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- PDB-2xzb: Pig Gastric H,K-ATPase with bound BeF and SCH28080 -

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Basic information

Entry
Database: PDB / ID: 2xzb
TitlePig Gastric H,K-ATPase with bound BeF and SCH28080
Components
  • POTASSIUM-TRANSPORTING ATPASE ALPHA CHAIN 1
  • POTASSIUM-TRANSPORTING ATPASE SUBUNIT BETA
KeywordsHYDROLASE / ION PUMP / H/K-ATPASE / P-TYPE ATPASE / MEMBRANE PROTEIN / BERYLLIUM FLUORIDE / ATP-BINDING / ACID SUPPRESSANT
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 / ATPase activator activity / potassium ion binding / 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 / Cation-transporting P-type ATPase, C-terminal ...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: 7 Å
AuthorsAbe, K. / Tani, K. / Fujiyoshi, Y.
CitationJournal: Nat Commun / Year: 2011
Title: Conformational rearrangement of gastric H(+),K(+)-ATPase induced by an acid suppressant.
Authors: Kazuhiro Abe / Kazutoshi Tani / Yoshinori Fujiyoshi /
Abstract: Acid-related gastric diseases are associated with disorder of digestive tract acidification. The gastric proton pump, H(+),K(+)-ATPase, exports H(+) in exchange for luminal K(+) to generate a highly ...Acid-related gastric diseases are associated with disorder of digestive tract acidification. The gastric proton pump, H(+),K(+)-ATPase, exports H(+) in exchange for luminal K(+) to generate a highly acidic environment in the stomach, and is a main target for acid suppressants. Here, we report the three-dimensional structure of gastric H(+),K(+)-ATPase with bound SCH28080, a representative K(+)-competitive acid blocker, at 7 Å resolution based on electron crystallography of two-dimensional crystals. The density of the bound SCH28080 is found near transmembrane (TM) helices 4, 5 and 6, in the luminal cavity. The SCH28080-binding site is formed by the rearrangement of TM helices, which is in turn transmitted to the cytoplasmic domains, resulting in a luminal-open conformation. These results represent the first structural evidence for a binding site of an acid suppressant on H(+),K(+)-ATPase, and the conformational change induced by this class of drugs.
History
DepositionNov 24, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Other / Version format compliance
Revision 1.2Apr 11, 2012Group: Other
Revision 1.3Sep 16, 2020Group: Author supporting evidence / Data collection / Derived calculations
Category: diffrn_radiation / em_image_scans ...diffrn_radiation / em_image_scans / em_single_particle_entity / pdbx_struct_sheet_hbond / struct_conf / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _diffrn_radiation.pdbx_scattering_type

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Assembly

Deposited unit
A: POTASSIUM-TRANSPORTING ATPASE ALPHA CHAIN 1
B: POTASSIUM-TRANSPORTING ATPASE SUBUNIT BETA


Theoretical massNumber of molelcules
Total (without water)147,5142
Polymers147,5142
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)140.900, 111.300, 320.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein POTASSIUM-TRANSPORTING ATPASE ALPHA CHAIN 1 / H\ / K-ATPASE / GASTRIC H(+)/K(+) ATPASE SUBUNIT ALPHA / PROTON PUMP


Mass: 114399.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: STOMACH / References: UniProt: P19156, H+/K+-exchanging ATPase
#2: Protein POTASSIUM-TRANSPORTING ATPASE SUBUNIT BETA / H\ / K-ATPASE / GASTRIC H(+)/K(+) ATPASE SUBUNIT BETA / PROTON PUMP BETA CHAIN / GP60-90


Mass: 33113.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: STOMACH / References: UniProt: P18434, H+/K+-exchanging ATPase

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY / Number of used crystals: 515
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: Gastric H,K-ATPase with bound BeF and SCH28080 / Type: COMPLEX
Buffer solutionpH: 5.5
Details: 20mM MES, 20mM Mg(CH3COO)2, 5mM ATP, 10%(v/v) glycerol, 3mM DTT
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: REICHERT-JUNG PLUNGER / Cryogen name: NITROGEN
Crystal growpH: 5.5 / Details: pH 5.5

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Data collection

MicroscopyModel: JEOL KYOTO-3000SFF / Date: Mar 29, 2010
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 40000 X / Nominal defocus max: 4130 nm / Nominal defocus min: 580 nm
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM
DiffractionMean temperature: 4.5 K
DetectorDate: Mar 29, 2010
RadiationScattering type: electron
Radiation wavelengthRelative weight: 1
ReflectionResolution: 7→140.9 Å / Num. obs: 6801 / Redundancy: 12.9 %

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Processing

SoftwareName: MRC / Classification: data scaling
3D reconstructionResolution: 7 Å / Resolution method: OTHER / Symmetry type: 2D CRYSTAL
RefinementResolution: 7→129 Å / Num. reflection obs: 6801 / σ(F): 0
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1831.
Refinement stepCycle: LAST / Resolution: 7→129 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8983 0 0 0 8983

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