+Open data
-Basic information
Entry | Database: PDB / ID: 2yn9 | ||||||
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Title | Cryo-EM structure of gastric H+,K+-ATPase with bound rubidium | ||||||
Components |
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Keywords | HYDROLASE / P-TYPE ATPASE / PROTON PUMP | ||||||
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: 8 Å | ||||||
Authors | Abe, K. / Tani, K. / Friedrich, T. / Fujiyoshi, Y. | ||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2012 Title: Cryo-EM structure of gastric H+,K+-ATPase with a single occupied cation-binding site. Authors: Kazuhiro Abe / Kazutoshi Tani / Thomas Friedrich / Yoshinori Fujiyoshi / Abstract: Gastric H(+),K(+)-ATPase is responsible for gastric acid secretion. ATP-driven H(+) uptake into the stomach is efficiently accomplished by the exchange of an equal amount of K(+), resulting in a ...Gastric H(+),K(+)-ATPase is responsible for gastric acid secretion. ATP-driven H(+) uptake into the stomach is efficiently accomplished by the exchange of an equal amount of K(+), resulting in a luminal pH close to 1. Because of the limited free energy available for ATP hydrolysis, the stoichiometry of transported cations is thought to vary from 2H(+)/2K(+) to 1H(+)/1K(+) per hydrolysis of one ATP molecule as the luminal pH decreases, although direct evidence for this hypothesis has remained elusive. Here, we show, using the phosphate analog aluminum fluoride (AlF) and a K(+) congener (Rb(+)), the 8-Å resolution structure of H(+),K(+)-ATPase in the transition state of dephosphorylation, (Rb(+))E2~AlF, which is distinct from the preceding Rb(+)-free E2P state. A strong density located in the transmembrane cation-binding site of (Rb(+))E2~AlF highly likely represents a single bound Rb(+) ion, which is clearly different from the Rb(+)-free E2AlF or K(+)-bound (K(+))E2~AlF structures. Measurement of radioactive (86)Rb(+) binding suggests that the binding stoichiometry varies depending on the pH, and approximately half of the amount of Rb(+) is bound under acidic crystallization conditions compared with at a neutral pH. These data represent structural and biochemical evidence for the 1H(+)/1K(+)/1ATP transport mode of H(+),K(+)-ATPase, which is a prerequisite for generation of the 10(6)-fold proton gradient in terms of thermodynamics. Together with the released E2P-stabilizing interaction between the β subunit's N terminus and the P domain observed in the (Rb(+))E2~AlF structure, we propose a refined vectorial transport model of H(+),K(+)-ATPase, which must prevail against the highly acidic state of the gastric lumen. | ||||||
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 | 2yn9.cif.gz | 225.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yn9.ent.gz | 174.3 KB | Display | PDB format |
PDBx/mmJSON format | 2yn9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yn9_validation.pdf.gz | 717.1 KB | Display | wwPDB validaton report |
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Full document | 2yn9_full_validation.pdf.gz | 893 KB | Display | |
Data in XML | 2yn9_validation.xml.gz | 66.4 KB | Display | |
Data in CIF | 2yn9_validation.cif.gz | 93.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yn/2yn9 ftp://data.pdbj.org/pub/pdb/validation_reports/yn/2yn9 | HTTPS FTP |
-Related structure data
Related structure data | 2219MC 2220C 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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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 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON CRYSTALLOGRAPHY / Number of used crystals: 248 |
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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 rubidium / Type: COMPLEX |
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Buffer solution | pH: 4.8 Details: 20mM propionate, 1mM ADP, 3mM DTT,pH 4.8-4.9 adjusted by Tris, 1mM MgCl2, 1mM AlCl3, 4mM NaF, 10mM RbCl |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: LEICA KF80 / Cryogen name: NITROGEN |
Crystal grow | pH: 4.8 / Details: pH 4.8 |
-Data collection
Microscopy | Model: JEOL KYOTO-3000SFF / Date: Mar 23, 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: 3480 nm / Nominal defocus min: 830 nm |
Image recording | Film or detector model: KODAK SO-163 FILM |
Diffraction | Mean temperature: 4 K |
Detector | Date: Mar 23, 2010 |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 8→129 Å / Num. obs: 39197 / % possible obs: 73.2 % |
-Processing
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3D reconstruction | Resolution: 8 Å / Symmetry type: 2D CRYSTAL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 8→129 Å / Num. reflection obs: 4166 / σ(F): 0 Details: ALL REGIONS WERE MODELED STEREOCHEMICALLY. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2219. (DEPOSITION ID: 11197). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 8→129 Å
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