+Open data
-Basic information
Entry | Database: PDB / ID: 7.0E+20 | |||||||||
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Title | Cryo EM structure of a K+-bound Na+,K+-ATPase in the E2 state | |||||||||
Components | (Sodium/potassium-transporting ATPase subunit ...) x 3 | |||||||||
Keywords | MEMBRANE PROTEIN / Na+ / K+-ATPase | |||||||||
Function / homology | Function and homology information negative regulation of glucocorticoid biosynthetic process / protein transport into plasma membrane raft / positive regulation of calcium:sodium antiporter activity / positive regulation of heart contraction / positive regulation of potassium ion transmembrane transporter activity / positive regulation of P-type sodium:potassium-exchanging transporter activity / Na+/K+-exchanging ATPase / positive regulation of striated muscle contraction / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane ...negative regulation of glucocorticoid biosynthetic process / protein transport into plasma membrane raft / positive regulation of calcium:sodium antiporter activity / positive regulation of heart contraction / positive regulation of potassium ion transmembrane transporter activity / positive regulation of P-type sodium:potassium-exchanging transporter activity / Na+/K+-exchanging ATPase / positive regulation of striated muscle contraction / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / response to glycoside / membrane repolarization during cardiac muscle cell action potential / photoreceptor inner segment membrane / negative regulation of heart contraction / P-type sodium:potassium-exchanging transporter activity / steroid hormone binding / sodium ion binding / sodium:potassium-exchanging ATPase complex / membrane repolarization / regulation of the force of heart contraction / establishment or maintenance of transmembrane electrochemical gradient / sodium ion export across plasma membrane / osmosensory signaling pathway / cell communication by electrical coupling involved in cardiac conduction / intracellular potassium ion homeostasis / intracellular sodium ion homeostasis / cardiac muscle cell action potential involved in contraction / regulation of cardiac muscle contraction by calcium ion signaling / positive regulation of ATP-dependent activity / relaxation of cardiac muscle / Basigin interactions / cellular response to steroid hormone stimulus / organelle membrane / potassium ion import across plasma membrane / Ion transport by P-type ATPases / phosphatase activity / monoatomic cation transmembrane transport / potassium ion binding / ATPase activator activity / intercalated disc / lateral plasma membrane / sperm flagellum / sodium channel regulator activity / sodium ion transmembrane transport / Ion homeostasis / regulation of sodium ion transport / cardiac muscle contraction / ATP metabolic process / T-tubule / proton transmembrane transport / protein localization to plasma membrane / sarcolemma / transmembrane transport / regulation of blood pressure / intracellular calcium ion homeostasis / extracellular vesicle / melanosome / MHC class II protein complex binding / protein-macromolecule adaptor activity / protein-folding chaperone binding / ATPase binding / regulation of gene expression / basolateral plasma membrane / transmembrane transporter binding / Potential therapeutics for SARS / postsynaptic density / cell adhesion / protein stabilization / response to xenobiotic stimulus / apical plasma membrane / protein heterodimerization activity / membrane raft / axon / innate immune response / protein kinase binding / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / extracellular exosome / ATP binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Guo, Y.Y. / Zhang, Y.Y. / Yan, R.H. / Huang, B.D. / Ye, F.F. / Wu, L.S. / Chi, X.M. / Zhou, Q. | |||||||||
Funding support | China, 2items
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Citation | Journal: Nat Commun / Year: 2022 Title: Cryo-EM structures of recombinant human sodium-potassium pump determined in three different states. Authors: Yingying Guo / Yuanyuan Zhang / Renhong Yan / Bangdong Huang / Fangfei Ye / Liushu Wu / Ximin Chi / Yi Shi / Qiang Zhou / Abstract: Sodium-Potassium Pump (Na/K-ATPase, NKA) is an ion pump that generates an electrochemical gradient of sodium and potassium ions across the plasma membrane by hydrolyzing ATP. During each Post-Albers ...Sodium-Potassium Pump (Na/K-ATPase, NKA) is an ion pump that generates an electrochemical gradient of sodium and potassium ions across the plasma membrane by hydrolyzing ATP. During each Post-Albers cycle, NKA exchanges three cytoplasmic sodium ions for two extracellular potassium ions through alternating changes between the E1 and E2 states. Hitherto, several steps remained unknown during the complete working cycle of NKA. Here, we report cryo-electron microscopy (cryo-EM) structures of recombinant human NKA (hNKA) in three distinct states at 2.7-3.2 Å resolution, representing the E1·3Na and E1·3Na·ATP states with cytosolic gates open and the basic E2·[2K] state, respectively. This work provides the insights into the cytoplasmic Na entrance pathway and the mechanism of cytoplasmic gate closure coupled with ATP hydrolysis, filling crucial gaps in the structural elucidation of the Post-Albers cycle of NKA. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7e20.cif.gz | 249.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e20.ent.gz | 197.8 KB | Display | PDB format |
PDBx/mmJSON format | 7e20.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7e20_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7e20_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7e20_validation.xml.gz | 47.2 KB | Display | |
Data in CIF | 7e20_validation.cif.gz | 67.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/7e20 ftp://data.pdbj.org/pub/pdb/validation_reports/e2/7e20 | HTTPS FTP |
-Related structure data
Related structure data | 30948MC 7e1zC 7e21C M: map data used to model this data C: citing same article (ref.) |
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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
-Sodium/potassium-transporting ATPase subunit ... , 3 types, 3 molecules ABC
#1: Protein | Mass: 113012.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ATP1A1 / Production host: Homo sapiens (human) / References: UniProt: P05023, Na+/K+-exchanging ATPase |
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#2: Protein | Mass: 35108.258 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ATP1B1, ATP1B / Production host: Homo sapiens (human) / References: UniProt: P05026 |
#3: Protein | Mass: 7292.322 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FXYD2, ATP1C, ATP1G1 / Production host: Homo sapiens (human) / References: UniProt: P54710 |
-Sugars , 2 types, 2 molecules
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#9: Sugar | ChemComp-NAG / |
-Non-polymers , 5 types, 12 molecules
#5: Chemical | #6: Chemical | ChemComp-MG / | #7: Chemical | ChemComp-Y01 / #8: Chemical | ChemComp-PC1 / | #10: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: cryo EM structure of a K+-bound Na+,K+-ATPase in the E2 state Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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 defocus max: 2200 nm / Nominal defocus min: 1200 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software | Name: RELION / Version: 3.0.6 / Category: 3D reconstruction |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53681 / Symmetry type: POINT |