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Yorodumi- PDB-7x24: Cryo-EM structure of non gastric H,K-ATPase alpha2 SPWC mutant in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7x24 | ||||||
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Title | Cryo-EM structure of non gastric H,K-ATPase alpha2 SPWC mutant in (2K+)E2-AlF state | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / P-type ATPase / transporter / proton pump / kidney / colon / airway | ||||||
Function / homology | Function and homology information Basigin interactions / H+/K+-exchanging ATPase / Ion transport by P-type ATPases / Na+/K+-exchanging ATPase / P-type potassium:proton transporter activity / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / metal ion transport / P-type sodium:potassium-exchanging transporter activity / membrane repolarization ...Basigin interactions / H+/K+-exchanging ATPase / Ion transport by P-type ATPases / Na+/K+-exchanging ATPase / P-type potassium:proton transporter activity / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / metal ion transport / P-type sodium:potassium-exchanging transporter activity / membrane repolarization / sodium:potassium-exchanging ATPase complex / regulation of pH / regulation of calcium ion transmembrane transport / sodium ion export across plasma membrane / intracellular potassium ion homeostasis / potassium ion homeostasis / intracellular sodium ion homeostasis / regulation of cardiac muscle contraction by calcium ion signaling / response to metal ion / relaxation of cardiac muscle / organelle membrane / Ion homeostasis / sodium ion transport / potassium ion import across plasma membrane / monoatomic cation transmembrane transport / ATPase activator activity / blastocyst development / intercalated disc / lateral plasma membrane / sperm flagellum / sodium ion transmembrane transport / cardiac muscle contraction / ATP metabolic process / T-tubule / proton transmembrane transport / potassium ion transport / caveola / protein localization to plasma membrane / response to organic cyclic compound / sarcolemma / intracellular calcium ion homeostasis / ATPase binding / regulation of gene expression / protein-macromolecule adaptor activity / basolateral plasma membrane / response to hypoxia / protein stabilization / cell adhesion / apical plasma membrane / protein heterodimerization activity / innate immune response / protein kinase binding / ATP hydrolysis activity / ATP binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
Authors | Abe, K. / Nakanishi, H. / Young, V. / Artigas, P. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structure and function of H/K pump mutants reveal Na/K pump mechanisms. Authors: Victoria C Young / Hanayo Nakanishi / Dylan J Meyer / Tomohiro Nishizawa / Atsunori Oshima / Pablo Artigas / Kazuhiro Abe / Abstract: Ion-transport mechanisms evolve by changing ion-selectivity, such as switching from Na to H selectivity in secondary-active transporters or P-type-ATPases. Here we study primary-active transport via ...Ion-transport mechanisms evolve by changing ion-selectivity, such as switching from Na to H selectivity in secondary-active transporters or P-type-ATPases. Here we study primary-active transport via P-type ATPases using functional and structural analyses to demonstrate that four simultaneous residue substitutions transform the non-gastric H/K pump, a strict H-dependent electroneutral P-type ATPase, into a bona fide Na-dependent electrogenic Na/K pump. Conversion of a H-dependent primary-active transporter into a Na-dependent one provides a prototype for similar studies of ion-transport proteins. Moreover, we solve the structures of the wild-type non-gastric H/K pump, a suitable drug target to treat cystic fibrosis, and of its Na/K pump-mimicking mutant in two major conformations, providing insight on how Na binding drives a concerted mechanism leading to Na/K pump phosphorylation. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7x24.cif.gz | 244.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7x24.ent.gz | 190.5 KB | Display | PDB format |
PDBx/mmJSON format | 7x24.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7x24_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7x24_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7x24_validation.xml.gz | 51.1 KB | Display | |
Data in CIF | 7x24_validation.cif.gz | 75 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x2/7x24 ftp://data.pdbj.org/pub/pdb/validation_reports/x2/7x24 | HTTPS FTP |
-Related structure data
Related structure data | 32957MC 7x20C 7x21C 7x22C 7x23C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 109145.664 Da / Num. of mol.: 1 / Mutation: K794S,A797P,I943W,R949C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Atp12a, Atp1al1 / Production host: Homo sapiens (human) References: UniProt: P54708, H+/K+-exchanging ATPase, Na+/K+-exchanging ATPase |
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#2: Protein | Mass: 37516.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Atp1b1 / Production host: Homo sapiens (human) / References: UniProt: P07340 |
-Sugars , 1 types, 1 molecules
#8: Sugar | ChemComp-NAG / |
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-Non-polymers , 5 types, 13 molecules
#3: Chemical | #4: Chemical | ChemComp-PCW / #5: Chemical | #6: Chemical | ChemComp-ALF / | #7: Chemical | ChemComp-MG / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: non gastric H,K-ATPase / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Value: 150 kDa/nm / Experimental value: YES |
Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 6.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 48 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 769755 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.95 Å2 | ||||||||||||||||||||||||
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