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- PDB-9viz: Cryo-EM structure of palytoxin-bound Na+,K+-ATPase in the transie... -

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Basic information

Entry
Database: PDB / ID: 9viz
TitleCryo-EM structure of palytoxin-bound Na+,K+-ATPase in the transient state of dephosphorylation (E2~P)
Components
  • FXYD domain-containing ion transport regulator
  • Na+,K+-ATPase beta subunit
  • Na, K-ATPase alpha subunit
KeywordsMEMBRANE PROTEIN / ion pump / P-type ATPase
Function / homology
Function and homology information


regulation of monoatomic ion transport / P-type sodium:potassium-exchanging transporter activity / sodium:potassium-exchanging ATPase complex / sodium ion export across plasma membrane / intracellular sodium ion homeostasis / potassium ion import across plasma membrane / intracellular potassium ion homeostasis / ATPase activator activity / sodium channel regulator activity / monoatomic ion transport ...regulation of monoatomic ion transport / P-type sodium:potassium-exchanging transporter activity / sodium:potassium-exchanging ATPase complex / sodium ion export across plasma membrane / intracellular sodium ion homeostasis / potassium ion import across plasma membrane / intracellular potassium ion homeostasis / ATPase activator activity / sodium channel regulator activity / monoatomic ion transport / proton transmembrane transport / ATP hydrolysis activity / ATP binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
Ion-transport regulator, FXYD motif / : / ATP1G1/PLM/MAT8 family / FXYD family signature. / 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. / Sodium and potassium ATPases beta subunits signature 2. ...Ion-transport regulator, FXYD motif / : / ATP1G1/PLM/MAT8 family / FXYD family signature. / 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. / Sodium and potassium ATPases beta subunits signature 2. / 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 / Cation transport ATPase (P-type) / E1-E2 ATPase / 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 / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
: / TETRAFLUOROALUMINATE ION / CHOLESTEROL / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Sodium/potassium-transporting ATPase subunit beta / Sodium/potassium-transporting ATPase subunit alpha / FXYD domain-containing ion transport regulator
Similarity search - Component
Biological speciesSqualus acanthias (spiny dogfish)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsKanai, R. / Vilsen, B. / Cornelius, F. / Toyoshima, C.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP23K27136 Japan
Japan Society for the Promotion of Science (JSPS)JP24K01985 Japan
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: How palytoxin transforms the Na,K pump into a cation channel.
Authors: Ryuta Kanai / Naoki Tsunekawa / Flemming Cornelius / Bente Vilsen / Chikashi Toyoshima /
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 ...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, 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·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.
History
DepositionJun 19, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Na, K-ATPase alpha subunit
B: Na+,K+-ATPase beta subunit
G: FXYD domain-containing ion transport regulator
C: Na, K-ATPase alpha subunit
D: Na+,K+-ATPase beta subunit
E: FXYD domain-containing ion transport regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)350,46154
Polymers317,3646
Non-polymers33,09748
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "C" or chain "D" or chain "E"
d_2ens_1chain "A" or chain "B" or chain "G"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ASPASPTYRTYRCD31 - 102336 - 1028
d_12CLRCLRCLRCLRCIA1301
d_13CLRCLRCLRCLRCJA1302
d_14PCWPCWPCWPCWCKA1303
d_15PCWPCWPCWPCWCLA1304
d_16PCWPCWPCWPCWCMA1305
d_17PCWPCWPCWPCWCNA1306
d_18PCWPCWPCWPCWCOA1307
d_19PCWPCWPCWPCWCPA1308
d_110PCWPCWPCWPCWCQA1310
d_111PCWPCWPCWPCWCRA1311
d_112PCWPCWPCWPCWCSA1312
d_113PCWPCWPCWPCWCTA1313
d_114PCWPCWPCWPCWCUA1314
d_115ALFALFALFALFCVA2002
d_116MGMGMGMGCWA2003
d_117NANANANACXA2005
d_118NANANANACYA2008
d_119PTXPTXPTXPTXCZA2011
d_120GLYGLYSERSERDE12 - 30512 - 305
d_121NAGNAGNAGNAGKK1
d_122NAGNAGNAGNAGKK2
d_123FUCFUCFUCFUCKK6
d_124BMABMABMABMAKK3
d_125MANMANMANMANKK4
d_126MANMANMANMANKK5
d_127NAGNAGNAGNAGLL1
d_128NAGNAGNAGNAGLL2
d_129BMABMABMABMALL3
d_130MANMANMANMANLL6
d_131MANMANMANMANLL4
d_132NAGNAGNAGNAGLL5
d_133NAGNAGNAGNAGMM1
d_134NAGNAGNAGNAGMM2
d_135FUCFUCFUCFUCMM5
d_136BMABMABMABMAMM3
d_137MANMANMANMANMM4
d_138NAGNAGNAGNAGNN1
d_139NAGNAGNAGNAGNN2
d_140CLRCLRCLRCLRDAB501
d_141CLRCLRCLRCLRDBB502
d_142GLUGLUCYSCYSEF4 - 4324 - 63
d_21ASPASPTYRTYRAA31 - 102336 - 1028
d_22CLRCLRCLRCLRAO1301
d_23CLRCLRCLRCLRAP1302
d_24PCWPCWPCWPCWAQ1303
d_25PCWPCWPCWPCWAR1304
d_26PCWPCWPCWPCWAS1305
d_27PCWPCWPCWPCWAT1306
d_28PCWPCWPCWPCWAU1307
d_29PCWPCWPCWPCWAV1308
d_210PCWPCWPCWPCWAW1310
d_211PCWPCWPCWPCWAX1311
d_212PCWPCWPCWPCWAY1312
d_213PCWPCWPCWPCWAZ1313
d_214PCWPCWPCWPCWAAA1314
d_215ALFALFALFALFABA2002
d_216MGMGMGMGACA2003
d_217NANANANAADA2005
d_218NANANANAAEA2008
d_219PTXPTXPTXPTXAFA2011
d_220GLYGLYSERSERBB12 - 30512 - 305
d_221NAGNAGNAGNAGFG1
d_222NAGNAGNAGNAGFG2
d_223FUCFUCFUCFUCFG6
d_224BMABMABMABMAFG3
d_225MANMANMANMANFG4
d_226MANMANMANMANFG5
d_227NAGNAGNAGNAGHH1
d_228NAGNAGNAGNAGHH2
d_229BMABMABMABMAHH3
d_230MANMANMANMANHH6
d_231MANMANMANMANHH4
d_232NAGNAGNAGNAGHH5
d_233NAGNAGNAGNAGII1
d_234NAGNAGNAGNAGII2
d_235FUCFUCFUCFUCII5
d_236BMABMABMABMAII3
d_237MANMANMANMANII4
d_238NAGNAGNAGNAGJJ1
d_239NAGNAGNAGNAGJJ2
d_240CLRCLRCLRCLRBGA501
d_241CLRCLRCLRCLRBHA502
d_242GLUGLUCYSCYSGC4 - 4324 - 63

NCS oper: (Code: givenMatrix: (-0.999987025637, -0.00238963225512, -0.00449869032913), (0.00236900676832, -0.999986684833, 0.00458453534131), (-0.00450958578185, 0.00457381843205, 0.999979371698) ...NCS oper: (Code: given
Matrix: (-0.999987025637, -0.00238963225512, -0.00449869032913), (0.00236900676832, -0.999986684833, 0.00458453534131), (-0.00450958578185, 0.00457381843205, 0.999979371698)
Vector: 258.9996111, 257.319772771, 0.0184862742002)

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Components

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Protein , 3 types, 6 molecules ACBDGE

#1: Protein Na, K-ATPase alpha subunit


Mass: 113309.891 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Squalus acanthias (spiny dogfish) / References: UniProt: Q4H132
#2: Protein Na+,K+-ATPase beta subunit / Sodium/potassium-transporting ATPase subunit beta-1


Mass: 35176.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Squalus acanthias (spiny dogfish) / References: UniProt: C4IX13
#3: Protein FXYD domain-containing ion transport regulator


Mass: 10195.847 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Squalus acanthias (spiny dogfish) / References: UniProt: Q70Q12

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Sugars , 4 types, 8 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose- ...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


Type: oligosaccharide / Mass: 1114.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-1-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#7: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 6 types, 40 molecules

#8: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H46O
#9: Chemical...
ChemComp-PCW / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / (Z,Z)-4-HYDROXY-N,N,N-TRIMETHYL-10-OXO-7-[(1-OXO-9-OCTADECENYL)OXY]-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-18-EN-1-AMINIUM-4-OXIDE


Mass: 787.121 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM
#10: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF4
#11: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#12: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#13: Chemical ChemComp-A1MA6 / palytoxin


Mass: 2680.139 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C129H223N3O54 / Feature type: SUBJECT OF INVESTIGATION

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Details

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, #1, #3 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Squalus acanthias (spiny dogfish)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
11 mMmagnesium chlorideMgCl21
226 mMsodium chlorideNaCl1
30.2 mMphosphoric acidH3PO41
420 mMHEPESC8H18N2O4S1
50.01 %C12E8C28H58O91
61 mMDTTC4H10O2S21
71 mMaluminium chlorideAlCl31
84 mMsodium fluorideNaF1
90.3 mMpalytoxinC129H223N3O541
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 99.9 % / Chamber temperature: 279 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION4.0.1particle selection
2PHENIX1.21.2_5419model refinement
5CTFFIND4CTF correction
10RELION4.0.1initial Euler assignment
11RELION4.0.1final Euler assignment
12RELION4.0.1classification
13RELION4.0.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 62516 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 2zxe

2zxe


Accession code: 2zxe / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 76.08 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.006123310
ELECTRON MICROSCOPYf_angle_d1.233231494
ELECTRON MICROSCOPYf_chiral_restr0.22893690
ELECTRON MICROSCOPYf_plane_restr0.00916466
ELECTRON MICROSCOPYf_dihedral_angle_d19.23339658
Refine LS restraints NCSType: NCS constraints / Rms dev position: 3.60775654359E-13 Å

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