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- PDB-7ddk: Crystal structures of Na+,K+-ATPase in complex with rostafuroxin -

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Basic information

Entry
Database: PDB / ID: 7ddk
TitleCrystal structures of Na+,K+-ATPase in complex with rostafuroxin
Components
  • (Sodium/potassium-transporting ATPase subunit ...) x 2
  • FXYD domain-containing ion transport regulator
KeywordsMEMBRANE PROTEIN / Na+ / K+-ATPase / ion transport / Cardiotonic steroids
Function / homology
Function and homology information


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 / transmembrane transport / sarcolemma / 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
: / : / 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
CHOLESTEROL / Chem-E4R / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 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 / Resolution: 3.5 Å
AuthorsOgawa, H. / Cornelius, F. / Kanai, R. / Motoyama, K. / Vilsen, B. / Toyoshima, C.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16K18500 Japan
Japan Society for the Promotion of Science (JSPS)16H02499 Japan
Japan Society for the Promotion of Science (JSPS)19H00975 Japan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
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
DepositionOct 29, 2020Deposition site: PDBJ / Processing site: PDBJ
SupersessionJan 27, 2021ID: 6KQ0
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: FXYD domain-containing ion transport regulator
C: Sodium/potassium-transporting ATPase subunit alpha-1
D: Sodium/potassium-transporting ATPase subunit beta-1
E: FXYD domain-containing ion transport regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)324,99039
Polymers309,4056
Non-polymers15,58533
Water18010
1
A: Sodium/potassium-transporting ATPase subunit alpha-1
B: Sodium/potassium-transporting ATPase subunit beta-1
G: FXYD domain-containing ion transport regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,10119
Polymers154,7023
Non-polymers7,39916
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11310 Å2
ΔGint-71 kcal/mol
Surface area59520 Å2
MethodPISA
2
C: Sodium/potassium-transporting ATPase subunit alpha-1
D: Sodium/potassium-transporting ATPase subunit beta-1
E: FXYD domain-containing ion transport regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,88820
Polymers154,7023
Non-polymers8,18617
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11640 Å2
ΔGint-77 kcal/mol
Surface area59160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.357, 118.176, 494.668
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain 'A'A21 - 1016
211chain 'C'C21 - 1016
112(chain 'B' and (resid 13 through 161 or resid 168 through 303 or resid 1001 through 1021))B13 - 160
122(chain 'B' and (resid 13 through 161 or resid 168 through 303 or resid 1001 through 1021))B168 - 303
132(chain 'B' and (resid 13 through 161 or resid 168 through 303 or resid 1001 through 1021))B1001 - 1002
142(chain 'B' and (resid 13 through 161 or resid 168 through 303 or resid 1001 through 1021))B1011 - 1012
152(chain 'B' and (resid 13 through 161 or resid 168 through 303 or resid 1001 through 1021))B1021
212chain 'D'D13 - 160
222chain 'D'D168 - 303
232chain 'D'D1001 - 1002
242chain 'D'D1011 - 1012
252chain 'D'D1021
113chain 'E'E17 - 48
213chain 'G'G17 - 48
114(chain 'H' and (resid 1105 through 1106 or resid 1202 through 3000))H1105 - 1106
124(chain 'H' and (resid 1105 through 1106 or resid 1202 through 3000))H1202 - 1205
134(chain 'H' and (resid 1105 through 1106 or resid 1202 through 3000))H1212
144(chain 'H' and (resid 1105 through 1106 or resid 1202 through 3000))H1215
154(chain 'H' and (resid 1105 through 1106 or resid 1202 through 3000))H3000
214(chain 'I' and (resid 1106 through 1107 or resid 1203 through 3000))I1106 - 1107
224(chain 'I' and (resid 1106 through 1107 or resid 1203 through 3000))I1203
234(chain 'I' and (resid 1106 through 1107 or resid 1203 through 3000))I1205
244(chain 'I' and (resid 1106 through 1107 or resid 1203 through 3000))I1207 - 1208
254(chain 'I' and (resid 1106 through 1107 or resid 1203 through 3000))I1212
264(chain 'I' and (resid 1106 through 1107 or resid 1203 through 3000))I1215
274(chain 'I' and (resid 1106 through 1107 or resid 1203 through 3000))I3000

NCS ensembles :
ID
1
2
3
4

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Components

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Sodium/potassium-transporting ATPase subunit ... , 2 types, 4 molecules ACBD

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


Mass: 112403.945 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P05024, Na+/K+-exchanging ATPase
#2: Protein Sodium/potassium-transporting ATPase subunit beta-1 / Sodium/potassium-dependent ATPase subunit beta-1


Mass: 35204.402 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P05027

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Protein , 1 types, 2 molecules GE

#3: Protein FXYD domain-containing ion transport regulator / Na+/K+ ATPase gamma subunit transcript variant a


Mass: 7094.115 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q58K79

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Sugars , 2 types, 6 molecules

#4: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#10: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 37 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical
ChemComp-PCW / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / (Z,Z)-4-HYDROXY-N,N,N-TRIMETHYL-10-OXO-7-[(1-OXO-9-OCTADECENYL)OXY]-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-18-EN-1-AMINIUM-4-OXIDE


Mass: 787.121 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM
#8: Chemical ChemComp-E4R / (3S,5R,8R,9S,10S,13S,14S,17S)-17-(furan-3-yl)-10,13-dimethyl-2,3,4,5,6,7,8,9,11,12,15,16-dodecahydro-1H-cyclopenta[a]phenanthrene-3,14,17-triol / Rostafuroxin


Mass: 374.514 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H34O4 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H46O
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 5.67 Å3/Da / Density % sol: 78.32 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 16% PEG2000 MME, 10% GLYCEROL, 200 mM MAGNESIUM CHLORIDE, 5 mM GSH, 0.1 mMDTT, 0.0001% BHT, 100 mM MES-NMDG, PH 6.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 18, 2014
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 49973 / % possible obs: 58.3 % / Redundancy: 16.4 % / Biso Wilson estimate: 89.53 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 10.2
Reflection shellResolution: 3.5→3.61 Å / Rmerge(I) obs: 0.177 / Num. unique obs: 570

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KPU

6kpu
PDB Unreleased entry


Resolution: 3.5→16 Å / SU ML: 0.4788 / Cross valid method: FREE R-VALUE / σ(F): 1.63 / Phase error: 26.413
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2686 2434 4.97 %
Rwork0.2199 46549 -
obs0.2223 48983 57.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 110 Å2
Refinement stepCycle: LAST / Resolution: 3.5→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20690 0 654 10 21354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004821787
X-RAY DIFFRACTIONf_angle_d0.883329591
X-RAY DIFFRACTIONf_chiral_restr0.05223357
X-RAY DIFFRACTIONf_plane_restr0.00786356
X-RAY DIFFRACTIONf_dihedral_angle_d16.7318167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.570.4743130.3523299X-RAY DIFFRACTION6.34
3.57-3.650.3847280.374494X-RAY DIFFRACTION10.75
3.65-3.730.4388290.3579754X-RAY DIFFRACTION15.9
3.73-3.820.4229670.31571075X-RAY DIFFRACTION23.1
3.82-3.930.4222740.31711347X-RAY DIFFRACTION28.98
3.93-4.040.3597860.28831691X-RAY DIFFRACTION36.23
4.04-4.170.40781110.28931932X-RAY DIFFRACTION41.56
4.17-4.310.3391240.27032293X-RAY DIFFRACTION48.91
4.31-4.480.29951260.24312631X-RAY DIFFRACTION55.7
4.48-4.680.26651660.22562913X-RAY DIFFRACTION61.86
4.68-4.920.26841550.21423355X-RAY DIFFRACTION70.58
4.92-5.220.29682120.21323878X-RAY DIFFRACTION82.23
5.22-5.610.30462270.23984577X-RAY DIFFRACTION96.31
5.61-6.140.272540.24444774X-RAY DIFFRACTION99.98
6.14-6.970.26642260.21784818X-RAY DIFFRACTION100
6.97-8.550.22352840.19074800X-RAY DIFFRACTION99.94
8.55-160.19292520.16764918X-RAY DIFFRACTION98.72

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