+
Open data
-
Basic information
Entry | Database: PDB / ID: 7ddl | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structures of Na+,K+-ATPase in complex with bufalin | ||||||||||||
![]() |
| ||||||||||||
![]() | MEMBRANE PROTEIN / Na+ / K+-ATPase / ion transport / Cardiotonic steroids | ||||||||||||
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 | ![]() ![]() ![]() | ||||||||||||
![]() | Ogawa, H. / Cornelius, F. / Kanai, R. / Motoyama, K. / Vilsen, B. / Toyoshima, C. | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() Title: Binding of cardiotonic steroids to Na + ,K + -ATPase in the E2P state. Authors: Kanai, R. / Cornelius, F. / Ogawa, H. / Motoyama, K. / Vilsen, B. / Toyoshima, C. | ||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 668.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 441.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 5.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 4.9 MB | Display | |
Data in XML | ![]() | 98.8 KB | Display | |
Data in CIF | ![]() | 129.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7d91C ![]() 7d92C ![]() 7d93C ![]() 7d94C ![]() 7ddfC ![]() 7ddhC ![]() 7ddiC ![]() 7ddkC ![]() 6kpu ![]() 6kpy ![]() 6kpz C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
|
-
Components
-Sodium/potassium-transporting ATPase subunit ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 112403.945 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | Mass: 35204.402 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|
-Protein , 1 types, 2 molecules GE
#3: Protein | Mass: 7094.115 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|
-Sugars , 2 types, 6 molecules ![](data/chem/img/NAG.gif)
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #10: Sugar | |
---|
-Non-polymers , 6 types, 35 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PCW.gif)
![](data/chem/img/BUF.gif)
![](data/chem/img/CLR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PCW.gif)
![](data/chem/img/BUF.gif)
![](data/chem/img/CLR.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-MG / #6: Chemical | #7: Chemical | ChemComp-PCW / #8: Chemical | #9: Chemical | ChemComp-CLR / #11: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 5.68 Å3/Da / Density % sol: 78.36 % |
---|---|
Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop Details: 16% PEG 2000 MME, 10% GLYCEROL, 200mM MAGNESIUM CHLORIDE, 5mM GSH, 0.1mM DTT, 0.0001% BHT, 100mM MES-NMDG, PH 6.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 20, 2020 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 51448 / % possible obs: 46 % / Redundancy: 4.4 % / Biso Wilson estimate: 104.65 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.045 / Rrim(I) all: 0.1 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 3.2→3.635 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.731 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2572 / CC1/2: 0.279 / Rpim(I) all: 0.437 / Rrim(I) all: 0.857 / % possible all: 7.3 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6KPU ![]() 6kpu Resolution: 3.2→14.99 Å / SU ML: 0.4802 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.4043 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 115.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→14.99 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|