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- EMDB-27168: Human alpha3 Na+/K+-ATPase in its exoplasmic side-open state -

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Basic information

Entry
Database: EMDB / ID: EMD-27168
TitleHuman alpha3 Na+/K+-ATPase in its exoplasmic side-open state
Map dataHuman alpha3 Na+/K+-ATPase in its exoplasmic side-open state
Sample
  • Complex: Na+/K+-ATPase
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit alpha-3
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit beta-1
    • Protein or peptide: FXYD domain-containing ion transport regulator 6
KeywordsNa/K-ATPase / a3 / b1 / FXYD6 / occluded state / TRANSPORT PROTEIN / TRANSLOCASE-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


neuron to neuron synapse / protein transport into plasma membrane raft / Na+/K+-exchanging ATPase / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / photoreceptor inner segment membrane / membrane repolarization during cardiac muscle cell action potential / steroid hormone binding / P-type sodium:potassium-exchanging transporter activity / sodium:potassium-exchanging ATPase complex ...neuron to neuron synapse / protein transport into plasma membrane raft / Na+/K+-exchanging ATPase / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / photoreceptor inner segment membrane / membrane repolarization during cardiac muscle cell action potential / steroid hormone binding / P-type sodium:potassium-exchanging transporter activity / sodium:potassium-exchanging ATPase complex / membrane repolarization / establishment or maintenance of transmembrane electrochemical gradient / regulation of resting membrane potential / cell communication by electrical coupling involved in cardiac conduction / sodium ion export across plasma membrane / intracellular sodium ion homeostasis / regulation of calcium ion transmembrane transport / relaxation of cardiac muscle / response to glycoside / regulation of cardiac muscle contraction by calcium ion signaling / Basigin interactions / neuronal cell body membrane / cellular response to steroid hormone stimulus / sodium ion transport / organelle membrane / potassium ion import across plasma membrane / intracellular potassium ion homeostasis / ATPase activator activity / Ion transport by P-type ATPases / intercalated disc / lateral plasma membrane / sodium channel regulator activity / sperm flagellum / transporter activator activity / ATP metabolic process / cardiac muscle contraction / Ion homeostasis / photoreceptor inner segment / neuron projection maintenance / T-tubule / sodium ion transmembrane transport / proton transmembrane transport / protein localization to plasma membrane / sarcolemma / caveola / potassium ion transport / cellular response to amyloid-beta / intracellular calcium ion homeostasis / MHC class II protein complex binding / extracellular vesicle / protein-folding chaperone binding / amyloid-beta binding / presynaptic membrane / ATPase binding / regulation of gene expression / protein-macromolecule adaptor activity / basolateral plasma membrane / Potential therapeutics for SARS / postsynaptic membrane / response to hypoxia / cell adhesion / protein stabilization / apical plasma membrane / protein heterodimerization activity / axon / innate immune response / neuronal cell body / synapse / protein kinase binding / glutamatergic synapse / endoplasmic reticulum / Golgi apparatus / ATP hydrolysis activity / extracellular exosome / ATP binding / metal ion binding / membrane / 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. / : ...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 / 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 / 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: 3.9 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-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27168.png

Downloads & links

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Map

FileDownload / File: emd_27168.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman alpha3 Na+/K+-ATPase in its exoplasmic side-open state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 220 pix.
= 237.6 Å		1.08 Å/pix.
x 220 pix.
= 237.6 Å		1.08 Å/pix.
x 220 pix.
= 237.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.03
Minimum - Maximum-0.08163329 - 0.13734849
Average (Standard dev.)0.00020289245 (±0.0052679693)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 237.6 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 exoplasmic side-open state

Fileemd_27168_half_map_1.map
AnnotationHuman alpha3 Na+/K+-ATPase in its exoplasmic side-open 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 exoplasmic side-open state

Fileemd_27168_half_map_2.map
AnnotationHuman alpha3 Na+/K+-ATPase in its exoplasmic side-open 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+-ATPase
Components
  • Complex: Na+/K+-ATPase
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit alpha-3
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit beta-1
    • Protein or peptide: FXYD domain-containing ion transport regulator 6

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Supramolecule #1: Na+/K+-ATPase

SupramoleculeName: Na+/K+-ATPase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Sodium/potassium-transporting ATPase subunit alpha-3

MacromoleculeName: Sodium/potassium-transporting ATPase subunit alpha-3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: Na+/K+-exchanging ATPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 111.725195 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 NVPAGL LATVTVCLTL TAKRMARKNC LVKNLEAVET LGSTSTICS(BFD) KTGTLTQNRM TVAHMWFDNQ IHEADTTEDQ SGTSFDKSS HTWVALSHIA GLCNRAVFKG GQDNIPVLKR DVAGDASESA LLKCIELSSG SVKLMRERNK KVAEIPFNST N KYQLSIHE TEDPNDNRYL LVMKGAPERI LDRCSTILLQ GKEQPLDEEM KEAFQNAYLE LGGLGERVLG FCHYYLPEEQ FP KGFAFDC DDVNFTTDNL CFVGLMSMID PPRAAVPDAV GKCRSAGIKV IMVTGDHPIT AKAIAKGVGI ISEGNETVED IAA RLNIPV SQVNPRDAKA CVIHGTDLKD FTSEQIDEIL QNHTEIVFAR TSPQQKLIIV EGCQRQGAIV AVTGDGVNDS PALK KADIG VAMGIAGSDV SKQAADMILL DDNFASIVTG VEEGRLIFDN LKKSIAYTLT SNIPAITPFL LFIMANIPLP LGTIT ILCI ALGTAMVPAI SLAYEAAESD IMKRQPRNPR TDKLVNERLI SMAYGQIGMI QALGGFFSYF VILAENGFLP GNLVGI RLN WDDRTVNDLE DSYGQQWTYE QRKVVEFTCH TAFFVSIVVV QWADLIICKT RRNSVFQQGM KNKILIFGLF EETALAA FL SYCPGMDVAL RMYPLKPSWW FCAFPYSFLI FVYDEIRKLI LRRNPGGWVE KETYY

UniProtKB: Sodium/potassium-transporting ATPase subunit alpha-3

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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: 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

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

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Macromolecule #3: FXYD domain-containing ion transport regulator 6

MacromoleculeName: FXYD domain-containing ion transport regulator 6 / type: protein_or_peptide / ID: 3 / 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

UniProtKB: FXYD domain-containing ion transport regulator 6

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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 / Pretreatment - Time: 90 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

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

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Image processing

Particle selectionNumber selected: 1559941
Startup modelType of model: OTHER / Details: With RELION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 84639
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION

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