+
Open data
-
Basic information
Entry | Database: PDB / ID: 8d3u | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Human alpha3 Na+/K+-ATPase in its Na+-occluded state | |||||||||
![]() |
| |||||||||
![]() | TRANSLOCASE/TRANSPORT PROTEIN / Na/K-ATPase / a3 / b1 / FXYD6 / occluded state / TRANSPORT PROTEIN / TRANSLOCASE-TRANSPORT PROTEIN complex | |||||||||
Function / homology | ![]() 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 / membrane repolarization during cardiac muscle cell action potential ...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 / 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 / P-type sodium:potassium-exchanging transporter activity / sodium:potassium-exchanging ATPase complex / establishment or maintenance of transmembrane electrochemical gradient / sodium ion export across plasma membrane / intracellular potassium ion homeostasis / intracellular sodium ion homeostasis / positive regulation of ATP-dependent activity / regulation of cardiac muscle contraction by calcium ion signaling / Basigin interactions / relaxation of cardiac muscle / cell communication by electrical coupling involved in cardiac conduction / cellular response to steroid hormone stimulus / neuronal cell body membrane / monoatomic cation transmembrane transport / potassium ion import across plasma membrane / organelle membrane / Ion transport by P-type ATPases / ATPase activator activity / intercalated disc / sodium ion transmembrane transport / lateral plasma membrane / sperm flagellum / sodium channel regulator activity / cardiac muscle contraction / ATP metabolic process / monoatomic ion transmembrane transport / Ion homeostasis / proton transmembrane transport / T-tubule / neuron projection maintenance / photoreceptor inner segment / protein localization to plasma membrane / sarcolemma / intracellular calcium ion homeostasis / cellular response to amyloid-beta / extracellular vesicle / MHC class II protein complex binding / protein-macromolecule adaptor activity / presynaptic membrane / amyloid-beta binding / protein-folding chaperone binding / ATPase binding / regulation of gene expression / basolateral plasma membrane / postsynaptic membrane / Potential therapeutics for SARS / protein stabilization / cell adhesion / apical plasma membrane / protein heterodimerization activity / axon / innate immune response / neuronal cell body / glutamatergic synapse / synapse / protein kinase binding / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / extracellular exosome / ATP binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
![]() | Nguyen, P.T. / Bai, X. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 309.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 237.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 47.7 KB | Display | |
Data in CIF | ![]() | 69.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 27164MC ![]() 8d3vC ![]() 8d3wC ![]() 8d3xC ![]() 8d3yC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
#1: Protein | Mass: 111864.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: Mammalian expression vector Flag-MCS-pcDNA3.1 (others) References: UniProt: P13637, Na+/K+-exchanging ATPase |
---|---|
#2: Protein | Mass: 35108.258 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: Mammalian expression vector Flag-MCS-pcDNA3.1 (others) References: UniProt: P05026 |
#3: Protein | Mass: 10855.645 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: Mammalian expression vector Flag-MCS-pcDNA3.1 (others) References: UniProt: Q9H0Q3 |
#4: Chemical | ChemComp-ADP / |
#5: Chemical | ChemComp-ALF / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: Na+/K+-ATPase / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: Mammalian expression vector Flag-MCS-pcDNA3.1 (others) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 1600 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-
Processing
EM software |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||
Particle selection | Num. of particles selected: 1889299 | |||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 108246 / Symmetry type: POINT |