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- PDB-8d3y: Human alpha3 Na+/K+-ATPase in its exoplasmic side-open state -

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Basic information

Entry
Database: PDB / ID: 8d3y
TitleHuman alpha3 Na+/K+-ATPase in its exoplasmic side-open state
Components
  • FXYD domain-containing ion transport regulator 6
  • Sodium/potassium-transporting ATPase subunit alpha-3
  • Sodium/potassium-transporting ATPase subunit beta-1
KeywordsTRANSLOCASE/TRANSPORT PROTEIN / Na/K-ATPase / a3 / b1 / FXYD6 / occluded state / TRANSPORT PROTEIN / TRANSLOCASE-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


positive regulation of P-type sodium:potassium-exchanging transporter activity / neuron to neuron synapse / protein transport into plasma membrane raft / positive regulation of potassium ion transmembrane transporter activity / Na+/K+-exchanging ATPase / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / membrane repolarization during cardiac muscle cell action potential / photoreceptor inner segment membrane / steroid hormone binding ...positive regulation of P-type sodium:potassium-exchanging transporter activity / neuron to neuron synapse / protein transport into plasma membrane raft / positive regulation of potassium ion transmembrane transporter activity / Na+/K+-exchanging ATPase / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / membrane repolarization during cardiac muscle cell action potential / photoreceptor inner segment membrane / steroid hormone binding / response to glycoside / 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 / sodium ion export across plasma membrane / cell communication by electrical coupling involved in cardiac conduction / regulation of calcium ion transmembrane transport / intracellular sodium ion homeostasis / positive regulation of ATP-dependent activity / intracellular potassium ion homeostasis / regulation of cardiac muscle contraction by calcium ion signaling / relaxation of cardiac muscle / Basigin interactions / neuronal cell body membrane / sodium ion transport / cellular response to steroid hormone stimulus / organelle membrane / potassium ion import across plasma membrane / monoatomic cation transmembrane transport / Ion transport by P-type ATPases / ATPase activator activity / sperm flagellum / intercalated disc / sodium channel regulator activity / lateral plasma membrane / ATP metabolic process / cardiac muscle contraction / Ion homeostasis / photoreceptor inner segment / T-tubule / neuron projection maintenance / sodium ion transmembrane transport / proton transmembrane transport / protein localization to plasma membrane / potassium ion transport / sarcolemma / intracellular calcium ion homeostasis / cellular response to amyloid-beta / 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 / postsynaptic membrane / Potential therapeutics for SARS / cell adhesion / protein stabilization / apical plasma membrane / protein heterodimerization activity / axon / innate immune response / neuronal cell body / synapse / protein kinase binding / glutamatergic synapse / Golgi apparatus / endoplasmic reticulum / 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 / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsNguyen, P.T. / Bai, X.
Funding support United States, 2items
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, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sodium/potassium-transporting ATPase subunit alpha-3
B: Sodium/potassium-transporting ATPase subunit beta-1
G: FXYD domain-containing ion transport regulator 6


Theoretical massNumber of molelcules
Total (without water)157,6893
Polymers157,6893
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Sodium/potassium-transporting ATPase subunit alpha-3 / Na(+)/K(+) ATPase alpha-3 subunit / Na(+)/K(+) ATPase alpha(III) subunit / Sodium pump subunit alpha-3


Mass: 111725.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATP1A3
Production host: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
References: UniProt: P13637, Na+/K+-exchanging ATPase
#2: Protein Sodium/potassium-transporting ATPase subunit beta-1 / Sodium/potassium-dependent ATPase subunit beta-1


Mass: 35108.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATP1B1, ATP1B
Production host: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
References: UniProt: P05026
#3: Protein FXYD domain-containing ion transport regulator 6 / Phosphohippolin


Mass: 10855.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FXYD6, UNQ521/PRO1056
Production host: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
References: UniProt: Q9H0Q3
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Na+/K+-ATPase / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
Buffer solutionpH: 7.4
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 1600 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM software
IDNameCategory
1RELIONparticle selection
2SerialEMimage acquisition
4GctfCTF correction
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1559941
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 84639 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00310097
ELECTRON MICROSCOPYf_angle_d0.55713715
ELECTRON MICROSCOPYf_dihedral_angle_d3.7781387
ELECTRON MICROSCOPYf_chiral_restr0.0411584
ELECTRON MICROSCOPYf_plane_restr0.0031765

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