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Yorodumi- EMDB-37391: Cryo-EM structure of the gastric proton pump Y799W/E936Q mutant i... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37391 | |||||||||
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Title | Cryo-EM structure of the gastric proton pump Y799W/E936Q mutant in K+-occluded (K+)E2-AlF state | |||||||||
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Sample |
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Keywords | P-type ATPase / gastric proton pump / membrane protein / primary transporter / transporter | |||||||||
Function / homology | Function and homology information regulation of proton transport / pH reduction / potassium:proton exchanging ATPase complex / P-type potassium:proton transporter activity / Ion transport by P-type ATPases / 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 ...regulation of proton transport / pH reduction / potassium:proton exchanging ATPase complex / P-type potassium:proton transporter activity / Ion transport by P-type ATPases / 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 transmembrane transport / proton transmembrane transport / cell adhesion / response to xenobiotic stimulus / apical plasma membrane / magnesium ion binding / ATP hydrolysis activity / ATP binding Similarity search - Function | |||||||||
Biological species | Sus scrofa (pig) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.51 Å | |||||||||
Authors | Abe K | |||||||||
Funding support | Japan, 1 items
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Citation | Journal: J Biol Chem / Year: 2024 Title: Specific protonation of acidic residues confers K selectivity to the gastric proton pump. Authors: Hridya Valia Madapally / Kazuhiro Abe / Vikas Dubey / Himanshu Khandelia / Abstract: The gastric proton pump (H,K-ATPase) transports a proton into the stomach lumen for every K ion exchanged in the opposite direction. In the lumen-facing state of the pump (E2), the pump selectively ...The gastric proton pump (H,K-ATPase) transports a proton into the stomach lumen for every K ion exchanged in the opposite direction. In the lumen-facing state of the pump (E2), the pump selectively binds K despite the presence of a 10-fold higher concentration of Na. The molecular basis for the ion selectivity of the pump is unknown. Using molecular dynamics simulations, free energy calculations, and Na and K-dependent ATPase activity assays, we demonstrate that the K selectivity of the pump depends upon the simultaneous protonation of the acidic residues E343 and E795 in the ion-binding site. We also show that when E936 is protonated, the pump becomes Na sensitive. The protonation-mimetic mutant E936Q exhibits weak Na-activated ATPase activity. A 2.5-Å resolution cryo-EM structure of the E936Q mutant in the K-occluded E2-Pi form shows, however, no significant structural difference compared with wildtype except less-than-ideal coordination of K in the mutant. The selectivity toward a specific ion correlates with a more rigid and less fluctuating ion-binding site. Despite being exposed to a pH of 1, the fundamental principle driving the K ion selectivity of H,K-ATPase is similar to that of Na,K-ATPase: the ionization states of the acidic residues in the ion-binding sites determine ion selectivity. Unlike the Na,K-ATPase, however, protonation of an ion-binding glutamate residue (E936) confers Na sensitivity. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37391.map.gz | 266.9 MB | EMDB map data format | |
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Header (meta data) | emd-37391-v30.xml emd-37391.xml | 17.9 KB 17.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_37391_fsc.xml | 13.8 KB | Display | FSC data file |
Images | emd_37391.png | 52.5 KB | ||
Masks | emd_37391_msk_1.map | 282.6 MB | Mask map | |
Filedesc metadata | emd-37391.cif.gz | 6.6 KB | ||
Others | emd_37391_half_map_1.map.gz emd_37391_half_map_2.map.gz | 262.5 MB 262.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37391 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37391 | HTTPS FTP |
-Validation report
Summary document | emd_37391_validation.pdf.gz | 840.8 KB | Display | EMDB validaton report |
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Full document | emd_37391_full_validation.pdf.gz | 840.3 KB | Display | |
Data in XML | emd_37391_validation.xml.gz | 23 KB | Display | |
Data in CIF | emd_37391_validation.cif.gz | 29.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37391 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37391 | HTTPS FTP |
-Related structure data
Related structure data | 8wa5MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_37391.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_37391_msk_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_37391_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_37391_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : alpha-beta complex of the gastric proton pump
+Supramolecule #1: alpha-beta complex of the gastric proton pump
+Macromolecule #1: Sodium/potassium-transporting ATPase subunit alpha
+Macromolecule #2: Potassium-transporting ATPase subunit beta
+Macromolecule #3: POTASSIUM ION
+Macromolecule #4: TETRAFLUOROALUMINATE ION
+Macromolecule #5: MAGNESIUM ION
+Macromolecule #6: CHOLESTEROL
+Macromolecule #7: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose
+Macromolecule #9: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 64.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |