+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30948 | |||||||||
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Title | Cryo EM structure of a K+-bound Na+,K+-ATPase in the E2 state | |||||||||
Map data | ||||||||||
Sample |
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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 / membrane repolarization during cardiac muscle cell action potential / response to glycoside / photoreceptor inner segment membrane / P-type sodium:potassium-exchanging transporter activity / steroid hormone binding / membrane repolarization / sodium ion binding / sodium:potassium-exchanging ATPase complex / negative regulation of heart contraction / establishment or maintenance of transmembrane electrochemical gradient / regulation of the force of heart contraction / sodium ion export across plasma membrane / intracellular potassium ion homeostasis / intracellular sodium ion homeostasis / cardiac muscle cell action potential involved in contraction / osmosensory signaling pathway / positive regulation of ATP-dependent activity / regulation of cardiac muscle contraction by calcium ion signaling / relaxation of cardiac muscle / cell communication by electrical coupling involved in cardiac conduction / Basigin interactions / cellular response to steroid hormone stimulus / potassium ion import across plasma membrane / monoatomic cation transmembrane transport / phosphatase activity / organelle membrane / potassium ion binding / Ion transport by P-type ATPases / ATPase activator activity / intercalated disc / lateral plasma membrane / sodium ion transmembrane transport / sperm flagellum / sodium channel regulator activity / cardiac muscle contraction / regulation of sodium ion transport / ATP metabolic process / Ion homeostasis / proton transmembrane transport / T-tubule / 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 / protein stabilization / cell adhesion / response to xenobiotic stimulus / membrane raft / apical plasma membrane / protein heterodimerization activity / 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 | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Guo YY / Zhang YY / Yan RH / Huang BD / Ye FF / Wu LS / Chi XM / Zhou Q | |||||||||
Funding support | China, 2 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_30948.map.gz | 28.5 MB | EMDB map data format | |
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Header (meta data) | emd-30948-v30.xml emd-30948.xml | 15.6 KB 15.6 KB | Display Display | EMDB header |
Images | emd_30948.png | 44.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30948 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30948 | HTTPS FTP |
-Validation report
Summary document | emd_30948_validation.pdf.gz | 489.1 KB | Display | EMDB validaton report |
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Full document | emd_30948_full_validation.pdf.gz | 488.6 KB | Display | |
Data in XML | emd_30948_validation.xml.gz | 5.7 KB | Display | |
Data in CIF | emd_30948_validation.cif.gz | 6.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30948 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30948 | HTTPS FTP |
-Related structure data
Related structure data | 7e20MC 7e1zC 7e21C 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_30948.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.087 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : cryo EM structure of a K+-bound Na+,K+-ATPase in the E2 state
+Supramolecule #1: cryo EM structure of a K+-bound Na+,K+-ATPase in the E2 state
+Macromolecule #1: Sodium/potassium-transporting ATPase subunit alpha-1
+Macromolecule #2: Sodium/potassium-transporting ATPase subunit beta-1
+Macromolecule #3: Sodium/potassium-transporting ATPase subunit gamma
+Macromolecule #5: POTASSIUM ION
+Macromolecule #6: MAGNESIUM ION
+Macromolecule #7: CHOLESTEROL HEMISUCCINATE
+Macromolecule #8: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #9: 2-acetamido-2-deoxy-beta-D-glucopyranose
+Macromolecule #10: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.6) / Number images used: 53681 |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |