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Yorodumi- PDB-7y46: Cryo-EM structure of the Na+,K+-ATPase in the E2.2K+ state after ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7y46 | |||||||||||||||||||||
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Title | Cryo-EM structure of the Na+,K+-ATPase in the E2.2K+ state after addition of ATP | |||||||||||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / Na+ / K+-ATPase / ion transport / TRANSPORT PROTEIN | |||||||||||||||||||||
Function / homology | Function and homology information regulation of monoatomic ion transport / P-type potassium transmembrane transporter activity / sodium:potassium-exchanging ATPase complex / ion channel regulator activity / sodium ion transport / monoatomic ion transport / potassium ion transport / ATP hydrolysis activity / ATP binding / membrane ...regulation of monoatomic ion transport / P-type potassium transmembrane transporter activity / sodium:potassium-exchanging ATPase complex / ion channel regulator activity / sodium ion transport / monoatomic ion transport / potassium ion transport / ATP hydrolysis activity / ATP binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||||||||||||||
Biological species | Squalus acanthias (spiny dogfish) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.2 Å | |||||||||||||||||||||
Authors | Kanai, R. / Cornelius, F. / Vilsen, B. / Toyoshima, C. | |||||||||||||||||||||
Funding support | Japan, Denmark, 6items
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Citation | Journal: FEBS Lett / Year: 2022 Title: Cryo-electron microscopy of Na ,K -ATPase reveals how the extracellular gate locks in the E2·2K state. Authors: Ryuta Kanai / Flemming Cornelius / Bente Vilsen / Chikashi Toyoshima / Abstract: Na ,K -ATPase (NKA) is one of the most important members of the P-type ion-translocating ATPases and plays a pivotal role in establishing electrochemical gradients for Na and K across the cell ...Na ,K -ATPase (NKA) is one of the most important members of the P-type ion-translocating ATPases and plays a pivotal role in establishing electrochemical gradients for Na and K across the cell membrane. Presented here is a 3.3 Å resolution structure of NKA in the E2·2K state solved by cryo-electron microscopy. It is a stable state with two occluded K after transferring three Na into the extracellular medium and releasing inorganic phosphate bound to the cytoplasmic P domain. We describe how the extracellular ion pathway wide open in the E2P state becomes closed and locked in E2·2K , linked to events at the phosphorylation site more than 50 Å away. We also show, although at low resolution, how ATP binding to NKA in E2·2K relaxes the gating machinery and thereby accelerates the transition into the next step, that is, the release of K into the cytoplasm, more than 100 times. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7y46.cif.gz | 499.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7y46.ent.gz | 399.1 KB | Display | PDB format |
PDBx/mmJSON format | 7y46.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y4/7y46 ftp://data.pdbj.org/pub/pdb/validation_reports/y4/7y46 | HTTPS FTP |
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-Related structure data
Related structure data | 33602MC 7y45C 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: givenMatrix: (-0.999926569858, 0.0049598677153, -0.0110568803619), (-0.00507754645572, -0.999930496835, 0.0106404897325), (-0.0110033364523, 0.0106958502235, 0.999882255756)Vector: ...NCS oper: (Code: given Matrix: (-0.999926569858, 0.0049598677153, -0.0110568803619), Vector: |
-Components
-Protein , 3 types, 6 molecules CADBEG
#1: Protein | Mass: 113309.891 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Squalus acanthias (spiny dogfish) / References: UniProt: Q4H132 #2: Protein | Mass: 35176.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Squalus acanthias (spiny dogfish) / References: UniProt: C4IX13 #3: Protein | Mass: 10195.847 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Squalus acanthias (spiny dogfish) / References: UniProt: Q70Q12 |
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-Sugars , 4 types, 8 molecules
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Polysaccharide | Source method: isolated from a genetically manipulated source #7: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 5 types, 22 molecules
#8: Chemical | #9: Chemical | ChemComp-K / #10: Chemical | ChemComp-CLR / #11: Chemical | #12: 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: Sodium/potassium-transporting ATPase / Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL | |||||||||||||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||||||||||||||||||||||
Source (natural) | Organism: Squalus acanthias (spiny dogfish) | |||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: C-flat-1.2/1.3 | |||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 99.9 % / Chamber temperature: 279 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 FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27915 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 268 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation Coeeficient | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 2ZXE | ||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 463.77 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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