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- PDB-7d94: Crystal Structure of the Na+,K+-ATPase in the E2P state with boun... -

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Basic information

Entry
Database: PDB / ID: 7d94
TitleCrystal Structure of the Na+,K+-ATPase in the E2P state with bound one Mg2+ and one Rb+ in the presence of bufalin
Components
  • (Sodium/potassium-transporting ATPase subunit ...) x 2
  • FXYD domain-containing ion transport regulator
KeywordsTRANSPORT PROTEIN / Na+ / K+-ATPase / membrane protein / ion transport / 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
bufalin / CHOLESTEROL / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / RUBIDIUM ION / 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
AuthorsKanai, R. / Cornelius, F. / Ogawa, H. / Motoyama, K. / Vilsen, B. / Toyoshima, C.
Funding support Japan, Denmark, 7items
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
Danish Council for Independent ResearchDFF7016-00193B Denmark
Danish Council for Independent ResearchDFF4183-00011A Denmark
Novo Nordisk FoundationNNF13OC0013409 Denmark
Novo Nordisk FoundationNNF13OC0006555 Denmark
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 12, 2020Deposition site: PDBJ / Processing site: PDBJ
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)320,86235
Polymers309,4056
Non-polymers11,45729
Water1448
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)161,02518
Polymers154,7023
Non-polymers6,32315
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7070 Å2
ΔGint-22 kcal/mol
Surface area58250 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)159,83717
Polymers154,7023
Non-polymers5,13514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7040 Å2
ΔGint-24 kcal/mol
Surface area57970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.570, 117.310, 490.705
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

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

NCS ensembles :
ID
1
2
3

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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: isolated from a genetically manipulated source
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
#11: 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 / N-Acetylglucosamine


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 , 7 types, 31 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-RB / RUBIDIUM ION / Rubidium


Mass: 85.468 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Rb
#8: Chemical
ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C27H46O
#9: 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.: 8 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM
#10: Chemical ChemComp-BUF / bufalin / Bufalin


Mass: 386.524 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H34O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: toxin*YM
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 5.38 Å3/Da / Density % sol: 77.12 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 125-150 mM MgCl2, 18% (w/v) PEG2000MME, 10% (w/v) glycerol, 5 mM GSH, 0.1 mM DTT and 1 mg/ml butylhydroxytoluen, 100 mM MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.813 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 20, 2020
RadiationMonochromator: Si double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.813 Å / Relative weight: 1
ReflectionResolution: 3.4→30 Å / Num. obs: 90801 / % possible obs: 53 % / Redundancy: 3.1 % / Biso Wilson estimate: 93.11 Å2 / CC1/2: 0.973 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.117 / Rrim(I) all: 0.21 / Net I/σ(I): 5.7
Reflection shellResolution: 3.4→3.51 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 0.94 / Num. unique obs: 95 / CC1/2: 0.08 / Rpim(I) all: 0.542 / Rrim(I) all: 0.767 / % possible all: 1.1

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Processing

Software
NameVersionClassification
BSSdata collection
DENZOdata reduction
SCALEPACKdata scaling
STARANISOdata scaling
PHASERphasing
Cootmodel building
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KPZ

6kpz
PDB Unreleased entry


Resolution: 3.5→15 Å / SU ML: 0.5484 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.2726
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2628 3667 4.09 %
Rwork0.2235 85242 -
obs0.2251 85262 55.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 112.31 Å2
Refinement stepCycle: LAST / Resolution: 3.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20690 0 520 8 21218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00521653
X-RAY DIFFRACTIONf_angle_d0.924529398
X-RAY DIFFRACTIONf_chiral_restr0.05373343
X-RAY DIFFRACTIONf_plane_restr0.00786345
X-RAY DIFFRACTIONf_dihedral_angle_d16.72158083
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.550.578390.3446181X-RAY DIFFRACTION3.13
3.55-3.590.3362170.3856333X-RAY DIFFRACTION5.81
3.6-3.640.4281190.3798554X-RAY DIFFRACTION9.34
3.65-3.70.3555310.3437783X-RAY DIFFRACTION13.27
3.7-3.760.4093520.3284967X-RAY DIFFRACTION16.61
3.76-3.820.3649590.35981186X-RAY DIFFRACTION20.25
3.82-3.880.3291570.34041409X-RAY DIFFRACTION23.89
3.88-3.950.3347760.32471565X-RAY DIFFRACTION26.76
3.95-4.030.3304710.3061803X-RAY DIFFRACTION29.95
4.03-4.110.3485670.30021994X-RAY DIFFRACTION33.79
4.11-4.190.2917950.30122204X-RAY DIFFRACTION37.52
4.19-4.290.3172890.27012437X-RAY DIFFRACTION41.01
4.29-4.390.2791060.2612702X-RAY DIFFRACTION45.8
4.39-4.510.32911260.24553084X-RAY DIFFRACTION51.73
4.51-4.640.26481710.24423524X-RAY DIFFRACTION59.9
4.64-4.780.29261730.24474103X-RAY DIFFRACTION69.72
4.78-4.950.28041790.23584549X-RAY DIFFRACTION76.69
4.95-5.140.24992330.24255157X-RAY DIFFRACTION87.1
5.14-5.360.29742480.23745494X-RAY DIFFRACTION93.88
5.36-5.630.28362470.24565768X-RAY DIFFRACTION97.36
5.63-5.960.30582480.24415903X-RAY DIFFRACTION99.95
5.96-6.390.28952570.23875966X-RAY DIFFRACTION99.95
6.39-6.970.24092600.20975835X-RAY DIFFRACTION99.82
6.97-7.850.25392550.18375935X-RAY DIFFRACTION99.97
7.85-9.460.19062370.15685882X-RAY DIFFRACTION99.97
9.46-150.19612570.16745924X-RAY DIFFRACTION99.69

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