8D3X | pdb_00008d3x

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

• PDB DOI: https://doi.org/10.2210/pdb8D3X/pdb
• EM Map EMD-27167: EMDB EMDataResource

• Classification: TRANSLOCASE/TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Mammalian expression vector Flag-MCS-pcDNA3.1
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMmpstruc


• Deposited: 2022-06-01 Released: 2022-09-21 
• Deposition Author(s): Nguyen, P.T., Bai, X.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Welch Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for gating mechanism of the human sodium-potassium pump.

Nguyen, P.T., Deisl, C., Fine, M., Tippetts, T.S., Uchikawa, E., Bai, X.C., Levine, B.

(2022) Nat Commun 13: 5293-5293

• PubMed: 36075933 
• DOI: https://doi.org/10.1038/s41467-022-32990-x
• Primary Citation Related Structures: 
  8D3U, 8D3V, 8D3W, 8D3X, 8D3Y


• PubMed 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 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 ₄ ^- trapped Na ⁺ -occluded (E1•P-ADP), BeF ₃ ^- trapped exoplasmic side-open (E2P) and MgF ₄ ^2- trapped K ⁺ -occluded (E2•P _i ) states. Our work reveals the atomically resolved structural detail of the cytoplasmic gating mechanism of the Na ⁺ /K ⁺ -ATPase.

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Organizational Affiliation: 
• Howard Hughes Medical Institute and Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA. [e-mail].
Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA. [e-mail].
Howard Hughes Medical Institute and Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 157.93 kDa 
• Atom Count: 10,219 
• Modeled Residue Count: 1,305 
• Deposited Residue Count: 1,414 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium/potassium-transporting ATPase subunit beta-1	A [auth B]	303	Homo sapiens	Mutation(s): 0  Gene Names: ATP1B1, ATP1B Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P05026 (Homo sapiens) Explore P05026  Go to UniProtKB:  P05026
PHAROS:  P05026 GTEx:  ENSG00000143153

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
FXYD domain-containing ion transport regulator 6	B [auth G]	98	Homo sapiens	Mutation(s): 0  Gene Names: FXYD6, UNQ521/PRO1056 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H0Q3 (Homo sapiens) Explore Q9H0Q3  Go to UniProtKB:  Q9H0Q3
PHAROS:  Q9H0Q3 GTEx:  ENSG00000137726

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium/potassium-transporting ATPase subunit alpha-3	C [auth A]	1,013	Homo sapiens	Mutation(s): 0  Gene Names: ATP1A3 EC: 7.2.2.13 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P13637 (Homo sapiens) Explore P13637  Go to UniProtKB:  P13637
PHAROS:  P13637 GTEx:  ENSG00000105409

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MF4 (Subject of Investigation/LOI)	D [auth A]	TETRAFLUOROMAGNESATE(2-) F4 Mg XVYWAXYEHHUKQW-UHFFFAOYSA-J

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-09-21 
Deposition Author(s): Nguyen, P.T., Bai, X.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM136976
Welch Foundation	United States	I-1944

Revision History  

• Version 1.0: 2022-09-21
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Structure summary
• Version 1.2: 2025-05-28
  Changes: Data collection