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- EMDB-32956: Cryo-EM structure of non gastric H,K-ATPase alpha2 SPWC mutant in... -

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Basic information

Entry
Database: EMDB / ID: EMD-32956
TitleCryo-EM structure of non gastric H,K-ATPase alpha2 SPWC mutant in 3Na+E1-AMPPCPF state
Map data
Sample
  • Complex: non gastric H,K-ATPase
    • Protein or peptide: Potassium-transporting ATPase alpha chain 2
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit beta-1
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
  • Ligand: SODIUM ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
KeywordsP-type ATPase / transporter / proton pump / kidney / colon / airway / MEMBRANE PROTEIN
Function / homology
Function and homology information


Basigin interactions / H+/K+-exchanging ATPase / Ion transport by P-type ATPases / P-type potassium:proton transporter activity / Na+/K+-exchanging ATPase / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / P-type sodium:potassium-exchanging transporter activity / sodium:potassium-exchanging ATPase complex / membrane repolarization ...Basigin interactions / H+/K+-exchanging ATPase / Ion transport by P-type ATPases / P-type potassium:proton transporter activity / Na+/K+-exchanging ATPase / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / P-type sodium:potassium-exchanging transporter activity / sodium:potassium-exchanging ATPase complex / membrane repolarization / metal ion transport / regulation of pH / sodium ion export across plasma membrane / potassium ion homeostasis / positive regulation of potassium ion transmembrane transport / intracellular sodium ion homeostasis / regulation of calcium ion transmembrane transport / response to metal ion / relaxation of cardiac muscle / regulation of cardiac muscle contraction by calcium ion signaling / Ion homeostasis / positive regulation of sodium ion transmembrane transport / sodium ion transport / organelle membrane / potassium ion import across plasma membrane / intracellular potassium ion homeostasis / ATPase activator activity / intercalated disc / lateral plasma membrane / blastocyst development / sperm flagellum / transporter activator activity / ATP metabolic process / cardiac muscle contraction / T-tubule / sodium ion transmembrane transport / proton transmembrane transport / protein localization to plasma membrane / sarcolemma / caveola / potassium ion transport / transmembrane transport / intracellular calcium ion homeostasis / ATPase binding / regulation of gene expression / protein-macromolecule adaptor activity / basolateral plasma membrane / response to hypoxia / cell adhesion / protein stabilization / apical plasma membrane / protein heterodimerization activity / innate immune response / protein kinase binding / ATP hydrolysis activity / ATP binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
Sodium/potassium-transporting ATPase subunit beta / Sodium/potassium-transporting ATPase subunit beta superfamily / Sodium / potassium ATPase beta chain / Sodium and potassium ATPases beta subunits signature 1. / Sodium and potassium ATPases beta subunits signature 2. / : / P-type ATPase subfamily IIC, subunit alpha / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus ...Sodium/potassium-transporting ATPase subunit beta / Sodium/potassium-transporting ATPase subunit beta superfamily / Sodium / potassium ATPase beta chain / Sodium and potassium ATPases beta subunits signature 1. / Sodium and potassium ATPases beta subunits signature 2. / : / P-type ATPase subfamily IIC, subunit alpha / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / P-type ATPase, cytoplasmic domain N / P-type ATPase actuator domain / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Sodium/potassium-transporting ATPase subunit beta-1 / Potassium-transporting ATPase alpha chain 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsAbe K / Nakanishi H / Young V / Artigas P
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21H02426 Japan
CitationJournal: 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
DepositionFeb 25, 2022-
Header (metadata) releaseOct 5, 2022-
Map releaseOct 5, 2022-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32956.png

Downloads & links

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Map

FileDownload / File: emd_32956.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.011
Minimum - Maximum-0.09517897 - 0.14368623
Average (Standard dev.)0.00028081192 (±0.0033966906)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_32956_msk_1.map
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Half map: #1

Fileemd_32956_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_32956_half_map_2.map
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Sample components

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Entire : non gastric H,K-ATPase

EntireName: non gastric H,K-ATPase
Components
  • Complex: non gastric H,K-ATPase
    • Protein or peptide: Potassium-transporting ATPase alpha chain 2
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit beta-1
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
  • Ligand: SODIUM ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: non gastric H,K-ATPase

SupramoleculeName: non gastric H,K-ATPase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 150 kDa/nm

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Macromolecule #1: Potassium-transporting ATPase alpha chain 2

MacromoleculeName: Potassium-transporting ATPase alpha chain 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: H+/K+-exchanging ATPase
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 109.145664 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GMDLDDHRLS NTELEQKYGT NIIQGLSSVR ATELLARDGP NTLTPPKQTP EIIKFLKQMV GGFSILLWIG AALCWIAFVI QYVNNSASL DNVYLGAILV LVVILTGIFA YYQEAKSTNI MASFSKMIPQ QALVIRDAEK KVISAEQLVV GDVVEIKGGD Q IPADIRLV ...String:
GMDLDDHRLS NTELEQKYGT NIIQGLSSVR ATELLARDGP NTLTPPKQTP EIIKFLKQMV GGFSILLWIG AALCWIAFVI QYVNNSASL DNVYLGAILV LVVILTGIFA YYQEAKSTNI MASFSKMIPQ QALVIRDAEK KVISAEQLVV GDVVEIKGGD Q IPADIRLV FSQGCKVDNS SLTGESEPQA RSTEFTHENP LETKNIGFYS TTCLEGTATG IVINTGDRTI IGRIASLASG VG SEKTPIA IEIEHFVHIV AGVAVSIDII FFITAVCMKY YVLDAIIFLI SIIVANVPEG LLATVTVTLS LTAKRMAKKN CLV KNLEAV ETLGSTSIIC SDKTGTLTQN RMTVAHLWFD NQIFVADTSE NQTKQAFDQS SGTWASLSKI ITLCNRAEFR PGQE SVPIM KRTVVGDASE TALLKFSEVI LGDVMGIRKR NHKVAEIPFN STNKFQLSIH ETEDPNNKRF LVVMKGAPER ILEKC STIM INGQEQPLDK SSADSFHTAY MELGGLGERV LGFCHLYLPA EQFPQSYIFD VDSVNFPTSN FCFVGLLSMI DPPRST VPD AVSKCRSAGI KVIMVTGDHP ITAKAIAKSV GIISANNETV EDIAKRRNIA VEQVNKREAK AAVVTGMELK DMTPEQL DE LLTNYQEIVF ARTSPQQKLI IVEGCQRQDA IVAVTGDGVN DSPALKKADI GIAMGIAGSD AAKNAADMVL LDDNFASI V TGVEEGRLIF DNLKKTIAYT LTSNIPELCP FLIYIVAGLP LPIGTITILF IDLGTDIIPS IALAYEKAES DIMNRKPRH KKKDRLVNTQ LAIYSYLHIG LMQALGGFLV YFTVYAQQGF WPTSLINLRV AWETDDINDL EDSYGQEWTR YQRKYLEWTG STAFFVAIM IQQWADLIIC KTRRNSIFQQ GLFRNKVIWV GIASQVIVAL ILSYGLGSVP ALSFTMLRVQ YWFVAVPHAI L IWVYDEMR KLFIRLYPGS WWDKNMYY

UniProtKB: Potassium-transporting ATPase alpha chain 2

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Macromolecule #2: Sodium/potassium-transporting ATPase subunit beta-1

MacromoleculeName: Sodium/potassium-transporting ATPase subunit beta-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 37.516859 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGDYKDDDDK SSGENLYFQG MARGKAKEEG SWKKFIWNSE KKEFLGRTGG SWFKILLFYV IFYGCLAGIF IGTIQVMLLT ISELKPTYQ DRVAPPGLTQ IPQIQKTEIS FRPNDPKSYE AYVLNIIRFL EKYKDSAQKD DMIFEDCGSM PSEPKERGEF N HERGERKV ...String:
MGDYKDDDDK SSGENLYFQG MARGKAKEEG SWKKFIWNSE KKEFLGRTGG SWFKILLFYV IFYGCLAGIF IGTIQVMLLT ISELKPTYQ DRVAPPGLTQ IPQIQKTEIS FRPNDPKSYE AYVLNIIRFL EKYKDSAQKD DMIFEDCGSM PSEPKERGEF N HERGERKV CRFKLDWLGN CSGLNDESYG YKEGKPCIII KLNRVLGFKP KPPKNESLET YPLTMKYNPN VLPVQCTGKR DE DKDKVGN IEYFGMGGFY GFPLQYYPYY GKLLQPKYLQ PLLAVQFTNL TLDTEIRIEC KAYGENIGYS EKDRFQGRFD VKI EVKS

UniProtKB: Sodium/potassium-transporting ATPase subunit beta-1

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Macromolecule #3: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER

MacromoleculeName: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 1 / Formula: ACP
Molecular weightTheoretical: 505.208 Da
Chemical component information

ChemComp-ACP:
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / AMP-PCP, energy-carrying molecule analogue*YM

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Macromolecule #4: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 4 / Number of copies: 3
Molecular weightTheoretical: 22.99 Da

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 7 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1010045
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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