9VJ2: Palytoxin-bound Na+,K+-ATPase in the E2P state

Crystal structure of palytoxin-bound Na+,K+-ATPase in the E2P state. Determined by X-ray diffraction at 3.79 Å resolution. Released 1 Oct 2025.

Method: X-ray diffraction
Resolution: 3.79 Å
Organism: Sus scrofa
Chains: 3
Atoms: 10,796
Mol. weight: 164.11 kDa
Ligands: A1MA6, BEF, PCW, CLR
Released: 1 Oct 2025

Explore 9VJ2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9VJ2 contains 71 α-helices and 54 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 56 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	22-30	9
α-helix	32-33	2
α-helix	41-48	8
β-strand	51	1	1
β-strand	55	1	1
α-helix	58-68	11
α-helix	73-78	6
α-helix	81-90	10
α-helix	93-112	20
α-helix	123-154	32
β-strand	162-166	5	2
β-strand	169-173	5	2
α-helix	175-177	3
β-strand	183-186	4	2
β-strand	191	1	3
β-strand	195-201	7	2
β-strand	204-207	4	3
α-helix	217	1
β-strand	218-220	3	3
β-strand	235-236	2	2
β-strand	241-244	4	3
β-strand	247-253	7	2
α-helix	255-257	3
α-helix	259-268	10
α-helix	276-305	30
α-helix	310-323	14
α-helix	329-346	18
β-strand	349-351	3	4
α-helix	354-357	4
α-helix	359-362	4
β-strand	365-368	4	4
α-helix	370-374	5
β-strand	375	1	5
β-strand	380-386	7	6
β-strand	389-392	4	6
α-helix	409-420	12
β-strand	426	1	7
β-strand	440	1	7
α-helix	444-456	13
α-helix	461-465	5
β-strand	469-473	5	6
β-strand	482-487	6	6
β-strand	496-502	7	6
α-helix	504-509	6
β-strand	511-516	6	6
β-strand	519-521	3	6
α-helix	525-540	16
β-strand	544	1	6
β-strand	547-551	5	6
β-strand	576-585	10	6
α-helix	586-587	2
β-strand	588	1	5
α-helix	589	1
α-helix	592-601	10
α-helix	604	1
β-strand	605-609	5	4
α-helix	614-624	11
α-helix	634-641	8
α-helix	650-652	3
β-strand	655-659	5	4
α-helix	660-664	5
α-helix	668-677	10
β-strand	680-684	5	4
α-helix	688-700	13
β-strand	705-709	5	4
α-helix	712-714	3
α-helix	715-720	6
β-strand	723-727	5	4
α-helix	733-738	6
β-strand	741-743	3	4
α-helix	750-774	25
α-helix	777-788	12
α-helix	797-802	6
α-helix	803-807	5
α-helix	809-814	6
α-helix	824-826	3
α-helix	828-831	4
α-helix	840-843	4
α-helix	844-850	7
α-helix	851-868	18
α-helix	874-876	3
α-helix	880-883	4
β-strand	891-892	2	8
β-strand	898-899	2	8
α-helix	901-930	30
α-helix	937-940	4
α-helix	945-963	19
α-helix	967-970	4
α-helix	974-977	4
α-helix	978-980	3
α-helix	985-1004	20
α-helix	1009-1014	6

Chain B: 14 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	24	1	9
β-strand	27	1	9
α-helix	29-60	32
α-helix	70-72	3
β-strand	77-80	4	10
α-helix	84-86	3
β-strand	87-90	4	11
α-helix	99-109	11
α-helix	110-112	3
β-strand	123-124	2	12
β-strand	148-149	2	12
α-helix	153-155	3
α-helix	169-171	3
β-strand	175	1	13
β-strand	177-180	4	10
α-helix	181-182	2
β-strand	184	1	14
α-helix	190-192	3
α-helix	193-195	3
β-strand	208-210	3	15
β-strand	211-214	4	11
α-helix	218-224	7
β-strand	226-230	5	13
α-helix	232-234	3
β-strand	237-239	3	15
α-helix	240-242	3
β-strand	245	1	14
α-helix	247-250	4
β-strand	258-259	2	10
β-strand	260-264	5	13
β-strand	271-278	8	11
β-strand	294-301	8	11

Chain G: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	23-45	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sodium/potassium-transporting ATPase subunit alpha	A	protein	1021	Sus scrofa	D2WKD6 (AlphaFold model)
Sodium/potassium-transporting ATPase subunit beta-1	B	protein	303	Sus scrofa	P05027 (AlphaFold model)
FXYD domain-containing ion transport regulator	G	protein	65	Sus scrofa	Q58K79 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9VJ2_1 Sodium/potassium-transporting ATPase subunit alpha (chains A)
MGKGVGRDKYEPAAVSEHGDKKKAKKERDMDELKKEVSMDDHKLSLDELHRKYGTDLSRG
LTPARAAEILARDGPNALTPPPTTPEWVKFCRQLFGGFSMLLWIGAILCFLAYGIQAATE
EEPQNDNLYLGVVLSAVVIITGCFSYYQEAKSSKIMESFKNMVPQQALVIRNGEKMSINA
EEVVVGDLVEVKGGDRIPADLRIISANGCKVDNSSLTGESEPQTRSPDFTNENPLETRNI
AFFSTNCVEGTARGIVVYTGDRTVMGRIATLASGLEGGQTPIAAEIEHFIHIITGVAVFL
GVSFFILSLILEYTWLEAVIFLIGIIVANVPEGLLATVTVCLTLTAKRMARKNCLVKNLE
AVETLGSTSTICSDKTGTLTQNRMTVAHMWFDNQIHEADTTENQSGVSFDKTSATWLALS
RIAGLCNRAVFQANQENLPILKRAVAGDASESALLKCIELCCGSVKEMRERYTKIVEIPF
NSTNKYQLSIHKNPNTAEPRHLLVMKGAPERILDRCSSILIHGKEQPLDEELKDAFQNAY
LELGGLGERVLGFCHLFLPDEQFPEGFQFDTDDVNFPLDNLCFVGLISMIDPPRAAVPDA
VGKCRSAGIKVIMVTGDHPITAKAIAKGVGIISEGNETVEDIAARLNIPVSQVNPRDAKA
CVVHGSDLKDMTSEQLDDILKYHTEIVFARTSPQQKLIIVEGCQRQGAIVAVTGDGVNDS
PALKKADIGVAMGIAGSDVSKQAADMILLDDNFASIVTGVEEGRLIFDNLKKSIAYTLTS
NIPEITPFLIFIIANIPLPLGTVTILCIDLGTDMVPAISLAYEQAESDIMKRQPRNPKTD
KLVNERLISMAYGQIGMIQALGGFFTYFVILAENGFLPIHLLGLRVNWDDRWINDVEDSY
GQQWTYEQRKIVEFTCHTAFFVSIVVVQWADLVICKTRRNSVFQQGMKNKILIFGLFEET
ALAAFLSYCPGMGVALRMYPLKPTWWFCAFPYSLLIFVYDEVRKLIIRRRPGGWVEKETY
Y

Sequence of entity 2 (B), FASTA

>9VJ2_2 Sodium/potassium-transporting ATPase subunit beta-1 (chains B)
MARGKAKEEGSWKKFIWNSEKKEFLGRTGGSWFKILLFYVIFYGCLAGIFIGTIQVMLLT
ISEFKPTYQDRVAPPGLTQIPQSQKTEISFRPNDPQSYESYVVSIVRFLEKYKDLAQKDD
MIFEDCGNVPSELKERGEYNNERGERKVCRFRLEWLGNCSGLNDETYGYKDGKPCVIIKL
NRVLGFKPKPPKNESLETYPVMKYNPYVLPVHCTGKRDEDKEKVGTMEYFGLGGYPGFPL
QYYPYYGKLLQPKYLQPLMAVQFTNLTMDTEIRIECKAYGENIGYSEKDRFQGRFDVKIE
VKS

Sequence of entity 3 (G), FASTA

>9VJ2_3 FXYD domain-containing ion transport regulator (chains G)
MAGLSTDDGGSPKGDVDPFYYDYETVRNGGLIFAALAFIVGLIIILSKRLRCGGKKHRPI
NEDEL

Ligands and cofactors

ID	Name	Formula	Copies
A1MA6	palytoxin	C129 H223 N3 O54	1
BEF	Beryllium trifluoride ion	Be F3	1
PCW	1,2-dioleoyl-sn-glycero-3-phosphocholine	C44 H85 N O8 P	6
CLR	Cholesterol	C27 H46 O	2
MG	Magnesium ion	Mg	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

How palytoxin transforms the Na + ,K + pump into a cation channel. Kanai, R., Tsunekawa, N., Cornelius, F. et al. Proc Natl Acad Sci U S A (2025) 122:e2506450122-e2506450122. DOI 10.1073/pnas.2506450122 · PubMed

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