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- PDB-3n23: Crystal structure of the high affinity complex between ouabain an... -

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Basic information

Entry
Database: PDB / ID: 3n23
TitleCrystal structure of the high affinity complex between ouabain and the E2P form of the sodium-potassium pump
Components
  • Na+/K+ ATPase gamma subunit transcript variant a
  • Sodium/potassium-transporting ATPase subunit alpha-1
  • Sodium/potassium-transporting ATPase subunit beta-1
KeywordsHYDROLASE / sodium-potassium pump / P-type ATPase / ouabain / cardiotonic steroids
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 / lateral plasma membrane / sperm flagellum / 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
: / : / Ion-transport regulator, FXYD motif / ATP1G1/PLM/MAT8 family / FXYD family signature. / Sodium/potassium-transporting ATPase subunit beta / Sodium/potassium-transporting ATPase subunit beta superfamily / Sodium / potassium ATPase beta chain / Sodium and potassium ATPases beta subunits signature 1. / Sodium and potassium ATPases beta subunits signature 2. ...: / : / Ion-transport regulator, FXYD motif / ATP1G1/PLM/MAT8 family / FXYD family signature. / Sodium/potassium-transporting ATPase subunit beta / Sodium/potassium-transporting ATPase subunit beta superfamily / Sodium / potassium ATPase beta chain / Sodium and potassium ATPases beta subunits signature 1. / Sodium and potassium ATPases beta subunits signature 2. / P-type ATPase subfamily IIC, subunit alpha / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / Cation transport ATPase (P-type) / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
OUABAIN / Sodium/potassium-transporting ATPase subunit alpha-1 / Sodium/potassium-transporting ATPase subunit beta-1 / FXYD domain-containing ion transport regulator
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / ML / Resolution: 4.6 Å
AuthorsYatime, L. / Laursen, M. / Morth, J.P. / Esmann, M. / Nissen, P. / Fedosova, N.U.
CitationJournal: J.Struct.Biol. / Year: 2011
Title: Structural insights into the high affinity binding of cardiotonic steroids to the Na+,K+-ATPase.
Authors: Yatime, L. / Laursen, M. / Morth, J.P. / Esmann, M. / Nissen, P. / Fedosova, N.U.
History
DepositionMay 17, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 17, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sodium/potassium-transporting ATPase subunit alpha-1
B: Sodium/potassium-transporting ATPase subunit beta-1
G: Na+/K+ ATPase gamma subunit transcript variant a
C: Sodium/potassium-transporting ATPase subunit alpha-1
D: Sodium/potassium-transporting ATPase subunit beta-1
E: Na+/K+ ATPase gamma subunit transcript variant a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)291,74910
Polymers290,5326
Non-polymers1,2184
Water0
1
A: Sodium/potassium-transporting ATPase subunit alpha-1
B: Sodium/potassium-transporting ATPase subunit beta-1
G: Na+/K+ ATPase gamma subunit transcript variant a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,8755
Polymers145,2663
Non-polymers6092
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-37 kcal/mol
Surface area58680 Å2
MethodPISA
2
C: Sodium/potassium-transporting ATPase subunit alpha-1
D: Sodium/potassium-transporting ATPase subunit beta-1
E: Na+/K+ ATPase gamma subunit transcript variant a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,8755
Polymers145,2663
Non-polymers6092
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-37 kcal/mol
Surface area58620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.160, 118.930, 494.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sodium/potassium-transporting ATPase subunit alpha-1 / Na(+)/K(+) ATPase alpha-1 subunit / Sodium pump subunit alpha-1


Mass: 109669.891 Da / Num. of mol.: 2 / Fragment: ALPHA chain (UNP RESIDUES 30-1021) / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P05024, EC: 3.6.3.9
#2: Protein Sodium/potassium-transporting ATPase subunit beta-1 / Sodium/potassium-dependent ATPase subunit beta-1


Mass: 32129.859 Da / Num. of mol.: 2 / Fragment: BETA chain (UNP RESIDUES 27-303) / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P05027
#3: Protein/peptide Na+/K+ ATPase gamma subunit transcript variant a


Mass: 3466.012 Da / Num. of mol.: 2 / Fragment: GAMMA chain (UNP RESIDUES 17-47) / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q58K79
#4: Chemical ChemComp-OBN / OUABAIN / Ouabain


Mass: 584.652 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H44O12
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.92 Å3/Da / Density % sol: 79.24 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 16% PEG 2000 MME, 10% glycerol, 0.2M magnesium chloride, 100mM MES, 1.5mM N-decanoylsucrose, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 18, 2009
RadiationMonochromator: Si(311) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 4.6→50 Å / Num. all: 39359 / Num. obs: 39359 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.5 % / Biso Wilson estimate: 190 Å2 / Rsym value: 0.133 / Net I/σ(I): 10.85
Reflection shellResolution: 4.6→4.8 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 2.06 / Num. unique all: 4646 / Rsym value: 0.944 / % possible all: 99.9

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Phasing

PhasingMethod: ML

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
CNSrefinement
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
MxCuBEdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.6→39.554 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.716 / SU ML: 0.75 / σ(F): 1.99 / Phase error: 33.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.302 1972 5.02 %random
Rwork0.272 ---
all0.273 39261 --
obs0.273 39261 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 227.296 Å2 / ksol: 0.297 e/Å3
Displacement parametersBiso max: 549.87 Å2 / Biso mean: 277.661 Å2 / Biso min: 63.27 Å2
Baniso -1Baniso -2Baniso -3
1-108.735 Å20 Å2-0 Å2
2--16.747 Å2-0 Å2
3----60.135 Å2
Refinement stepCycle: LAST / Resolution: 4.6→39.554 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20188 0 84 0 20272
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00720710
X-RAY DIFFRACTIONf_angle_d0.89528102
X-RAY DIFFRACTIONf_chiral_restr0.0553200
X-RAY DIFFRACTIONf_plane_restr0.0053594
X-RAY DIFFRACTIONf_dihedral_angle_d18.2997686
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.6-4.7150.3591400.35626182758100
4.715-4.8420.3721450.33625902735100
4.842-4.9840.4011350.31426312766100
4.984-5.1450.3531440.30426292773100
5.145-5.3280.3491250.29126342759100
5.328-5.5410.311370.30526372774100
5.541-5.7930.3441360.2926142750100
5.793-6.0970.3131460.29926512797100
6.097-6.4770.3311510.27226492800100
6.477-6.9750.2881350.24426902825100
6.975-7.6720.2531390.20926602799100
7.672-8.7720.211340.18327152849100
8.772-11.0120.2031640.16927182882100
11.012-39.5550.3151410.3112853299499

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