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Yorodumi- PDB-7yg1: Cryo-EM structure of the C-terminal domain of the human sodium-ch... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yg1 | ||||||
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Title | Cryo-EM structure of the C-terminal domain of the human sodium-chloride cotransporter | ||||||
Components | Solute carrier family 12 member 3 | ||||||
Keywords | MEMBRANE PROTEIN / transporter / cation-chloride cotransporter | ||||||
Function / homology | Function and homology information 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 ...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 | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.77 Å | ||||||
Authors | Nan, J. / Yang, X.M. / Shan, Z.Y. / Yuan, Y.F. / Zhang, Y.Q. | ||||||
Funding support | China, 1items
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Citation | Journal: Sci Adv / Year: 2022 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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yg1.cif.gz | 172.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yg1.ent.gz | 122.1 KB | Display | PDB format |
PDBx/mmJSON format | 7yg1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yg1_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7yg1_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7yg1_validation.xml.gz | 43 KB | Display | |
Data in CIF | 7yg1_validation.cif.gz | 61.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yg/7yg1 ftp://data.pdbj.org/pub/pdb/validation_reports/yg/7yg1 | HTTPS FTP |
-Related structure data
Related structure data | 33804MC 7y6iC 7yg0C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 116921.461 Da / Num. of mol.: 2 / Mutation: A264G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P55017 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Sodium-chloride cotransporter / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293 |
Buffer solution | pH: 8 |
Specimen | Conc.: 9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2300 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 52.8 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
EM imaging optics | Energyfilter name: GIF Quantum ER / Energyfilter slit width: 20 eV |
-Processing
EM software |
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CTF correction | Type: NONE | |||||||||
3D reconstruction | Resolution: 3.77 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 79225 / Symmetry type: POINT |