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- PDB-7yzr: 50 mM Rb+ soak of beryllium fluoride inhibited Na+,K+-ATPase, E2-... -

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Basic information

Entry
Database: PDB / ID: 7yzr
Title50 mM Rb+ soak of beryllium fluoride inhibited Na+,K+-ATPase, E2-BeFx (rigid body model)
Components
  • FXYD domain-containing ion transport regulator
  • Sodium/potassium-transporting ATPase subunit alpha-1
  • Sodium/potassium-transporting ATPase subunit beta-1
KeywordsMEMBRANE PROTEIN / Pig kidney Na+ / K+-ATPase
Function / homology
Function and homology information


Basigin interactions / Ion homeostasis / Na+/K+-exchanging ATPase / Ion transport by P-type ATPases / positive regulation of sodium ion export across plasma membrane / regulation of monoatomic ion transport / positive regulation of potassium ion import across plasma membrane / sodium ion binding / P-type sodium:potassium-exchanging transporter activity / sodium:potassium-exchanging ATPase complex ...Basigin interactions / Ion homeostasis / Na+/K+-exchanging ATPase / Ion transport by P-type ATPases / positive regulation of sodium ion export across plasma membrane / regulation of monoatomic ion transport / positive regulation of potassium ion import across plasma membrane / sodium ion binding / P-type sodium:potassium-exchanging transporter activity / sodium:potassium-exchanging ATPase complex / membrane repolarization / establishment or maintenance of transmembrane electrochemical gradient / sodium ion export across plasma membrane / positive regulation of potassium ion transmembrane transport / regulation of calcium ion transmembrane transport / intracellular sodium ion homeostasis / ion channel regulator activity / relaxation of cardiac muscle / regulation of cardiac muscle contraction by calcium ion signaling / positive regulation of sodium ion transmembrane transport / organelle membrane / potassium ion import across plasma membrane / potassium ion binding / intracellular potassium ion homeostasis / ATPase activator activity / intercalated disc / lateral plasma membrane / sperm flagellum / transporter activator activity / 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 / ATPase binding / regulation of gene expression / protein-macromolecule adaptor activity / basolateral plasma membrane / cell adhesion / protein stabilization / 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 and potassium ATPases beta subunits signature 2. / 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. ...: / Ion-transport regulator, FXYD motif / : / ATP1G1/PLM/MAT8 family / FXYD family signature. / Sodium and potassium ATPases beta subunits signature 2. / 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. / : / 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 / P-type ATPase, cytoplasmic domain N / P-type ATPase actuator domain / 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
BERYLLIUM TRIFLUORIDE 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: 6.92 Å
AuthorsFruergaard, M.U. / Dach, I. / Andersen, J.L. / Ozol, M. / Shasavar, A. / Quistgaard, E.M. / Poulsen, H. / Fedosova, N.U. / Nissen, P.
Funding support Denmark, 1items
OrganizationGrant numberCountry
LundbeckfondenR155-2015-2666 Denmark
CitationJournal: J.Biol.Chem. / Year: 2022
Title: The Na + ,K + -ATPase in complex with beryllium fluoride mimics an ATPase phosphorylated state.
Authors: Fruergaard, M.U. / Dach, I. / Andersen, J.L. / Ozol, M. / Shahsavar, A. / Quistgaard, E.M. / Poulsen, H. / Fedosova, N.U. / Nissen, P.
History
DepositionFeb 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)309,58610
Polymers309,4056
Non-polymers1814
Water00
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)154,7935
Polymers154,7033
Non-polymers902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-39 kcal/mol
Surface area59900 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)154,7935
Polymers154,7033
Non-polymers902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-40 kcal/mol
Surface area61430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.940, 118.920, 496.900
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: 112666.375 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 / Na(+)/K(+) ATPase beta-1 subunit


Mass: 35073.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P05027
#3: Protein FXYD domain-containing ion transport regulator / Na+/K+ ATPase gamma subunit transcript variant a


Mass: 6962.919 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q58K79
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: 5.97 Å3/Da / Density % sol: 79.4 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: The protein sample was mixed in a 1:1 ratio with reservoir solution containing 16.5 % (wt/vol) polyethylene glycol 2000 monomethyl ether (PEG 2000 MME), 10 % (vol/vol) glycerol, 175 mM ...Details: The protein sample was mixed in a 1:1 ratio with reservoir solution containing 16.5 % (wt/vol) polyethylene glycol 2000 monomethyl ether (PEG 2000 MME), 10 % (vol/vol) glycerol, 175 mM MgCl2, 150 mM NaCl, 20 mM HEPES/MES pH 6.2 and 2 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.8141 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8141 Å / Relative weight: 1
ReflectionResolution: 6.92→24.99 Å / Num. obs: 12121 / % possible obs: 99.5 % / Redundancy: 14.185 % / Biso Wilson estimate: 288.27 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.263 / Rrim(I) all: 0.273 / Χ2: 0.727 / Net I/σ(I): 8.17 / Num. measured all: 171942 / Scaling rejects: 28
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
6.92-7.113.9592.2681.29121168798680.7582.35498.7
7.1-7.2914.5021.9841.56124288578570.782.056100
7.29-7.514.1711.8011.72118198348340.741.869100
7.5-7.7314.5571.32.33115297947920.8971.34799.7
7.73-7.9914.1651.0662.6116158218200.9681.10699.9
7.99-8.2714.9030.9173.33110587427420.9440.95100
8.27-8.5814.790.6634.47111377537530.9630.687100
8.58-8.9314.8530.5335.31104277027020.980.552100
8.93-9.3314.7430.3866.8102616966960.9880.4100
9.33-9.7814.5280.3118.4295016546540.990.322100
9.78-10.3114.6840.24110.3389726116110.9960.249100
10.31-10.9414.3640.20811.5588346156150.9960.216100
10.94-11.6914.3250.19711.9880655635630.9960.204100
11.69-12.6314.2390.17113.7273905195190.9980.177100
12.63-13.8314.0020.13815.8869594974970.9970.143100
13.83-15.4713.5150.11318.4960414474470.9980.117100
15.47-17.8613.5320.09521.2654404024020.9990.099100
17.86-21.8712.5460.07624.943413463460.9980.079100
21.87-30.9311.1560.07227.0431462822820.9970.076100
24.99-30.937.1320.04825.7286317212110.05270.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QTV

7qtv


Resolution: 6.92→24.99 Å / SU ML: 0.9 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 33.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3094 1173 9.92 %
Rwork0.2888 10651 -
obs0.2907 11824 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 698.68 Å2 / Biso mean: 407.5024 Å2 / Biso min: 297.88 Å2
Refinement stepCycle: final / Resolution: 6.92→24.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20660 0 10 0 20670
Biso mean--439.93 --
Num. residues----2630
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
6.92-7.220.41691400.41961292143299
7.22-7.590.38431450.363813061451100
7.59-8.060.31291450.30021324146999
8.06-8.650.27291440.278113011445100
8.65-9.480.27011490.249113211470100
9.48-10.760.27741470.235913541501100
10.76-13.210.26951500.254313561506100
13.21-24.990.3471530.31541397155099

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