+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29103 | |||||||||
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Title | Cryo-EM structure of human NCC | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information Defective SLC12A3 causes Gitelman syndrome (GS) / sodium:chloride symporter activity / salt transmembrane transporter activity / sodium:potassium:chloride symporter activity / : / Cation-coupled Chloride cotransporters / sodium ion homeostasis / renal sodium ion absorption / chloride ion homeostasis / potassium ion homeostasis ...Defective SLC12A3 causes Gitelman syndrome (GS) / sodium:chloride symporter activity / salt transmembrane transporter 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 / sodium ion transport / response to aldosterone / 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 | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.02 Å | |||||||||
Authors | Zhang J / Fan M / Feng L | |||||||||
Funding support | 1 items
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Citation | Journal: Nature / Year: 2023 Title: Structure and thiazide inhibition mechanism of the human Na-Cl cotransporter. Authors: Minrui Fan / Jianxiu Zhang / Chien-Ling Lee / Jinru Zhang / Liang Feng / Abstract: The sodium-chloride cotransporter (NCC) is critical for kidney physiology. The NCC has a major role in salt reabsorption in the distal convoluted tubule of the nephron, and mutations in the NCC cause ...The sodium-chloride cotransporter (NCC) is critical for kidney physiology. The NCC has a major role in salt reabsorption in the distal convoluted tubule of the nephron, and mutations in the NCC cause the salt-wasting disease Gitelman syndrome. As a key player in salt handling, the NCC regulates blood pressure and is the target of thiazide diuretics, which have been widely prescribed as first-line medications to treat hypertension for more than 60 years. Here we determined the structures of human NCC alone and in complex with a commonly used thiazide diuretic using cryo-electron microscopy. These structures, together with functional studies, reveal major conformational states of the NCC and an intriguing regulatory mechanism. They also illuminate how thiazide diuretics specifically interact with the NCC and inhibit its transport function. Our results provide critical insights for understanding the Na-Cl cotransport mechanism of the NCC, and they establish a framework for future drug design and for interpreting disease-related mutations. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29103.map.gz | 64.4 MB | EMDB map data format | |
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Header (meta data) | emd-29103-v30.xml emd-29103.xml | 14.4 KB 14.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29103_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_29103.png | 81.2 KB | ||
Masks | emd_29103_msk_1.map | 125 MB | Mask map | |
Others | emd_29103_half_map_1.map.gz emd_29103_half_map_2.map.gz | 116 MB 116 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29103 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29103 | HTTPS FTP |
-Validation report
Summary document | emd_29103_validation.pdf.gz | 858.3 KB | Display | EMDB validaton report |
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Full document | emd_29103_full_validation.pdf.gz | 857.9 KB | Display | |
Data in XML | emd_29103_validation.xml.gz | 19 KB | Display | |
Data in CIF | emd_29103_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29103 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29103 | HTTPS FTP |
-Related structure data
Related structure data | 8fhtMC 8fhnC 8fhoC 8fhpC 8fhqC 8fhrC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_29103.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_29103_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_29103_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_29103_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : NCC
Entire | Name: NCC |
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Components |
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-Supramolecule #1: NCC
Supramolecule | Name: NCC / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-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: Homo sapiens (human) |
Molecular weight | Theoretical: 113.279719 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MAELPTTETP GDATLCSGRF TISTLLSSDE PSPPAAYDSS HPSHLTHSST FCMRDFGYND IDVVPTYEHY ANDTQPGEPR KVRPTLADL HSFLKQEGRH LHALAFDSRP SHEMTDGLVE GEAGTSSEKN PEEPVRFGWV NGVMIRCMLN IWGVILYLRL P WITAQAGI ...String: MAELPTTETP GDATLCSGRF TISTLLSSDE PSPPAAYDSS HPSHLTHSST FCMRDFGYND IDVVPTYEHY ANDTQPGEPR KVRPTLADL HSFLKQEGRH LHALAFDSRP SHEMTDGLVE GEAGTSSEKN PEEPVRFGWV NGVMIRCMLN IWGVILYLRL P WITAQAGI VLTWIIILLS VTVTSITGLS ISAISTNGKV KSGGTYFLIS RSLGPELGGS IGLIFAFANA VGVAMHTVGF AE TVRDLLQ EYGAPIVDPI NDIRIIGVVS VTVLLAISLA GMEWESKAQV LFFLVIMVSF ANYLVGTLIP PSEDKASKGF FSY RADIFV QNLVPDWRGP DGTFFGMFSI FFPSATGILA GANISGDLKD PAIAIPKGTL MAIFWTTISY LAISATIGSC VVRD ASGVL NDTVTPGWGA CEGLACSYGW NFTECTQQHS CHYGLINYYQ TMSMVSGFAP LITAGIFGAT LSSALACLVS AAKVF QCLC EDQLYPLIGF FGKGYGKNKE PVRGYLLAYA IAVAFIIIAE LNTIAPIISN FFLCSYALIN FSCFHASITN SPGWRP SFQ YYNKWAALFG AIISVVIMFL LTWWAALIAI GVVLFLLLYV IYKKPEVNWG SSVQAGSYNL ALSYSVGLNE VEDHIKN YR PQCLVLTGPP NFRPALVDFV GTFTRNLSLM ICGHVLIGPH KQRMPELQLI ANGHTKWLNK RKIKAFYSDV IAEDLRRG V QILMQAAGLG RMKPNILVVG FKKNWQSAHP ATVEDYIGIL HDAFDFNYGV CVMRMREGLN VSKMMQAHIN PVFDPAEDG KEASARVDPK ALVKEEQATT IFQSEQGKKT IDIYWLFDDG GLTLLIPYLL GRKRRWSKCK IRVFVGGQIN RMDQERKAII SLLSKFRLG FHEVHILPDI NQNPRAEHTK RFEDMIAPFR LNDGFKDEAT VNEMRRDCPW KISDEEITKN RVKSLRQVRL N EIVLDYSR DAALIVITLP IGRKGKCPSS LYMAWLETLS QDLRPPVILI RGNQENVLTF YCQ |
-Macromolecule #2: SODIUM ION
Macromolecule | Name: SODIUM ION / type: ligand / ID: 2 / Number of copies: 2 |
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Molecular weight | Theoretical: 22.99 Da |
-Macromolecule #3: CHLORIDE ION
Macromolecule | Name: CHLORIDE ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: CL |
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Molecular weight | Theoretical: 35.453 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 12 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |