9VJ1 | pdb_00009vj1

Cryo-EM structure of Na+,K+-ATPase that forms a cation channel with palytoxin (ADP form)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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
Na+,K+-ATPase beta subunitA [auth D],
D [auth B]
305Squalus acanthiasMutation(s): 0 
UniProt
Find proteins for C4IX13 (Squalus acanthias)
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Go to UniProtKB:  C4IX13
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4IX13
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Na, K-ATPase alpha subunitB [auth C],
E [auth A]
1,028Squalus acanthiasMutation(s): 0 
UniProt
Find proteins for Q4H132 (Squalus acanthias)
Explore Q4H132 
Go to UniProtKB:  Q4H132
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UniProt GroupQ4H132
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
FXYD domain-containing ion transport regulatorC [auth E],
F [auth G]
94Squalus acanthiasMutation(s): 0 
UniProt
Find proteins for Q70Q12 (Squalus acanthias)
Explore Q70Q12 
Go to UniProtKB:  Q70Q12
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UniProt GroupQ70Q12
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth F],
K
6N-Glycosylation
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
H, L
6N-Glycosylation
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
I, M
5N-Glycosylation
Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
J, N
2N-Glycosylation
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1MA6 (Subject of Investigation/LOI)
Query on A1MA6

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BB [auth A],
FA [auth C]
palytoxin
C129 H223 N3 O54
CWODDUGJZSCNGB-HQNRRURTSA-N
PCW
Query on PCW

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CB [auth G]
DB [auth G]
GA [auth E]
HA [auth E]
IA [auth B]
CB [auth G],
DB [auth G],
GA [auth E],
HA [auth E],
IA [auth B],
NA [auth A],
OA [auth A],
PA [auth A],
QA [auth A],
RA [auth A],
S [auth C],
SA [auth A],
T [auth C],
TA [auth A],
U [auth C],
V [auth C],
W [auth C],
X [auth C]
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H85 N O8 P
SNKAWJBJQDLSFF-NVKMUCNASA-O
ADP
Query on ADP

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AA [auth C],
WA [auth A]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
CLR
Query on CLR

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JA [auth B]
KA [auth B]
LA [auth A]
MA [auth A]
O [auth D]
JA [auth B],
KA [auth B],
LA [auth A],
MA [auth A],
O [auth D],
P [auth D],
Q [auth C],
R [auth C],
UA [auth A],
Y [auth C]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
MG
Query on MG

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VA [auth A],
Z [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

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AB [auth A]
BA [auth C]
CA [auth C]
DA [auth C]
EA [auth C]
AB [auth A],
BA [auth C],
CA [auth C],
DA [auth C],
EA [auth C],
XA [auth A],
YA [auth A],
ZA [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONRELION4.0.1

Structure Validation

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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