- PDB-3b8e: Crystal structure of the sodium-potassium pump -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3b8e
Title
Crystal structure of the sodium-potassium pump
Components
(Sodium/potassium-transporting ATPase subunit ...) x 2
Na+/K+ ATPase gamma subunit transcript variant a
Keywords
HYDROLASE/TRANSPORT PROTEIN / Na+ / K+-ATPASE / P-TYPE ATPASE / CATION PUMP / MEMBRANE PROTEIN / HYDROLASE / ATP-BINDING / CALCIUM TRANSPORT / ION TRANSPORT / MEMBRANE POTENTIAL / PHOSPHORYLATION / Magnesium / Metal-binding / Nucleotide-binding / Potassium / Potassium transport / Sodium / Sodium transport / Sodium/potassium transport / Transmembrane / Glycoprotein / Signal-anchor / HYDROLASE-TRANSPORT PROTEIN COMPLEX
Function / homology
Function and homology information
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 / positive regulation of potassium ion import across plasma membrane / Ion transport by P-type ATPases / P-type sodium:potassium-exchanging transporter activity / membrane repolarization / sodium ion binding / sodium:potassium-exchanging ATPase complex ...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 / positive regulation of potassium ion import across plasma membrane / Ion transport by P-type ATPases / P-type sodium:potassium-exchanging transporter activity / membrane repolarization / sodium ion binding / sodium:potassium-exchanging ATPase complex / sodium ion export across plasma membrane / regulation of calcium ion transmembrane transport / intracellular potassium ion homeostasis / establishment or maintenance of transmembrane electrochemical gradient / intracellular sodium ion homeostasis / regulation of cardiac muscle contraction by calcium ion signaling / ion channel regulator activity / relaxation of cardiac muscle / potassium ion import across plasma membrane / ATPase activator activity / potassium ion binding / organelle membrane / intercalated disc / sperm flagellum / lateral plasma membrane / ATP metabolic process / regulation of sodium ion transport / cardiac muscle contraction / T-tubule / proton transmembrane transport / protein localization to plasma membrane / sarcolemma / transmembrane transport / intracellular calcium ion homeostasis / melanosome / protein-macromolecule adaptor activity / ATPase binding / regulation of gene expression / basolateral plasma membrane / protein stabilization / cell adhesion / apical plasma membrane / axon / innate immune response / protein kinase binding / ATP hydrolysis activity / ATP binding / membrane / plasma membrane Similarity search - Function
Mass: 790.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
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Details
Nonpolymer details
THE AUTHORS ONLY SEE DENSITY FOR THE PHOSPHATIDYLCHOLINE LIPID HEAD GROUP AND THEY DO NOT HAVE ANY ...THE AUTHORS ONLY SEE DENSITY FOR THE PHOSPHATIDYLCHOLINE LIPID HEAD GROUP AND THEY DO NOT HAVE ANY EXPERIMENTAL EVIDENCE FOR PC1.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 6.35 Å3/Da / Density % sol: 80.63 %
Resolution: 3.5→3.6 Å / Redundancy: 14 % / Rmerge(I) obs: 1.2 / Mean I/σ(I) obs: 2.56 / Num. unique all: 6208 / % possible all: 100
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Processing
Software
Name
Version
Classification
SHARP
phasing
CNS
1.2
refinement
XDS
datareduction
XSCALE
datascaling
Refinement
Method to determine structure: MIR / Resolution: 3.5→20 Å / Isotropic thermal model: GROUPED B-factors / Stereochemistry target values: Engh & Huber
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.3129
1541
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RANDOM
Rwork
0.2774
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all
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77267
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obs
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76989
99.6 %
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Displacement parameters
Biso mean: 104 Å2
Baniso -1
Baniso -2
Baniso -3
1-
3.508 Å2
0 Å2
0 Å2
2-
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17.739 Å2
0 Å2
3-
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-21.247 Å2
Refine analyze
Free
Obs
Luzzati coordinate error
0.6 Å
0.54 Å
Luzzati d res low
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5 Å
Luzzati sigma a
1.1 Å
1.15 Å
Refinement step
Cycle: LAST / Resolution: 3.5→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
16676
0
42
0
16718
Refine LS restraints
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
c_bond_d
0.008002
X-RAY DIFFRACTION
c_angle_deg
1.51826
X-RAY DIFFRACTION
c_improper_angle_d
1.086
X-RAY DIFFRACTION
c_dihedral_angle_d
22.642
Refine LS restraints NCS
NCS model details: RESTRAINED NCS ON DOMAINS: A(resid 19:80 and 154:274 and 344:382 and 592:765), A(383:591), A(91:153), A(275:343 and 2003:2005), A(766:1016 and B and G) Rms dev Biso: 3 Å2 / Weight position: 500
LS refinement shell
Resolution: 3.5→3.54 Å
Rfactor
Num. reflection
Rfree
0.385
39
Rwork
0.4291
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obs
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2279
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