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- PDB-9vj1: Cryo-EM structure of Na+,K+-ATPase that forms a cation channel wi... -

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Basic information

Entry
Database: PDB / ID: 9vj1
TitleCryo-EM structure of Na+,K+-ATPase that forms a cation channel with palytoxin (ADP form)
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
: / ADENOSINE-5'-DIPHOSPHATE / 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. / Cornelius, F. / Vilsen, B. / 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
D: Na+,K+-ATPase beta subunit
C: Na, K-ATPase alpha subunit
E: FXYD domain-containing ion transport regulator
B: Na+,K+-ATPase beta subunit
A: Na, K-ATPase alpha subunit
G: FXYD domain-containing ion transport regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)348,82656
Polymers317,3646
Non-polymers31,46250
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 "A" or chain "B" or chain "G"
d_2ens_1chain "C" or chain "D" or chain "E"

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_11GLYGLYSERSERBD12 - 30512 - 305
d_12NAGNAGNAGNAGKK1
d_13NAGNAGNAGNAGKK2
d_14FUCFUCFUCFUCKK6
d_15BMABMABMABMAKK3
d_16MANMANMANMANKK4
d_17MANMANMANMANKK5
d_18NAGNAGNAGNAGLL1
d_19NAGNAGNAGNAGLL2
d_110BMABMABMABMALL3
d_111MANMANMANMANLL6
d_112MANMANMANMANLL4
d_113NAGNAGNAGNAGLL5
d_114NAGNAGNAGNAGMM1
d_115NAGNAGNAGNAGMM2
d_116FUCFUCFUCFUCMM5
d_117BMABMABMABMAMM3
d_118MANMANMANMANMM4
d_119NAGNAGNAGNAGNN1
d_120NAGNAGNAGNAGNN2
d_121CLRCLRCLRCLRBJA501
d_122CLRCLRCLRCLRBKA502
d_123ASPASPTYRTYRAE42 - 102347 - 1028
d_124CLRCLRCLRCLRALA1301
d_125CLRCLRCLRCLRAMA1302
d_126PCWPCWPCWPCWANA1303
d_127PCWPCWPCWPCWAOA1305
d_128PCWPCWPCWPCWAPA1306
d_129PCWPCWPCWPCWAQA1307
d_130PCWPCWPCWPCWARA1309
d_131PCWPCWPCWPCWASA1310
d_132PCWPCWPCWPCWATA1311
d_133PCWPCWPCWPCWAUA1312
d_134PCWPCWPCWPCWAVA1314
d_135CLRCLRCLRCLRAWA1315
d_136MGMGMGMGAXA2003
d_137ADPADPADPADPAYA2004
d_138NANANANAAZA2005
d_139NANANANAAAB2006
d_140NANANANAABB2007
d_141NANANANAACB2008
d_142PTXPTXPTXPTXADB2011
d_143GLUGLUCYSCYSGF4 - 4324 - 63
d_21GLYGLYSERSERDA12 - 30512 - 305
d_22NAGNAGNAGNAGFG1
d_23NAGNAGNAGNAGFG2
d_24FUCFUCFUCFUCFG6
d_25BMABMABMABMAFG3
d_26MANMANMANMANFG4
d_27MANMANMANMANFG5
d_28NAGNAGNAGNAGHH1
d_29NAGNAGNAGNAGHH2
d_210BMABMABMABMAHH3
d_211MANMANMANMANHH6
d_212MANMANMANMANHH4
d_213NAGNAGNAGNAGHH5
d_214NAGNAGNAGNAGII1
d_215NAGNAGNAGNAGII2
d_216FUCFUCFUCFUCII5
d_217BMABMABMABMAII3
d_218MANMANMANMANII4
d_219NAGNAGNAGNAGJJ1
d_220NAGNAGNAGNAGJJ2
d_221CLRCLRCLRCLRDO501
d_222CLRCLRCLRCLRDP502
d_223ASPASPTYRTYRCB42 - 102347 - 1028
d_224CLRCLRCLRCLRCQ1301
d_225CLRCLRCLRCLRCR1302
d_226PCWPCWPCWPCWCS1303
d_227PCWPCWPCWPCWCT1305
d_228PCWPCWPCWPCWCU1306
d_229PCWPCWPCWPCWCV1307
d_230PCWPCWPCWPCWCW1309
d_231PCWPCWPCWPCWCX1310
d_232PCWPCWPCWPCWCY1311
d_233PCWPCWPCWPCWCZ1312
d_234PCWPCWPCWPCWCAA1314
d_235CLRCLRCLRCLRCBA1315
d_236MGMGMGMGCCA2003
d_237ADPADPADPADPCDA2004
d_238NANANANACEA2005
d_239NANANANACFA2006
d_240NANANANACGA2007
d_241NANANANACHA2008
d_242PTXPTXPTXPTXCIA2011
d_243GLUGLUCYSCYSEC4 - 4324 - 63

NCS oper: (Code: givenMatrix: (-0.999957617888, -0.00158636174023, 0.00906895163815), (0.00160315569098, -0.999997013228, 0.00184483768281), (0.00906599797134, 0.00185929843612, 0.999957174428)Vector: ...NCS oper: (Code: given
Matrix: (-0.999957617888, -0.00158636174023, 0.00906895163815), (0.00160315569098, -0.999997013228, 0.00184483768281), (0.00906599797134, 0.00185929843612, 0.999957174428)
Vector: 257.220473277, 257.828626759, -1.17426950726)

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Components

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Protein , 3 types, 6 molecules DBCAEG

#1: 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
#2: 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
#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, 42 molecules

#8: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 10 / 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.: 18 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM
#10: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#11: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#12: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / 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
14 mMmagnesium chlorideMgCl21
220 mMHEPESC8H18N2O4S1
30.01 %C12E8C28H58O91
41 mMDTTC4H10O2S21
53 mMADP disodiumC10H13N5Na2O10P21
60.3 mMpalytoxinC129H223N3O541
794 mMsodium chlorideNaCl1
80.5 mMphosphoric acidH3PO41
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
5CTFFIND4.1.14CTF 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: 28472 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 8jfz

8jfz


Accession code: 8jfz / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 82.21 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.006523096
ELECTRON MICROSCOPYf_angle_d1.166331252
ELECTRON MICROSCOPYf_chiral_restr0.25683676
ELECTRON MICROSCOPYf_plane_restr0.00936406
ELECTRON MICROSCOPYf_dihedral_angle_d19.62259542
Refine LS restraints NCSType: NCS constraints / Rms dev position: 5.7348132263E-10 Å

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