+Open data
-Basic information
Entry | Database: PDB / ID: 2xzb | ||||||
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Title | Pig Gastric H,K-ATPase with bound BeF and SCH28080 | ||||||
Components |
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Keywords | HYDROLASE / 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 / 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 | ||||||
Biological species | SUS SCROFA (pig) | ||||||
Method | ELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 7 Å | ||||||
Authors | Abe, K. / Tani, K. / Fujiyoshi, Y. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 2xzb.cif.gz | 212.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xzb.ent.gz | 163.6 KB | Display | PDB format |
PDBx/mmJSON format | 2xzb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xzb_validation.pdf.gz | 782.9 KB | Display | wwPDB validaton report |
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Full document | 2xzb_full_validation.pdf.gz | 988.8 KB | Display | |
Data in XML | 2xzb_validation.xml.gz | 70.8 KB | Display | |
Data in CIF | 2xzb_validation.cif.gz | 97 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xz/2xzb ftp://data.pdbj.org/pub/pdb/validation_reports/xz/2xzb | HTTPS FTP |
-Related structure data
Related structure data | 1831MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Protein | 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 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON CRYSTALLOGRAPHY / Number of used crystals: 515 |
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EM experiment | Aggregation state: 2D ARRAY / 3D reconstruction method: electron crystallography |
-Sample preparation
Component | Name: Gastric H,K-ATPase with bound BeF and SCH28080 / Type: COMPLEX |
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Buffer solution | pH: 5.5 Details: 20mM MES, 20mM Mg(CH3COO)2, 5mM ATP, 10%(v/v) glycerol, 3mM DTT |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: REICHERT-JUNG PLUNGER / Cryogen name: NITROGEN |
Crystal grow | pH: 5.5 / Details: pH 5.5 |
-Data collection
Microscopy | Model: JEOL KYOTO-3000SFF / Date: Mar 29, 2010 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 40000 X / Nominal defocus max: 4130 nm / Nominal defocus min: 580 nm |
Image recording | Electron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Diffraction | Mean temperature: 4.5 K |
Detector | Date: Mar 29, 2010 |
Radiation | Scattering type: electron |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 7→140.9 Å / Num. obs: 6801 / Redundancy: 12.9 % |
-Processing
Software | Name: MRC / Classification: data scaling | ||||||||||||
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3D reconstruction | Resolution: 7 Å / Resolution method: OTHER / Symmetry type: 2D CRYSTAL | ||||||||||||
Refinement | Resolution: 7→129 Å / Num. reflection obs: 6801 / σ(F): 0 Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1831. | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 7→129 Å
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