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- PDB-3ixz: Pig gastric H+/K+-ATPase complexed with aluminium fluoride -

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Basic information

Entry
Database: PDB / ID: 3ixz
TitlePig gastric H+/K+-ATPase complexed with aluminium fluoride
Components
  • Potassium-transporting ATPase alpha
  • Potassium-transporting ATPase subunit beta
KeywordsHYDROLASE / ION PUMP / H+ / K+-ATPASE / P-TYPE ATPASE / MEMBRANE PROTEIN / E2 / ALUMINIUM FLUORIDE / ATP-binding / Hydrogen ion transport / Ion transport / Magnesium / Membrane / Metal-binding / Nucleotide-binding / Phosphoprotein / Potassium / Potassium transport / Transmembrane / Transport / Disulfide bond / Glycoprotein / Signal-anchor
Function / homology
Function and homology information


H+/K+-exchanging ATPase / potassium:proton exchanging ATPase complex / P-type potassium:proton transporter activity / Ion transport by P-type ATPases / P-type sodium:potassium-exchanging transporter activity / sodium:potassium-exchanging ATPase complex / sodium ion export across plasma membrane / intracellular potassium ion homeostasis / intracellular sodium ion homeostasis / potassium ion import across plasma membrane ...H+/K+-exchanging ATPase / potassium:proton exchanging ATPase complex / P-type potassium:proton transporter activity / Ion transport by P-type ATPases / P-type sodium:potassium-exchanging transporter activity / sodium:potassium-exchanging ATPase complex / 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 / potassium ion transmembrane transport / proton transmembrane transport / cell adhesion / apical plasma membrane / magnesium ion binding / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Gastric H+/K+-transporter P-type ATPase, N-terminal / Gastric H+/K+-ATPase, N terminal domain / 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 / haloacid dehalogenase-like hydrolase ...Gastric H+/K+-transporter P-type ATPase, N-terminal / Gastric H+/K+-ATPase, N terminal domain / 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 / haloacid dehalogenase-like hydrolase / 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
Potassium-transporting ATPase subunit beta / Potassium-transporting ATPase alpha chain 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 6.5 Å
AuthorsAbe, K. / Tani, K. / Nishizawa, T. / Fujiyoshi, Y.
CitationJournal: EMBO J / Year: 2009
Title: Inter-subunit interaction of gastric H+,K+-ATPase prevents reverse reaction of the transport cycle.
Authors: Kazuhiro Abe / Kazutoshi Tani / Tomohiro Nishizawa / Yoshinori Fujiyoshi /
Abstract: The gastric H(+),K(+)-ATPase is an ATP-driven proton pump responsible for generating a million-fold proton gradient across the gastric membrane. We present the structure of gastric H(+),K(+)-ATPase ...The gastric H(+),K(+)-ATPase is an ATP-driven proton pump responsible for generating a million-fold proton gradient across the gastric membrane. We present the structure of gastric H(+),K(+)-ATPase at 6.5 A resolution as determined by electron crystallography of two-dimensional crystals. The structure shows the catalytic alpha-subunit and the non-catalytic beta-subunit in a pseudo-E(2)P conformation. Different from Na(+),K(+)-ATPase, the N-terminal tail of the beta-subunit is in direct contact with the phosphorylation domain of the alpha-subunit. This interaction may hold the phosphorylation domain in place, thus stabilizing the enzyme conformation and preventing the reverse reaction of the transport cycle. Indeed, truncation of the beta-subunit N-terminus allowed the reverse reaction to occur. These results suggest that the beta-subunit N-terminus prevents the reverse reaction from E(2)P to E(1)P, which is likely to be relevant for the generation of a large H(+) gradient in vivo situation.
History
DepositionMar 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 18, 2018Group: Author supporting evidence / Data collection
Category: em_image_scans / em_single_particle_entity / em_software
Item: _em_software.image_processing_id
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Assembly

Deposited unit
A: Potassium-transporting ATPase alpha
B: Potassium-transporting ATPase subunit beta


Theoretical massNumber of molelcules
Total (without water)147,5142
Polymers147,5142
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)140.400, 109.000, 320.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Potassium-transporting ATPase alpha / Proton pump / Gastric H(+)/K(+) ATPase subunit alpha / Coordinate model: Cα atoms only


Mass: 114399.688 Da / Num. of mol.: 1 / Fragment: Gastric H+/K+ ATPase subunit alpha / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Strain: Stomach / References: UniProt: P19156, H+/K+-exchanging ATPase
#2: Protein Potassium-transporting ATPase subunit beta / Proton pump beta chain / Gastric H(+)/K(+) ATPase subunit beta / gp60-90 / Coordinate model: Cα atoms only


Mass: 33113.844 Da / Num. of mol.: 1 / Fragment: Gastric H+/K+ ATPase subunit beta / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Strain: Stomach / References: UniProt: P18434

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY / Number of used crystals: 346
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

Component
IDNameTypeDetailsParent-ID
1HK-ATPaseCOMPLEXThis sample was reconstituted into lipids.0
2HK-ATPase alpha subunit1
3HK-ATPase beta subunit1
Buffer solutionName: MES buffer / pH: 4.87 / Details: MES buffer
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: REICHERT-JUNG PLUNGER / Cryogen name: NITROGEN / Chamber temperature: 277 K
Crystal growMethod: microdialysis / pH: 4.87
Details: 20 mM propionate, 1 mM MgCl2, 0.5 mM AlCl3, 4 mM NaF, 0.3 mM ADP, 3 mM DTT, 10% (w/v) glycerol, pH 4.87, MICRODIALYSIS

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Data collection

MicroscopyModel: JEOL KYOTO-3000SFF
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 6000 X / Calibrated magnification: 59100 X / Nominal defocus max: 390 nm / Nominal defocus min: 3480 nm / Cs: 1.6 mm
Specimen holderTemperature: 4.2 K / Tilt angle max: 73.3 ° / Tilt angle min: 0 °
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM
DiffractionMean temperature: 4.2 K
DetectorDate: Apr 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: electron
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 4772

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Processing

Software
NameClassification
MRCmodel building
MRCphasing
EM software
IDNameCategory
1Situsmodel fitting
2MRC3D reconstruction
CTF correctionDetails: Each images were CTF corrected.
3D reconstructionMethod: crystallography / Resolution: 6.5 Å / Nominal pixel size: 1.17 Å / Actual pixel size: 1.17 Å / Magnification calibration: carbon grating / Symmetry type: 2D CRYSTAL
Atomic model building
IDProtocolSpaceTarget criteriaDetails
1RIGID BODY FITREALCross-correlation coefficientMETHOD--Local refinement REFINEMENT PROTOCOL--rigid body
2RIGID BODY FITREALCross-correlation coefficientMETHOD--Local refinement REFINEMENT PROTOCOL--rigid body
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
13B8E

3b8e

13B8E1PDBexperimental model
23B8E

3b8e

23B8E1PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms1044 0 0 0 1044

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