9VJ2 | pdb_00009vj2

Crystal structure of palytoxin-bound Na+,K+-ATPase in the E2P state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.79 Å
  • R-Value Free: 
    0.276 (Depositor), 0.271 (DCC) 
  • R-Value Work: 
    0.227 (Depositor), 0.253 (DCC) 
  • R-Value Observed: 
    0.229 (Depositor) 

Starting Model: experimental
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Literature

How palytoxin transforms the Na + ,K + pump into a cation channel.

Kanai, R.Tsunekawa, N.Cornelius, F.Vilsen, B.Toyoshima, C.

(2025) Proc Natl Acad Sci U S A 122: e2506450122-e2506450122

  • DOI: https://doi.org/10.1073/pnas.2506450122
  • Primary Citation of Related Structures:  
    9VIY, 9VIZ, 9VJ0, 9VJ1, 9VJ2

  • PubMed Abstract: 

    Palytoxin (PTX), a potent marine toxin, has long been known to transform Na + ,K + -ATPase (NKA), an indispensable ion pump, into a nonselective cation channel. It has been postulated that PTX takes control of the two gates on either side of a channel-like pore. These gates normally open and close alternately, synchronized with chemical events, never opening simultaneously. A critical question is whether palytoxin takes over the control of the two gates or creates a new pathway. Here, we present structures of NKA with bound palytoxin in three different states. PTX binds to NKA in E2P, occupying the physiological Na + exit pathway, similar to istaroxime, a new-generation cardiotonic steroid. Adding Na + and ATP/ADP to the NKA·PTX complex induces an open channel traversing the entire membrane alongside the physiological ion pathway. As AlF x , a stable transition state analog of phosphate replaces phosphate in the NKA·PTX complex preformed in E2P, the complex appears to undergo the normal reaction cycle from E2P to E1· n Na + . PTX occupies the space between the transmembrane helices M4 and M6, thereby preventing the closure of the extracellular half of the ion pathway. These structures demonstrate that the architecture of NKA is fundamentally different from "a pore with two gates." Each half of the ion pathway comprises three segments, including a movable component that plays a pivotal role in translocating the bound cations by connecting the constant part to an appropriate inlet. The ion pathway of NKA transforms dynamically, ensuring that the two halves never exist simultaneously.


  • Organizational Affiliation
    • Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku 113-0032, Tokyo, Japan.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium/potassium-transporting ATPase subunit alpha1,021Sus scrofaMutation(s): 0 
UniProt
Find proteins for D2WKD6 (Sus scrofa)
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Go to UniProtKB:  D2WKD6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD2WKD6
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium/potassium-transporting ATPase subunit beta-1303Sus scrofaMutation(s): 0 
UniProt
Find proteins for P05027 (Sus scrofa)
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Go to UniProtKB:  P05027
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UniProt GroupP05027
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
FXYD domain-containing ion transport regulatorC [auth G]65Sus scrofaMutation(s): 0 
UniProt
Find proteins for Q58K79 (Sus scrofa)
Explore Q58K79 
Go to UniProtKB:  Q58K79
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UniProt GroupQ58K79
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth C]2N-Glycosylation
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1MA6 (Subject of Investigation/LOI)
Query on A1MA6

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O [auth A]palytoxin
C129 H223 N3 O54
CWODDUGJZSCNGB-HQNRRURTSA-N
PCW
Query on PCW

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I [auth A]
J [auth A]
K [auth A]
L [auth A]
M [auth A]
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A]
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H85 N O8 P
SNKAWJBJQDLSFF-NVKMUCNASA-O
CLR
Query on CLR

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G [auth A],
H [auth A]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
NAG
Query on NAG

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P [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MG
Query on MG

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E [auth A],
F [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
BFD
Query on BFD
A
L-PEPTIDE LINKINGC4 H6 Be F3 N O4ASP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.79 Å
  • R-Value Free:  0.276 (Depositor), 0.271 (DCC) 
  • R-Value Work:  0.227 (Depositor), 0.253 (DCC) 
  • R-Value Observed: 0.229 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.022α = 90
b = 85.022β = 90
c = 646.129γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP23K27136
Japan Society for the Promotion of Science (JSPS)JapanJP24K01985

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-01
    Type: Initial release