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- PDB-7z04: 10 mM Rb+ soak of beryllium fluoride inhibited Na+,K+-ATPase, E2-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7z04 | ||||||
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Title | 10 mM Rb+ soak of beryllium fluoride inhibited Na+,K+-ATPase, E2-BeFx (rigid body model) | ||||||
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![]() | MEMBRANE PROTEIN / Pig kidney Na+ / K+-ATPase | ||||||
Function / homology | ![]() Basigin interactions / Ion homeostasis / positive regulation of P-type sodium:potassium-exchanging transporter activity / Na+/K+-exchanging ATPase / positive regulation of sodium ion export across plasma membrane / Ion transport by P-type ATPases / positive regulation of potassium ion import across plasma membrane / membrane repolarization / P-type sodium:potassium-exchanging transporter activity / sodium ion binding ...Basigin interactions / Ion homeostasis / positive regulation of P-type sodium:potassium-exchanging transporter activity / Na+/K+-exchanging ATPase / positive regulation of sodium ion export across plasma membrane / Ion transport by P-type ATPases / positive regulation of potassium ion import across plasma membrane / membrane repolarization / P-type sodium:potassium-exchanging transporter activity / sodium ion binding / sodium:potassium-exchanging ATPase complex / establishment or maintenance of transmembrane electrochemical gradient / sodium ion export across plasma membrane / intracellular potassium ion homeostasis / intracellular sodium ion homeostasis / potassium ion import across plasma membrane / potassium ion binding / ATPase activator activity / sodium channel regulator activity / regulation of sodium ion transport / proton transmembrane transport / sarcolemma / transmembrane transport / melanosome / protein-macromolecule adaptor activity / ATPase binding / basolateral plasma membrane / cell adhesion / apical plasma membrane / axon / innate immune response / ATP hydrolysis activity / ATP binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fruergaard, M.U. / Dach, I. / Andersen, J.L. / Ozol, M. / Shasavar, A. / Quistgaard, E.M. / Poulsen, H. / Fedosova, N.U. / Nissen, P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The Na + ,K + -ATPase in complex with beryllium fluoride mimics an ATPase phosphorylated state. Authors: Fruergaard, M.U. / Dach, I. / Andersen, J.L. / Ozol, M. / Shahsavar, A. / Quistgaard, E.M. / Poulsen, H. / Fedosova, N.U. / Nissen, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 536.6 KB | Display | ![]() |
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PDB format | ![]() | 426.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 733.8 KB | Display | ![]() |
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Full document | ![]() | 884.4 KB | Display | |
Data in XML | ![]() | 75.2 KB | Display | |
Data in CIF | ![]() | 107.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qtvSC ![]() 7yzrC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 112666.375 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | Mass: 35073.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | Mass: 6962.919 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Chemical | #5: Chemical | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.99 Å3/Da / Density % sol: 79.48 % |
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Crystal grow | Temperature: 288.15 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: The protein sample was mixed in a 1:1 ratio with reservoir solution containing 16.5 % (wt/vol) polyethylene glycol 2000 monomethyl ether (PEG 2000 MME), 10 % (vol/vol) glycerol, 175 mM ...Details: The protein sample was mixed in a 1:1 ratio with reservoir solution containing 16.5 % (wt/vol) polyethylene glycol 2000 monomethyl ether (PEG 2000 MME), 10 % (vol/vol) glycerol, 175 mM MgCl2, 150 mM NaCl, 20 mM HEPES/MES pH 6.2 and 2 mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 16, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8141 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 7.5→25 Å / Num. obs: 9614 / % possible obs: 99.4 % / Redundancy: 13.975 % / Biso Wilson estimate: 379.64 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.301 / Rrim(I) all: 0.313 / Χ2: 0.751 / Net I/σ(I): 7.78 / Num. measured all: 134354 / Scaling rejects: 12 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7QTV Resolution: 7.5→25 Å / SU ML: 1.17 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 35.9 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 752.14 Å2 / Biso mean: 480.1288 Å2 / Biso min: 43.67 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 7.5→25 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
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