+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5104 | |||||||||
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Title | Gastric H,K-ATPase complexed with aluminum fluoride | |||||||||
Map data | gastric HK-ATPase complexed with aluminium fluoride | |||||||||
Sample |
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Keywords | ION PUMP / H+ / K+-ATPASE / P-TYPE ATPASE / MEMBRANE PROTEIN / HYDROLASE / E2 / ALUMINUM FLUORIDE | |||||||||
Function / homology | Function and homology information proton transmembrane transport => GO:1902600 / 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 / ATP biosynthetic process / sodium ion export across plasma membrane / intracellular potassium ion homeostasis ...proton transmembrane transport => GO:1902600 / 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 / ATP biosynthetic process / 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 / potassium ion 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 / cryo EM / Resolution: 6.5 Å | |||||||||
Authors | Abe K / Tani K / Nishizawa T / Fujiyoshi Y | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5104.map.gz | 1.9 MB | EMDB map data format | |
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Header (meta data) | emd-5104-v30.xml emd-5104.xml | 13.9 KB 13.9 KB | Display Display | EMDB header |
Images | emd_5104_1.png | 403.4 KB | ||
Masks | emd_5104_msk_1.map | 2 MB | Mask map | |
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5104 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5104 | HTTPS FTP |
-Related structure data
Related structure data | 3ixzMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_5104.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | gastric HK-ATPase complexed with aluminium fluoride | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X: 2.06471 Å / Y: 2.09615 Å / Z: 2.22222 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Segmentation: HK-ATPase
Annotation | HK-ATPase | ||||||||||||
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File | emd_5104_msk_1.map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Gastric H,K-ATPase
Entire | Name: Gastric H,K-ATPase |
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Components |
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-Supramolecule #1000: Gastric H,K-ATPase
Supramolecule | Name: Gastric H,K-ATPase / type: sample / ID: 1000 / Oligomeric state: one alpha and one beta chain of HK-ATPase / Number unique components: 2 |
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Molecular weight | Theoretical: 150 KDa |
-Macromolecule #1: Potassium-transporting ATPase
Macromolecule | Name: Potassium-transporting ATPase / type: protein_or_peptide / ID: 1 / Name.synonym: HK-ATPase / Number of copies: 2 / Oligomeric state: dimer / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Sus scrofa (pig) / synonym: Pig / Tissue: stomach / Location in cell: plasma membrane |
Molecular weight | Theoretical: 150 KDa |
Sequence | GO: ATP biosynthetic process, proton transmembrane transport => GO:1902600, potassium ion transport InterPro: P-type ATPase, A domain superfamily, P-type ATPase subfamily IIC, subunit alpha, INTERPRO: IPR006069, Cation-transporting P-type ATPase, C-terminal, Cation-transporting P-type ATPase, N- ...InterPro: P-type ATPase, A domain superfamily, P-type ATPase subfamily IIC, subunit alpha, INTERPRO: IPR006069, Cation-transporting P-type ATPase, C-terminal, Cation-transporting P-type ATPase, N-terminal, Gastric H+/K+-transporter P-type ATPase, N-terminal, P-type ATPase, INTERPRO: IPR005834, Sodium/potassium-transporting ATPase subunit beta |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron crystallography |
Aggregation state | 2D array |
-Sample preparation
Concentration | 2.5 mg/mL |
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Buffer | 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 |
Grid | Details: molybdenum grid |
Vitrification | Cryogen name: NITROGEN / Chamber temperature: 4.2 K / Instrument: REICHERT-JUNG PLUNGER Details: Vitrification instrument: Reichert plunger. vitrification carried out in cold room at 4 degrees celsius. Method: carbon sandwich preparation |
Details | dialysis |
Crystal formation | Details: dialysis |
-Electron microscopy
Microscope | JEOL KYOTO-3000SFF |
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Temperature | Average: 4.2 K |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 346 / Average electron dose: 25 e/Å2 / Bits/pixel: 12 |
Tilt angle min | 0 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 59100 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.6 mm / Nominal defocus max: 3.48 µm / Nominal defocus min: 0.39 µm / Nominal magnification: 60000 |
Sample stage | Specimen holder: top entry / Specimen holder model: JEOL / Tilt angle max: 73.3 / Tilt series - Axis1 - Min angle: 0 ° / Tilt series - Axis1 - Max angle: 73.3 ° |
-Image processing
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: OTHER / Software - Name: MRC |
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Crystal parameters | Unit cell - A: 140.4 Å / Unit cell - B: 109.0 Å / Unit cell - C: 320.0 Å / Unit cell - γ: 90.0 ° / Unit cell - α: 90.0 ° / Unit cell - β: 90.0 ° / Plane group: P 2 21 21 |
CTF correction | Details: Each image |