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Yorodumi- PDB-4ux1: Cryo-EM structure of antagonist-bound E2P gastric H,K-ATPase (SCH... -
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-Basic information
Entry | Database: PDB / ID: 4ux1 | ||||||
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Title | Cryo-EM structure of antagonist-bound E2P gastric H,K-ATPase (SCH.E2. AlF) | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / POTASSIUM-TRANSPORTING ATPASE | ||||||
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. / Fujiyoshi, Y. | ||||||
Citation | Journal: J Biol Chem / Year: 2014 Title: Systematic comparison of molecular conformations of H+,K+-ATPase reveals an important contribution of the A-M2 linker for the luminal gating. Authors: Kazuhiro Abe / Kazutoshi Tani / Yoshinori Fujiyoshi / Abstract: Gastric H(+),K(+)-ATPase, an ATP-driven proton pump responsible for gastric acidification, is a molecular target for anti-ulcer drugs. Here we show its cryo-electron microscopy (EM) structure in an ...Gastric H(+),K(+)-ATPase, an ATP-driven proton pump responsible for gastric acidification, is a molecular target for anti-ulcer drugs. Here we show its cryo-electron microscopy (EM) structure in an E2P analog state, bound to magnesium fluoride (MgF), and its K(+)-competitive antagonist SCH28080, determined at 7 Å resolution by electron crystallography of two-dimensional crystals. Systematic comparison with other E2P-related cryo-EM structures revealed that the molecular conformation in the (SCH)E2·MgF state is remarkably distinguishable. Although the azimuthal position of the A domain of the (SCH)E2·MgF state is similar to that in the E2·AlF (aluminum fluoride) state, in which the transmembrane luminal gate is closed, the arrangement of transmembrane helices in the (SCH)E2·MgF state shows a luminal-open conformation imposed on by bound SCH28080 at its luminal cavity, based on observations of the structure in the SCH28080-bound E2·BeF (beryllium fluoride) state. The molecular conformation of the (SCH)E2·MgF state thus represents a mixed overall structure in which its cytoplasmic and luminal half appear to be independently modulated by a phosphate analog and an antagonist bound to the respective parts of the enzyme. Comparison of the molecular conformations revealed that the linker region connecting the A domain and the transmembrane helix 2 (A-M2 linker) mediates the regulation of luminal gating. The mechanistic rationale underlying luminal gating observed in H(+),K(+)-ATPase is consistent with that observed in sarcoplasmic reticulum Ca(2+)-ATPase and other P-type ATPases and is most likely conserved for the P-type ATPase family in general. | ||||||
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 | 4ux1.cif.gz | 218.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ux1.ent.gz | 175.7 KB | Display | PDB format |
PDBx/mmJSON format | 4ux1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ux1_validation.pdf.gz | 715.7 KB | Display | wwPDB validaton report |
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Full document | 4ux1_full_validation.pdf.gz | 918.9 KB | Display | |
Data in XML | 4ux1_validation.xml.gz | 65.8 KB | Display | |
Data in CIF | 4ux1_validation.cif.gz | 92.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ux/4ux1 ftp://data.pdbj.org/pub/pdb/validation_reports/ux/4ux1 | HTTPS FTP |
-Related structure data
Related structure data | 2759MC 2760C 4ux2C C: citing same article (ref.) M: map data used to model this data |
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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) / 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) / References: UniProt: P18434 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON CRYSTALLOGRAPHY / Number of used crystals: 267 |
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EM experiment | Aggregation state: 2D ARRAY / 3D reconstruction method: electron crystallography |
-Sample preparation
Component | Name: antagonist-bound E2P gastric H,K-ATPase / Type: COMPLEX |
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Buffer solution | pH: 4.8 |
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: Oct 29, 2013 |
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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: 2997 nm / Nominal defocus min: 808 nm |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Diffraction | Mean temperature: 4 K |
Detector | Date: Oct 29, 2013 |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 8→129 Å / Num. obs: 35798 / % possible obs: 52.6 % / Biso Wilson estimate: 32.4 Å2 |
-Processing
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3D reconstruction | Resolution: 8 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 2D CRYSTAL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 8→128.95 Å / Rfactor Rfree error: 0.043 / Data cutoff high absF: 876135.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: BULK SOLVENT MODEL USED SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2759. (DEPOSITION ID: 12786).
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 4098.69 Å2 / ksol: 0.1 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 0 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 8→128.95 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 8→8.5 Å / Rfactor Rfree error: 0.224 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP |