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- PDB-7x20: Crystal structure of non gastric H,K-ATPase alpha2 in (K+)E2-AlF state -

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Basic information

Entry
Database: PDB / ID: 7x20
TitleCrystal structure of non gastric H,K-ATPase alpha2 in (K+)E2-AlF state
Components
  • Potassium-transporting ATPase alpha chain 2
  • Sodium/potassium-transporting ATPase subunit beta-1
KeywordsMEMBRANE PROTEIN / P-type ATPase / transporter / proton pump / colon / kidney / airway
Function / homology
Function and homology information


Basigin interactions / H+/K+-exchanging ATPase / Ion transport by P-type ATPases / P-type potassium:proton transporter activity / Na+/K+-exchanging ATPase / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / P-type sodium:potassium-exchanging transporter activity / sodium:potassium-exchanging ATPase complex / membrane repolarization ...Basigin interactions / H+/K+-exchanging ATPase / Ion transport by P-type ATPases / P-type potassium:proton transporter activity / Na+/K+-exchanging ATPase / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / P-type sodium:potassium-exchanging transporter activity / sodium:potassium-exchanging ATPase complex / membrane repolarization / metal ion transport / regulation of pH / sodium ion export across plasma membrane / potassium ion homeostasis / positive regulation of potassium ion transmembrane transport / intracellular sodium ion homeostasis / regulation of calcium ion transmembrane transport / response to metal ion / relaxation of cardiac muscle / regulation of cardiac muscle contraction by calcium ion signaling / Ion homeostasis / positive regulation of sodium ion transmembrane transport / sodium ion transport / organelle membrane / potassium ion import across plasma membrane / intracellular potassium ion homeostasis / ATPase activator activity / intercalated disc / lateral plasma membrane / blastocyst development / sperm flagellum / transporter activator activity / ATP metabolic process / cardiac muscle contraction / T-tubule / sodium ion transmembrane transport / proton transmembrane transport / protein localization to plasma membrane / sarcolemma / caveola / potassium ion transport / transmembrane transport / intracellular calcium ion homeostasis / ATPase binding / regulation of gene expression / protein-macromolecule adaptor activity / basolateral plasma membrane / response to hypoxia / cell adhesion / protein stabilization / apical plasma membrane / protein heterodimerization activity / innate immune response / protein kinase binding / ATP hydrolysis activity / ATP binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
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 / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / Cation-transporting P-type ATPase, C-terminal ...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 / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TETRAFLUOROALUMINATE ION / : / Sodium/potassium-transporting ATPase subunit beta-1 / Potassium-transporting ATPase alpha chain 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsNakanishi, H. / Abe, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21H02426 Japan
CitationJournal: Nat Commun / Year: 2022
Title: Structure and function of H/K pump mutants reveal Na/K pump mechanisms.
Authors: Victoria C Young / Hanayo Nakanishi / Dylan J Meyer / Tomohiro Nishizawa / Atsunori Oshima / Pablo Artigas / Kazuhiro Abe /
Abstract: Ion-transport mechanisms evolve by changing ion-selectivity, such as switching from Na to H selectivity in secondary-active transporters or P-type-ATPases. Here we study primary-active transport via ...Ion-transport mechanisms evolve by changing ion-selectivity, such as switching from Na to H selectivity in secondary-active transporters or P-type-ATPases. Here we study primary-active transport via P-type ATPases using functional and structural analyses to demonstrate that four simultaneous residue substitutions transform the non-gastric H/K pump, a strict H-dependent electroneutral P-type ATPase, into a bona fide Na-dependent electrogenic Na/K pump. Conversion of a H-dependent primary-active transporter into a Na-dependent one provides a prototype for similar studies of ion-transport proteins. Moreover, we solve the structures of the wild-type non-gastric H/K pump, a suitable drug target to treat cystic fibrosis, and of its Na/K pump-mimicking mutant in two major conformations, providing insight on how Na binding drives a concerted mechanism leading to Na/K pump phosphorylation.
History
DepositionFeb 25, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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: Potassium-transporting ATPase alpha chain 2
B: Sodium/potassium-transporting ATPase subunit beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,0046
Polymers146,6022
Non-polymers4024
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-15 kcal/mol
Surface area56050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.970, 109.060, 267.670
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

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Potassium-transporting ATPase alpha chain 2 / HK alpha 2 / Non-gastric H(+)/K(+) ATPase subunit alpha / Non-gastric Na(+)/K(+) ATPase subunit ...HK alpha 2 / Non-gastric H(+)/K(+) ATPase subunit alpha / Non-gastric Na(+)/K(+) ATPase subunit alpha / Proton pump / Sodium pump


Mass: 109084.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Atp12a, Atp1al1 / Production host: Homo sapiens (human)
References: UniProt: P54708, H+/K+-exchanging ATPase, Na+/K+-exchanging ATPase
#2: Protein Sodium/potassium-transporting ATPase subunit beta-1 / Sodium/potassium-dependent ATPase subunit beta-1


Mass: 37516.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Atp1b1 / Production host: Homo sapiens (human) / References: UniProt: P07340

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Sugars , 1 types, 1 molecules

#5: 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.: 1 / 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 , 3 types, 4 molecules

#3: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.89 Å3/Da / Density % sol: 68.39 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 33% PEG 300, 50mM Glycine-NaOH pH 9.5, 100mM NaCl, 200mM KCl, 0.1mM AlCl3, 0.4mM NaF

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→48.06 Å / Num. obs: 68181 / % possible obs: 72.54 % / Redundancy: 2 % / Biso Wilson estimate: 49.39 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.049 / Net I/σ(I): 8.36
Reflection shellResolution: 3.3→3.42 Å / Rmerge(I) obs: 0.83 / Num. unique obs: 6682 / CC1/2: 0.768

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
Coot0.9.1model building
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6jxh

6jxh


Resolution: 3.3→48.06 Å / SU ML: 0.5458 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 33.2991
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.316 1264 5.07 %
Rwork0.2645 23655 -
obs0.2671 24919 72.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.9 Å2
Refinement stepCycle: LAST / Resolution: 3.3→48.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10019 0 21 1 10041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011510241
X-RAY DIFFRACTIONf_angle_d1.392313880
X-RAY DIFFRACTIONf_chiral_restr0.07471589
X-RAY DIFFRACTIONf_plane_restr0.01081766
X-RAY DIFFRACTIONf_dihedral_angle_d13.653792
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.430.5143250.4584540X-RAY DIFFRACTION15.07
3.43-3.590.4713580.3856895X-RAY DIFFRACTION25.43
3.59-3.780.3927820.32811526X-RAY DIFFRACTION42.87
3.78-4.010.34091380.28382586X-RAY DIFFRACTION72.24
4.01-4.320.34341780.2583420X-RAY DIFFRACTION95.9
4.32-4.760.29881940.24043606X-RAY DIFFRACTION99.35
4.76-5.450.27891810.24373624X-RAY DIFFRACTION99.53
5.45-6.860.33422050.2963652X-RAY DIFFRACTION99.82
6.86-48.060.2682030.23873806X-RAY DIFFRACTION99.28
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.267812079513-0.1612228030380.7087829451730.990640262593-1.457642809591.98444591128-0.030876856030.09703520859210.03128276222160.09123748400710.0908285074368-0.110520463442-0.324915176844-0.274747572685-0.05663605181940.3394396857170.1053603410270.1063921059780.20401105419-0.07914659065760.293472873949-14.73370558210.1273591538-40.3635732714
21.771088212650.328505252555-0.9557403938681.43555696244-0.3288656767923.77710352920.05018444827550.764014702950.280728627017-1.243926801430.0517000057561-0.07851779298140.542240087259-0.201419092396-0.1647431774761.126884021250.3043911962580.0389575581290.8637551634610.09802926481590.4631572679237.996083651969.49112440375-79.9241076325
30.446185390908-0.406426045508-0.2969228215760.62067380694-0.5862436434850.9146324337280.1243076623460.1002171763550.0189609977843-0.200395995644-0.05535471615350.03448979856030.5740085875660.231195123213-0.1048825031170.2300120041050.0986526424960.0381785598617-0.207140242966-0.0590007370710.301289836785-4.40311183142-8.34729612142-18.3816114474
41.17925309772-0.00823094932197-0.2747696401891.37854094697-0.1675190101880.0818149827472-0.1660594674910.758093789879-0.514094439665-0.637421294167-0.0633868550450.6210745913110.231957130372-0.1082425559680.0857331843052-0.0632170284001-0.7618358216890.06787284289150.600863396059-0.1369020451740.341666624143-8.50951277979-28.852044371-4.67786371236
50.85920867310.140104567856-0.4006755570280.4239691145330.2654502978361.605316112930.3760408793160.337664538341-0.1388176894670.178635055148-0.3523228831540.1977533045110.0190057014631-0.6270726570450.03553896020.3834728996390.0294921788042-0.2266741522580.701911927760.01499703051240.194547111114-11.0940822236-5.3723422789442.3418443859
64.64939216888-1.06751462349-0.9864173989033.07930611024-0.4375078639553.464081204420.0821171987463-0.5610099321190.2593845459250.456328833120.0495903674203-0.615846278294-0.122992320967-0.000453639805353-0.1399201234960.3507659108710.0996430647816-0.1390708909130.5824861075890.04109482446560.161653573058-1.67768014135-2.2687448446648.1357205845
72.40919127707-0.6493912893740.4138166137562.1619693344-0.4533170224831.63593914763-0.1713667256010.057449039750.131157863802-0.02488824136480.127085691426-0.0538058459483-0.8504833872680.02251708544750.01530222224770.57167715238-0.0301026018388-0.04584352141820.4155927010630.006947850666340.155085094225-7.394876965926.6900900542342.9295532844
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 51 through 462 )AA51 - 4621 - 412
22chain 'A' and (resid 463 through 610 )AA463 - 610413 - 560
33chain 'A' and (resid 611 through 1036 )AA611 - 1036561 - 986
44chain 'B' and (resid 17 through 60 )BC17 - 601 - 44
55chain 'B' and (resid 61 through 131 )BC61 - 13145 - 115
66chain 'B' and (resid 132 through 210 )BC132 - 210116 - 194
77chain 'B' and (resid 211 through 304 )BC211 - 304195 - 288

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