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- EMDB-27167: Human alpha3 Na+/K+-ATPase in its K+-occluded state -

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Basic information

Entry
Database: EMDB / ID: EMD-27167
TitleHuman alpha3 Na+/K+-ATPase in its K+-occluded state
Map dataHuman alpha3 Na+/K+-ATPase in its K+-occluded state
Sample
  • Complex: Na+/K+-ATPaseSodium–potassium pump
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit beta-1
    • Protein or peptide: FXYD domain-containing ion transport regulator 6
  • Protein or peptide: Sodium/potassium-transporting ATPase subunit alpha-3
  • Ligand: TETRAFLUOROMAGNESATE(2-)
Function / homology
Function and homology information


neuron to neuron synapse / protein transport into plasma membrane raft / positive regulation of calcium:sodium antiporter activity / positive regulation of potassium ion transmembrane transporter activity / positive regulation of P-type sodium:potassium-exchanging transporter activity / Na+/K+-exchanging ATPase / regulation of monoatomic ion transport / 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 ...neuron to neuron synapse / protein transport into plasma membrane raft / positive regulation of calcium:sodium antiporter activity / positive regulation of potassium ion transmembrane transporter activity / positive regulation of P-type sodium:potassium-exchanging transporter activity / Na+/K+-exchanging ATPase / regulation of monoatomic ion transport / 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 / membrane repolarization during cardiac muscle cell action potential / response to glycoside / regulation of resting membrane potential / photoreceptor inner segment membrane / steroid hormone binding / membrane repolarization / sodium:potassium-exchanging ATPase complex / sodium ion export across plasma membrane / intracellular potassium ion homeostasis / establishment or maintenance of transmembrane electrochemical gradient / intracellular sodium ion homeostasis / regulation of cardiac muscle contraction by calcium ion signaling / positive regulation of ATP-dependent activity / Basigin interactions / cell communication by electrical coupling involved in cardiac conduction / relaxation of cardiac muscle / neuronal cell body membrane / cellular response to steroid hormone stimulus / potassium ion import across plasma membrane / ATPase activator activity / monoatomic cation transmembrane transport / Ion transport by P-type ATPases / organelle membrane / sodium ion transmembrane transport / sodium channel regulator activity / intercalated disc / lateral plasma membrane / sperm flagellum / ATP metabolic process / Ion homeostasis / cardiac muscle contraction / T-tubule / proton transmembrane transport / photoreceptor inner segment / neuron projection maintenance / monoatomic ion transmembrane transport / protein localization to plasma membrane / sarcolemma / intracellular calcium ion homeostasis / cellular response to amyloid-beta / extracellular vesicle / protein-macromolecule adaptor activity / presynaptic membrane / MHC class II protein complex binding / amyloid-beta binding / ATPase binding / protein-folding chaperone binding / postsynaptic membrane / regulation of gene expression / basolateral plasma membrane / Potential therapeutics for SARS / protein stabilization / cell adhesion / apical plasma membrane / protein heterodimerization activity / axon / innate immune response / neuronal cell body / synapse / glutamatergic synapse / protein kinase binding / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / extracellular exosome / ATP binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
: / Ion-transport regulator, FXYD motif / ATP1G1/PLM/MAT8 family / FXYD family signature. / 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 ...: / Ion-transport regulator, FXYD motif / ATP1G1/PLM/MAT8 family / FXYD family signature. / 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 / Cation transport ATPase (P-type) / E1-E2 ATPase / 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 / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Sodium/potassium-transporting ATPase subunit beta-1 / Sodium/potassium-transporting ATPase subunit alpha-3 / FXYD domain-containing ion transport regulator 6
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsNguyen PT / Bai X
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM136976 United States
Welch FoundationI-1944 United States
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis for gating mechanism of the human sodium-potassium pump.
Authors: Phong T Nguyen / Christine Deisl / Michael Fine / Trevor S Tippetts / Emiko Uchikawa / Xiao-Chen Bai / Beth Levine /
Abstract: P2-type ATPase sodium-potassium pumps (Na/K-ATPases) are ion-transporting enzymes that use ATP to transport Na and K on opposite sides of the lipid bilayer against their electrochemical gradients to ...P2-type ATPase sodium-potassium pumps (Na/K-ATPases) are ion-transporting enzymes that use ATP to transport Na and K on opposite sides of the lipid bilayer against their electrochemical gradients to maintain ion concentration gradients across the membranes in all animal cells. Despite the available molecular architecture of the Na/K-ATPases, a complete molecular mechanism by which the Na and K ions access into and are released from the pump remains unknown. Here we report five cryo-electron microscopy (cryo-EM) structures of the human alpha3 Na/K-ATPase in its cytoplasmic side-open (E1), ATP-bound cytoplasmic side-open (E1•ATP), ADP-AlF trapped Na-occluded (E1•P-ADP), BeF trapped exoplasmic side-open (E2P) and MgF trapped K-occluded (E2•P) states. Our work reveals the atomically resolved structural detail of the cytoplasmic gating mechanism of the Na/K-ATPase.
History
DepositionJun 1, 2022-
Header (metadata) releaseSep 21, 2022-
Map releaseSep 21, 2022-
UpdateSep 21, 2022-
Current statusSep 21, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27167.png

Downloads & links

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Map

FileDownload / File: emd_27167.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman alpha3 Na+/K+-ATPase in its K+-occluded state
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.0216
Minimum - Maximum-0.051938236 - 0.08255704
Average (Standard dev.)0.00019646641 (±0.0035127625)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 215.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Human alpha3 Na+/K+-ATPase in its K+-occluded state

Fileemd_27167_half_map_1.map
AnnotationHuman alpha3 Na+/K+-ATPase in its K+-occluded state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Human alpha3 Na+/K+-ATPase in its K+-occluded state

Fileemd_27167_half_map_2.map
AnnotationHuman alpha3 Na+/K+-ATPase in its K+-occluded state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Na+/K+-ATPase

EntireName: Na+/K+-ATPaseSodium–potassium pump
Components
  • Complex: Na+/K+-ATPaseSodium–potassium pump
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit beta-1
    • Protein or peptide: FXYD domain-containing ion transport regulator 6
  • Protein or peptide: Sodium/potassium-transporting ATPase subunit alpha-3
  • Ligand: TETRAFLUOROMAGNESATE(2-)

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Supramolecule #1: Na+/K+-ATPase

SupramoleculeName: Na+/K+-ATPase / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)

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

MacromoleculeName: Sodium/potassium-transporting ATPase subunit beta-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.108258 KDa
Recombinant expressionOrganism: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
SequenceString: MARGKAKEEG SWKKFIWNSE KKEFLGRTGG SWFKILLFYV IFYGCLAGIF IGTIQVMLLT ISEFKPTYQD RVAPPGLTQI PQIQKTEIS FRPNDPKSYE AYVLNIVRFL EKYKDSAQRD DMIFEDCGDV PSEPKERGDF NHERGERKVC RFKLEWLGNC S GLNDETYG ...String:
MARGKAKEEG SWKKFIWNSE KKEFLGRTGG SWFKILLFYV IFYGCLAGIF IGTIQVMLLT ISEFKPTYQD RVAPPGLTQI PQIQKTEIS FRPNDPKSYE AYVLNIVRFL EKYKDSAQRD DMIFEDCGDV PSEPKERGDF NHERGERKVC RFKLEWLGNC S GLNDETYG YKEGKPCIII KLNRVLGFKP KPPKNESLET YPVMKYNPNV LPVQCTGKRD EDKDKVGNVE YFGLGNSPGF PL QYYPYYG KLLQPKYLQP LLAVQFTNLT MDTEIRIECK AYGENIGYSE KDRFQGRFDV KIEVKS

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Macromolecule #2: FXYD domain-containing ion transport regulator 6

MacromoleculeName: FXYD domain-containing ion transport regulator 6 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.855645 KDa
Recombinant expressionOrganism: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
SequenceString:
MATMELVLVF LCSLLAPMVL ASAAEKEKEM DPFHYDYQTL RIGGLVFAVV LFSVGILLIL SRRCKCSFNQ KPRAPGDEEA QVENLITAN ATEPQKAEN

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Macromolecule #3: Sodium/potassium-transporting ATPase subunit alpha-3

MacromoleculeName: Sodium/potassium-transporting ATPase subunit alpha-3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: Na+/K+-exchanging ATPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 111.864289 KDa
Recombinant expressionOrganism: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
SequenceString: MGDKKDDKDS PKKNKGKERR DLDDLKKEVA MTEHKMSVEE VCRKYNTDCV QGLTHSKAQE ILARDGPNAL TPPPTTPEWV KFCRQLFGG FSILLWIGAI LCFLAYGIQA GTEDDPSGDN LYLGIVLAAV VIITGCFSYY QEAKSSKIME SFKNMVPQQA L VIREGEKM ...String:
MGDKKDDKDS PKKNKGKERR DLDDLKKEVA MTEHKMSVEE VCRKYNTDCV QGLTHSKAQE ILARDGPNAL TPPPTTPEWV KFCRQLFGG FSILLWIGAI LCFLAYGIQA GTEDDPSGDN LYLGIVLAAV VIITGCFSYY QEAKSSKIME SFKNMVPQQA L VIREGEKM QVNAEEVVVG DLVEIKGGDR VPADLRIISA HGCKVDNSSL TGESEPQTRS PDCTHDNPLE TRNITFFSTN CV EGTARGV VVATGDRTVM GRIATLASGL EVGKTPIAIE IEHFIQLITG VAVFLGVSFF ILSLILGYTW LEAVIFLIGI IVA NVPEGL LATVTVCLTL TAKRMARKNC LVKNLEAVET LGSTSTICSD KTGTLTQNRM TVAHMWFDNQ IHEADTTEDQ SGTS FDKSS HTWVALSHIA GLCNRAVFKG GQDNIPVLKR DVAGDASESA LLKCIELSSG SVKLMRERNK KVAEIPFNST NKYQL SIHE TEDPNDNRYL LVMKGAPERI LDRCSTILLQ GKEQPLDEEM KEAFQNAYLE LGGLGERVLG FCHYYLPEEQ FPKGFA FDC DDVNFTTDNL CFVGLMSMID PPRAAVPDAV GKCRSAGIKV IMVTGDHPIT AKAIAKGVGI ISEGNETVED IAARLNI PV SQVNPRDAKA CVIHGTDLKD FTSEQIDEIL QNHTEIVFAR TSPQQKLIIV EGCQRQGAIV AVTGDGVNDS PALKKADI G VAMGIAGSDV SKQAADMILL DDNFASIVTG VEEGRLIFDN LKKSIAYTLT SNIPEITPFL LFIMANIPLP LGTITILCI DLGTDMVPAI SLAYEAAESD IMKRQPRNPR TDKLVNERLI SMAYGQIGMI QALGGFFSYF VILAENGFLP GNLVGIRLNW DDRTVNDLE DSYGQQWTYE QRKVVEFTCH TAFFVSIVVV QWADLIICKT RRNSVFQQGM KNKILIFGLF EETALAAFLS Y CPGMDVAL RMYPLKPSWW FCAFPYSFLI FVYDEIRKLI LRRNPGGWVE KETYY

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Macromolecule #4: TETRAFLUOROMAGNESATE(2-)

MacromoleculeName: TETRAFLUOROMAGNESATE(2-) / type: ligand / ID: 4 / Number of copies: 1 / Formula: MF4
Molecular weightTheoretical: 100.299 Da
Chemical component information

ChemComp-MF4:
TETRAFLUOROMAGNESATE(2-)

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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

Concentration4 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.6 µm
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2017712
CTF correctionSoftware - Name: Gctf
Startup modelType of model: OTHER / Details: With RELION
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 91096

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