{"@context":{"@vocab":"https://cir.nii.ac.jp/schema/1.0/","rdfs":"http://www.w3.org/2000/01/rdf-schema#","dc":"http://purl.org/dc/elements/1.1/","dcterms":"http://purl.org/dc/terms/","foaf":"http://xmlns.com/foaf/0.1/","prism":"http://prismstandard.org/namespaces/basic/2.0/","cinii":"http://ci.nii.ac.jp/ns/1.0/","datacite":"https://schema.datacite.org/meta/kernel-4/","ndl":"http://ndl.go.jp/dcndl/terms/","jpcoar":"https://github.com/JPCOAR/schema/blob/master/2.0/"},"@id":"https://cir.nii.ac.jp/crid/1360565166752351232.json","@type":"Article","productIdentifier":[{"identifier":{"@type":"DOI","@value":"10.1038/nature12578"}},{"identifier":{"@type":"URI","@value":"http://www.nature.com/articles/nature12578.pdf"}},{"identifier":{"@type":"URI","@value":"http://www.nature.com/articles/nature12578"}},{"identifier":{"@type":"PMID","@value":"24089211"}}],"resourceType":"学術雑誌論文(journal article)","dc:title":[{"@value":"Crystal structure of a Na+-bound Na+,K+-ATPase preceding the E1P state"}],"description":[{"notation":[{"@value":"Na(+),K(+)-ATPase pumps three Na(+) ions out of cells in exchange for two K(+) taken up from the extracellular medium per ATP molecule hydrolysed, thereby establishing Na(+) and K(+) gradients across the membrane in all animal cells. These ion gradients are used in many fundamental processes, notably excitation of nerve cells. Here we describe 2.8 Å-resolution crystal structures of this ATPase from pig kidney with bound Na(+), ADP and aluminium fluoride, a stable phosphate analogue, with and without oligomycin that promotes Na(+) occlusion. These crystal structures represent a transition state preceding the phosphorylated intermediate (E1P) in which three Na(+) ions are occluded. Details of the Na(+)-binding sites show how this ATPase functions as a Na(+)-specific pump, rejecting K(+) and Ca(2+), even though its affinity for Na(+) is low (millimolar dissociation constant). A mechanism for sequential, cooperative Na(+) binding can now be formulated in atomic detail."}]}],"creator":[{"@id":"https://cir.nii.ac.jp/crid/1420845751152054528","@type":"Researcher","personIdentifier":[{"@type":"KAKEN_RESEARCHERS","@value":"50598472"},{"@type":"NRID","@value":"1000050598472"},{"@type":"NRID","@value":"9000253183479"},{"@type":"NRID","@value":"9000000667453"},{"@type":"NRID","@value":"9000398805729"},{"@type":"RESEARCHMAP","@value":"https://researchmap.jp/rkanai"}],"foaf:name":[{"@value":"Ryuta Kanai"}]},{"@id":"https://cir.nii.ac.jp/crid/1420564276162668160","@type":"Researcher","personIdentifier":[{"@type":"KAKEN_RESEARCHERS","@value":"40292726"},{"@type":"NRID","@value":"1000040292726"},{"@type":"ORCID","@value":"0000-0001-5515-1533"},{"@type":"NRID","@value":"9000412291127"},{"@type":"RESEARCHMAP","@value":"https://researchmap.jp/haru_9000"}],"foaf:name":[{"@value":"Haruo Ogawa"}]},{"@id":"https://cir.nii.ac.jp/crid/1030285133809210116","@type":"Researcher","foaf:name":[{"@value":"Bente Vilsen"}]},{"@id":"https://cir.nii.ac.jp/crid/1030285133809210114","@type":"Researcher","foaf:name":[{"@value":"Flemming Cornelius"}]},{"@id":"https://cir.nii.ac.jp/crid/1420282801189100928","@type":"Researcher","personIdentifier":[{"@type":"KAKEN_RESEARCHERS","@value":"70172210"},{"@type":"NRID","@value":"1000070172210"},{"@type":"NRID","@value":"9000253201855"},{"@type":"NRID","@value":"9000007720005"},{"@type":"NRID","@value":"9000020690774"},{"@type":"NRID","@value":"9000364991902"},{"@type":"NRID","@value":"9000020936888"},{"@type":"NRID","@value":"9000246828560"},{"@type":"NRID","@value":"9000391619834"},{"@type":"NRID","@value":"9000396141497"},{"@type":"NRID","@value":"9000397693889"},{"@type":"NRID","@value":"9000253206203"},{"@type":"NRID","@value":"9000020045897"},{"@type":"NRID","@value":"9000391635633"},{"@type":"NRID","@value":"9000255728118"},{"@type":"NRID","@value":"9000000145050"},{"@type":"NRID","@value":"9000367031778"},{"@type":"NRID","@value":"9000391623649"},{"@type":"NRID","@value":"9000398805732"},{"@type":"NRID","@value":"9000252882557"},{"@type":"NRID","@value":"9000018351410"},{"@type":"NRID","@value":"9000253199552"},{"@type":"NRID","@value":"9000414753519"},{"@type":"NRID","@value":"9000011161307"},{"@type":"NRID","@value":"9000391623606"},{"@type":"NRID","@value":"9000404105651"},{"@type":"NRID","@value":"9000253206205"},{"@type":"NRID","@value":"9000253471019"},{"@type":"NRID","@value":"9000410154705"},{"@type":"RESEARCHMAP","@value":"https://researchmap.jp/read0006729"}],"foaf:name":[{"@value":"Chikashi Toyoshima"}]}],"publication":{"publicationIdentifier":[{"@type":"PISSN","@value":"00280836"},{"@type":"EISSN","@value":"14764687"}],"prism:publicationName":[{"@value":"Nature"}],"dc:publisher":[{"@value":"Springer Science and Business Media LLC"}],"prism:publicationDate":"2013-10","prism:volume":"502","prism:number":"7470","prism:startingPage":"201","prism:endingPage":"206"},"reviewed":"false","dc:rights":["http://www.springer.com/tdm"],"url":[{"@id":"http://www.nature.com/articles/nature12578.pdf"},{"@id":"http://www.nature.com/articles/nature12578"}],"createdAt":"2013-10-02","modifiedAt":"2023-05-18","foaf:topic":[{"@id":"https://cir.nii.ac.jp/all?q=Models,%20Molecular","dc:title":"Models, Molecular"},{"@id":"https://cir.nii.ac.jp/all?q=Binding%20Sites","dc:title":"Binding Sites"},{"@id":"https://cir.nii.ac.jp/all?q=Swine","dc:title":"Swine"},{"@id":"https://cir.nii.ac.jp/all?q=Sodium","dc:title":"Sodium"},{"@id":"https://cir.nii.ac.jp/all?q=Crystallography,%20X-Ray","dc:title":"Crystallography, X-Ray"},{"@id":"https://cir.nii.ac.jp/all?q=Kidney","dc:title":"Kidney"},{"@id":"https://cir.nii.ac.jp/all?q=Protein%20Structure,%20Tertiary","dc:title":"Protein Structure, Tertiary"},{"@id":"https://cir.nii.ac.jp/all?q=Na%20bindingssteder","dc:title":"Na bindingssteder"},{"@id":"https://cir.nii.ac.jp/all?q=Animals","dc:title":"Animals"},{"@id":"https://cir.nii.ac.jp/all?q=Sodium-Potassium-Exchanging%20ATPase","dc:title":"Sodium-Potassium-Exchanging ATPase"}],"project":[{"@id":"https://cir.nii.ac.jp/crid/1040000782139750272","@type":"Project","projectIdentifier":[{"@type":"KAKEN","@value":"23000014"},{"@type":"JGN","@value":"JP23000014"},{"@type":"URI","@value":"https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-23000014/"}],"notation":[{"@language":"ja","@value":"薬剤開発を視野に入れた膜輸送体の構造研究"},{"@language":"en","@value":"Structural biology of membrane transporters with a view to drug development"}]},{"@id":"https://cir.nii.ac.jp/crid/1040000782236308224","@type":"Project","projectIdentifier":[{"@type":"KAKEN","@value":"25136702"},{"@type":"JGN","@value":"JP25136702"},{"@type":"URI","@value":"https://kaken.nii.ac.jp/grant/KAKENHI-PUBLICLY-25136702/"}],"notation":[{"@language":"ja","@value":"PLN/SERCA2aレギュラトームによる心収縮調節機構の解明"}]},{"@id":"https://cir.nii.ac.jp/crid/1040000782267054464","@type":"Project","projectIdentifier":[{"@type":"KAKEN","@value":"25650020"},{"@type":"JGN","@value":"JP25650020"},{"@type":"URI","@value":"https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-25650020/"}],"notation":[{"@language":"ja","@value":"哺乳類超巨大膜蛋白質発現系の構築"},{"@language":"en","@value":"Establishment of an over-expression system for mammalian large membrane proteins"}]},{"@id":"https://cir.nii.ac.jp/crid/1040282257221373184","@type":"Project","projectIdentifier":[{"@type":"KAKEN","@value":"25291012"},{"@type":"JGN","@value":"JP25291012"},{"@type":"URI","@value":"https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-25291012/"}],"notation":[{"@language":"ja","@value":"心筋細胞のカルシウムイオン制御機構の結晶学的解明"},{"@language":"en","@value":"Structural analysis of PLN/SERCA regulatome toward understanding of the mechanism of Ca2+-regulation in the cardiac muscle cells"}]}],"relatedProduct":[{"@id":"https://cir.nii.ac.jp/crid/1360002216605271424","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Light-Driven Sodium-Pumping Rhodopsin: A New Concept of Active Transport"}]},{"@id":"https://cir.nii.ac.jp/crid/1360002216826854016","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Crystal structures of the gastric proton 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essential residue for active transport of sodium and potassium ions"}]},{"@id":"https://cir.nii.ac.jp/crid/1360298336565418880","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Cryoelectron microscopy of Na\n            <sup>+</sup>\n            ,K\n            <sup>+</sup>\n            -ATPase in the two E2P states with and without cardiotonic steroids"}]},{"@id":"https://cir.nii.ac.jp/crid/1360298754802302720","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Cryo‐electron microscopy of Na<sup>+</sup>,K<sup>+</sup>‐<scp>ATPase</scp> reveals how the extracellular gate locks in the <scp>E2</scp>·<scp>2K</scp><sup>+</sup> state"}]},{"@id":"https://cir.nii.ac.jp/crid/1360298757181483904","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Lipid peroxidation increases membrane tension, Piezo1 gating, and cation permeability to execute ferroptosis"}]},{"@id":"https://cir.nii.ac.jp/crid/1360567183934831616","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Systematic Comparison of Molecular Conformations of H+,K+-ATPase Reveals an Important Contribution of the A-M2 Linker for the Luminal Gating"}]},{"@id":"https://cir.nii.ac.jp/crid/1360567183941344512","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Distinct pH dependencies of Na+/K+ selectivity at the two faces of Na,K-ATPase"}]},{"@id":"https://cir.nii.ac.jp/crid/1360572092668218368","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Multi-Scale Flexible Fitting of Proteins to Cryo-EM Density Maps at Medium 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Ala of the rat kidney Na+,K+-ATPase displays low cation affinity and catalyzes ATP hydrolysis at a high rate in the absence of potassium ions"}]},{"@id":"https://cir.nii.ac.jp/crid/1360574096388246784","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Ion Selectivity of the Cytoplasmic Binding Sites of the Na,K-ATPase: II. Competition of Various Cations"}]},{"@id":"https://cir.nii.ac.jp/crid/1360576118787862272","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Gastric proton pump with two occluded K+ engineered with sodium pump-mimetic mutations"}]},{"@id":"https://cir.nii.ac.jp/crid/1360580232381494016","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Structure and function of H+/K+ pump mutants reveal Na+/K+ pump mechanisms"}]},{"@id":"https://cir.nii.ac.jp/crid/1360584339761753728","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"An unusual conformation from Na+-sensitive non-gastric proton pump mutants reveals molecular mechanisms of cooperative Na+-binding"}]},{"@id":"https://cir.nii.ac.jp/crid/1360584341825421952","@type":"Article","resourceType":"学術雑誌論文(journal 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Arg935"}]},{"@id":"https://cir.nii.ac.jp/crid/1360855569154518272","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Investigation of ion binding to the cytoplasmic binding sites of the Na,K-pump"}]},{"@id":"https://cir.nii.ac.jp/crid/1360855569679972096","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures"}]},{"@id":"https://cir.nii.ac.jp/crid/1360855569954178432","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Structural principles governing domain motions in proteins"}]},{"@id":"https://cir.nii.ac.jp/crid/1360855570767884800","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Thr-774 (Transmembrane Segment M5), Val-920 (M8), and Glu-954 (M9) Are Involved in Na+ Transport, and Gln-923 (M8) Is Essential for Na,K-ATPase Activity"}]},{"@id":"https://cir.nii.ac.jp/crid/1360855570849886336","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Identification and Function of a Cytoplasmic K+ Site of the Na+, K+-ATPase"}]},{"@id":"https://cir.nii.ac.jp/crid/1360855571062376960","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures"}]},{"@id":"https://cir.nii.ac.jp/crid/1360865814737627904","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Crystal structures of Na\n                    <sup>+</sup>\n                    ,K\n                    <sup>+</sup>\n                    ‐ATPase reveal the mechanism that converts the K\n                    <sup>+</sup>\n                    ‐bound form to Na\n                    <sup>+</sup>\n                    ‐bound form and opens and closes the cytoplasmic gate"}]},{"@id":"https://cir.nii.ac.jp/crid/1361137044526204288","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"The CCP4 suite: programs for protein crystallography"}]},{"@id":"https://cir.nii.ac.jp/crid/1361137045427077504","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Inter‐subunit interaction of gastric H+,K+‐ATPase prevents reverse reaction of the transport cycle"}]},{"@id":"https://cir.nii.ac.jp/crid/1361137046245094912","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"A structural overview of the plasma membrane Na+,K+-ATPase and H+-ATPase ion pumps"}]},{"@id":"https://cir.nii.ac.jp/crid/1361418520049425920","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Contribution to Tl<sup>+</sup>, K<sup>+</sup>, and Na<sup>+</sup> Binding of Asn<sup>776</sup>, Ser<sup>775</sup>, Thr<sup>774</sup>, Thr<sup>772</sup>, and Tyr<sup>771</sup> in Cytoplasmic Part of Fifth Transmembrane Segment in α-Subunit of Renal Na,K-ATPase"}]},{"@id":"https://cir.nii.ac.jp/crid/1361418520154679296","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Crystal structure of the sodium–potassium pump at 2.4 Å resolution"}]},{"@id":"https://cir.nii.ac.jp/crid/1361418520443380096","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"The Rapid-onset Dystonia Parkinsonism Mutation D923N of the Na+,K+-ATPase α3 Isoform Disrupts Na+ Interaction at the Third Na+ Site"}]},{"@id":"https://cir.nii.ac.jp/crid/1361418521280802944","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Crystal structure of the high-affinity Na\n            <sup>+</sup>\n            ,K\n            <sup>+</sup>\n            -ATPase–ouabain complex with Mg\n            <sup>2+</sup>\n            bound in the cation binding 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