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- PDB-7z04: 10 mM Rb+ soak of beryllium fluoride inhibited Na+,K+-ATPase, E2-... -

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Basic information

Entry
Database: PDB / ID: 7z04
Title10 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: 7.5 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 22, 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 6, 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

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)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 area6450 Å2
ΔGint-47 kcal/mol
Surface area62060 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 area6350 Å2
ΔGint-45 kcal/mol
Surface area62300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.000, 119.150, 498.240
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-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / 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: 5.99 Å3/Da / Density % sol: 79.48 %
Crystal growTemperature: 288.15 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: 7.5→25 Å / Num. obs: 9614 / % possible obs: 99.4 % / Redundancy: 13.975 % / Biso Wilson estimate: 379.64 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.301 / Rrim(I) all: 0.313 / Χ2: 0.751 / Net I/σ(I): 7.78 / Num. measured all: 134354 / Scaling rejects: 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
7.5-7.712.8032.6591.436990.5882.77299.3
7.7-7.9114.122.1532.086860.7932.233100
7.91-8.1414.3771.5592.686450.921.616100
8.14-8.3914.8951.4273.126550.8971.478100
8.39-8.6614.6991.0573.976140.9181.095100
8.66-8.9714.8420.8424.866070.9550.872100
8.97-9.3114.4390.6125.735900.980.635100
9.31-9.6914.7840.5147.25510.9780.532100
9.69-10.1214.4080.3948.235570.9870.409100
10.12-10.6114.6620.3628.925170.9920.375100
10.61-11.1814.2780.39.894970.9890.312100
11.18-11.8614.1240.27210.364830.9930.283100
11.86-12.6814.390.25311.114390.9940.263100
12.68-13.713.7760.21612.274160.9910.224100
13.7-15.0113.6170.17413.464070.990.181100
15.01-16.7813.6510.15115.13520.9870.157100
16.78-19.3712.9460.13116.153130.9960.137100
19.37-23.7312.0690.1118.982880.9830.115100
23.73-33.559.6070.0618.9621410.06499.5
33.55-48.985.8210.05317.018410.05861.8

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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: 7.5→25 Å / SU ML: 1.17 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 35.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.338 941 10.08 %
Rwork0.3025 8395 -
obs0.3062 9336 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 752.14 Å2 / Biso mean: 480.1288 Å2 / Biso min: 43.67 Å2
Refinement stepCycle: final / Resolution: 7.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20698 0 10 0 20708
Biso mean--553.61 --
Num. residues----2634
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
7.5-7.890.38641320.36411175130799
7.89-8.360.38341320.339911731305100
8.36-8.980.38821310.310511781309100
8.98-9.830.33851300.287712021332100
9.83-11.150.2971320.276412001332100
11.15-13.650.28531380.269512031341100
13.65-250.36321460.320412641410100

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