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- PDB-8d3w: Human alpha3 Na+/K+-ATPase in its AMPPCP-bound cytoplasmic side-o... -

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Basic information

Entry
Database: PDB / ID: 8d3w
TitleHuman alpha3 Na+/K+-ATPase in its AMPPCP-bound cytoplasmic 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
KeywordsTRANSPORT PROTEIN / Na/K-ATPase / a3 / b1 / FXYD6 / AMPPCP-bound / cytoplasmic side-open
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 / regulation of calcium ion transmembrane transport / intracellular sodium ion homeostasis / relaxation of cardiac muscle / regulation of cardiac muscle contraction by calcium ion signaling / response to glycoside / 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 and potassium ATPases beta subunits signature 2. / 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. / : ...Ion-transport regulator, FXYD motif / : / ATP1G1/PLM/MAT8 family / FXYD family signature. / Sodium and potassium ATPases beta subunits signature 2. / 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. / : / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / 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: 3.5 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 1.1Nov 13, 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

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,3334
Polymers157,8283
Non-polymers5051
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: 111864.289 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
#4: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PCP, energy-carrying molecule analogue*YM
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: #2-#3 / 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 / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
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

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: 2926310
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98088 / Symmetry type: POINT

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