activity / : / Cation-coupled Chloride cotransporters / sodium ion homeostasis / renal sodium ion absorption / chloride ion homeostasis / potassium ion homeostasis / cell volume homeostasis / response to aldosterone / sodium ion transport / potassium ion import across plasma membrane / response to dietary excess / sodium ion transmembrane transport / monoatomic ion transport / chloride transmembrane transport / apical plasma membrane / signal transduction / extracellular exosome / ATP binding / membrane / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.85 Å | |||||||||
![]() | Nan J / Yang X / Shan Z / Yuan Y / Zhang YQ | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of the human sodium-chloride cotransporter NCC. Authors: Jing Nan / Yafei Yuan / Xuemei Yang / Ziyang Shan / Huihui Liu / Feiwen Wei / Wei Zhang / Yanqing Zhang / ![]() Abstract: The sodium-chloride cotransporter NCC mediates the coupled import of sodium and chloride across the plasma membrane, playing vital roles in kidney extracellular fluid volume and blood pressure ...The sodium-chloride cotransporter NCC mediates the coupled import of sodium and chloride across the plasma membrane, playing vital roles in kidney extracellular fluid volume and blood pressure control. Here, we present the full-length structure of human NCC, with 2.9 Å for the transmembrane domain and 3.8 Å for the carboxyl-terminal domain. NCC adopts an inward-open conformation and a domain-swap dimeric assembly. Conserved ion binding sites among the cation-chloride cotransporters and the Na2 site are observed in our structure. A unique His residue in the substrate pocket in NCC potentially interacts with Na1 and Cl1 and might also mediate the coordination of Na2 through a Ser residue. Putative observed water molecules are indicated to participate in the coordination of ions and TM coupling. Together with transport activity assays, our structure provides the first glimpse of NCC and defines ion binding sites, promoting drug development for hypertension targeting on NCC. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.2 KB 18.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.4 KB | Display | ![]() |
Images | ![]() | 85.7 KB | ||
Others | ![]() ![]() | 59.2 MB 59.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7y6iMC ![]() 7yg0C ![]() 7yg1C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 1.046 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_33641_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33641_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Sodium-chloride cotransporter
Entire | Name: Sodium-chloride cotransporter |
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Components |
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-Supramolecule #1: Sodium-chloride cotransporter
Supramolecule | Name: Sodium-chloride cotransporter / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
-Macromolecule #1: Solute carrier family 12 member 3
Macromolecule | Name: Solute carrier family 12 member 3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 116.921461 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MAELPTTETP GDATLCSGRF TISTLLSSDE PSPPAAYDSS HPSHLTHSST FCMRTFGYNT IDVVPTYEHY ANSTQPGEPR KVRPTLADL HSFLKEGRHL HALAFDSRPS HEMTDGLVEG EAGTSSEKNP EEPVRFGWVK GVMIRCMLNI WGVILYLRLP W ITAQAGIV ...String: MAELPTTETP GDATLCSGRF TISTLLSSDE PSPPAAYDSS HPSHLTHSST FCMRTFGYNT IDVVPTYEHY ANSTQPGEPR KVRPTLADL HSFLKEGRHL HALAFDSRPS HEMTDGLVEG EAGTSSEKNP EEPVRFGWVK GVMIRCMLNI WGVILYLRLP W ITAQAGIV LTWIIILLSV TVTSITGLSI SAISTNGKVK SGGTYFLISR SLGPELGGSI GLIFAFANAV GVAMHTVGFA ET VRDLLQE YGAPIVDPIN DIRIIGVVSV TVLLAISLAG MEWESKAQVL FFLVIMVSFA NYLVGTLIPP SEDKASKGFF SYR ADIFVQ NLVPDWRGPD GTFFGMFSIF FPSATGILAG ANISGDLKDP AIAIPKGTLM AIFWTTISYL AISATIGSCV VRDA SGVLN DTVTPGWGAC EGLACSYGWN FTECTQQHSC HYGLINYYQT MSMVSGFAPL ITAGIFGATL SSALACLVSA AKVFQ CLCE DQLYPLIGFF GKGYGKNKEP VRGYLLAYAI AVAFIIIAEL NTIAPIISNF FLCSYALINF SCFHASITNS PGWRPS FQY YNKWAALFGA IISVVIMFLL TWWAALIAIG VVLFLLLYVI YKKPEVNWGS SVQAGSYNLA LSYSVGLNEV EDHIKNY RP QCLVLTGPPN FRPALVDFVG TFTRNLSLMI CGHVLIGPHK QRMPELQLIA NGHTKWLNKR KIKAFYSDVI AEDLRRGV Q ILMQAAGLGR MKPNILVVGF KKNWQSAHPA TVEDYIGILH DAFDFNYGVC VMRMREGLNV SKMMQAHINP VFDPAEDGK EASARVDPKA LVKEEQATTI FQSEQGKKTI DIYWLFDDGG LTLLIPYLLG RKRRWSKCKI RVFVGGQINR MDQERKAIIS LLSKFRLGF HEVHILPDIN QNPRAEHTKR FEDMIAPFRL NDGFKDEATV NEMRRDCPWK ISDEEITKNR VKSLRQVRLN E IVLDYSRD AALIVITLPI GRKGKCPSSL YMAWLETLSQ DLRPPVILIR GNQENVLTFY CQLEGSDEVD AGSHHHHHHH HH HGSVEDY KDDDDK |
-Macromolecule #3: CHLORIDE ION
Macromolecule | Name: CHLORIDE ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: CL |
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Molecular weight | Theoretical: 35.453 Da |
-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 |
-Macromolecule #5: CHOLESTEROL HEMISUCCINATE
Macromolecule | Name: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 5 / Number of copies: 6 / Formula: Y01 |
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Molecular weight | Theoretical: 486.726 Da |
Chemical component information | ![]() ChemComp-Y01: |
-Macromolecule #6: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Macromolecule | Name: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 6 / Number of copies: 8 / Formula: LPE |
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Molecular weight | Theoretical: 510.708 Da |
Chemical component information | ![]() ChemComp-LPE: |
-Macromolecule #7: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...
Macromolecule | Name: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate type: ligand / ID: 7 / Number of copies: 9 / Formula: POV |
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Molecular weight | Theoretical: 760.076 Da |
Chemical component information | ![]() ChemComp-POV: |
-Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 2 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Macromolecule #9: water
Macromolecule | Name: water / type: ligand / ID: 9 / Number of copies: 6 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 9 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum ER / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 52.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |