9KCJ: Human sodium pump E1003 in (3Na+)E1-AMPPCP state

Cryo-EM structure of human sodium pump E1003 in (3Na+)E1-AMPPCP state. Determined by electron microscopy at 3.1 Å resolution. Released 12 Nov 2025.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 3
Atoms: 10,507
Mol. weight: 168.23 kDa
Ligands: CLR, PC1, PCW, ACP
Released: 12 Nov 2025

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

Secondary structure: helices and β-sheets

9KCJ contains 66 α-helices and 48 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: 59 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	48-55	8
α-helix	65-75	11
α-helix	80-83	4
α-helix	88-96	9
α-helix	101-121	21
α-helix	128-162	35
β-strand	168-173	6	1
β-strand	176-181	6	1
α-helix	182-184	3
β-strand	190-193	4	1
β-strand	197-198	2	1
α-helix	199	1
β-strand	203-214	12	1
β-strand	225-226	2	1
β-strand	242-243	2	1
β-strand	248-258	11	1
α-helix	262-264	3
α-helix	266-269	4
α-helix	280-282	3
α-helix	283-312	30
α-helix	317-330	14
α-helix	336-353	18
β-strand	356-358	3	2
α-helix	361-363	3
α-helix	364-368	5
β-strand	372-375	4	2
β-strand	382	1	3
β-strand	387-393	7	4
β-strand	396-399	4	4
α-helix	416-428	13
β-strand	433	1	5
α-helix	434	1
β-strand	447	1	5
α-helix	451-463	13
α-helix	467-473	7
β-strand	476-480	5	4
β-strand	488-493	6	4
β-strand	504-509	6	4
α-helix	511-515	5
β-strand	518-523	6	4
β-strand	526-529	4	4
α-helix	532-547	16
β-strand	550-559	10	4
β-strand	583-592	10	4
α-helix	594	1
β-strand	595	1	3
α-helix	596	1
α-helix	599-608	10
α-helix	611	1
β-strand	612-616	5	2
α-helix	621-631	11
α-helix	641-647	7
α-helix	657-659	3
β-strand	662-666	5	2
α-helix	667-671	5
α-helix	675-684	10
β-strand	687-691	5	2
α-helix	695-707	13
β-strand	712-715	4	2
α-helix	719-721	3
α-helix	722-727	6
β-strand	730-734	5	2
α-helix	742-745	4
β-strand	748-750	3	2
α-helix	755-757	3
α-helix	758-780	23
α-helix	783-796	14
α-helix	798-800	3
α-helix	804-814	11
α-helix	817-820	4
α-helix	821-824	4
α-helix	825-828	4
α-helix	831-833	3
α-helix	835-838	4
α-helix	847-852	6
α-helix	853-857	5
α-helix	858-876	19
α-helix	880-883	4
α-helix	887-890	4
β-strand	898-899	2	6
β-strand	905-906	2	6
α-helix	908-937	30
α-helix	944-947	4
α-helix	952-970	19
α-helix	974-977	4
α-helix	982-984	3
α-helix	985-987	3
α-helix	989-991	3
α-helix	992-1011	20
α-helix	1016-1020	5

Chain B: 6 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	32-36	5
α-helix	37-64	28
β-strand	80	1	7
β-strand	81-84	4	8
β-strand	92-94	3	9
β-strand	96	1	10
β-strand	99	1	10
α-helix	104-113	10
β-strand	126	1	11
β-strand	144	1	11
α-helix	148-150	3
β-strand	170-175	6	8
α-helix	176-177	2
β-strand	179	1	12
β-strand	189-193	5	9
β-strand	200-201	2	13
α-helix	212-214	3
β-strand	217	1	12
β-strand	231-234	4	8
β-strand	235-236	2	13
β-strand	245-252	8	9
β-strand	268	1	7
β-strand	270-276	7	9

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	139-161	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sodium/potassium-transporting ATPase subunit alpha-1	A	protein	985	Homo sapiens	P05023 (AlphaFold model)
Sodium/potassium-transporting ATPase subunit beta-3	B	protein	279	Homo sapiens	P54709 (AlphaFold model)
FXYD domain-containing ion transport regulator 5	C	protein	178	Homo sapiens	Q96DB9 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9KCJ_1 Sodium/potassium-transporting ATPase subunit alpha-1 (chains A)
VSMDDHKLSLDELHRKYGTDLSRGLTSARAAEILARDGPNALTPPPTTPEWIKFCRQLFG
GFSMLLWIGAILCFLAYSIQAATEEEPQNDNLYLGVVLSAVVIITGCFSYYQEAKSSKIM
ESFKNMVPQQALVIRNGEKMSINAEEVVVGDLVEVKGGDRIPADLRIISANGCKVDNSSL
TGESEPQTRSPDFTNENPLETRNIAFFSTNCVEGTARGIVVYTGDRTVMGRIATLASGLE
GGQTPIAAEIEHFIHIITGVAVFLGVSFFILSLILEYTWLEAVIFLIGIIVANVPEGLLA
TVTVCLTLTAKRMARKNCLVKNLEAVETLGSTSTICSDKTGTLTQNRMTVAHMWFDNQIH
EADTTENQSGVSFDKTSATWLALSRIAGLCNRAVFQANQENLPILKRAVAGDASESALLK
CIELCCGSVKEMRERYAKIVEIPFNSTNKYQLSIHKNPNTSEPQHLLVMKGAPERILDRC
SSILLHGKEQPLDEELKDAFQNAYLELGGLGERVLGFCHLFLPDEQFPEGFQFDTDDVNF
PIDNLCFVGLISMIDPPRAAVPDAVGKCRSAGIKVIMVTGDHPITAKAIAKGVGIISEGN
ETVEDIAARLNIPVSQVNPRDAKACVVHGSDLKDMTSEQLDDILKYHTEIVFARTSPQQK
LIIVEGCQRQGAIVAVTGDGVNDSPALKKADIGVAMGIAGSDVSKQAADMILLDDNFASI
VTGVEEGRLIFDNLKKSIAYTLTSNIPEITPFLIFIIANIPLPLGTVTILCIDLGTDMVP
AISLAYEQAESDIMKRQPRNPKTDKLVNERLISMAYGQIGMIQALGGFFTYFVILAENGF
LPIHLLGLRVDWDDRWINDVEDSYGQQWTYEQRKIVEFTCHTAFFVSIVVVQWADLVICK
TRRNSVFQQGMKNKILIFGLFEETALAAFLSYCPGMGVALRMYPLKPTWWFCAFPYSLLI
FVYDKVRKLIIRRRPGGWVEKETYY

Sequence of entity 2 (B), FASTA

>9KCJ_2 Sodium/potassium-transporting ATPase subunit beta-3 (chains B)
MTKNEKKSLNQSLAEWKLFIYNPTTGEFLGRTAKSWGLILLFYLVFYGFLAALFSFTMWV
MLQTLNDEVPKYRDQIPSPGLMVFPKPVTALEYTFSRSDPTSYAGYIEDLKKFLKPYTLE
EQKNLTVCPDGALFEQKGPVYVACQFPISLLQACSGMNDPDFGYSQGNPCILVKMNRIIG
LKPEGVPRIDCVSKNEDIPNVAVYPHNGMIDLKYFPYYGKKLHVGYLQPLVAVQVSFAPN
NTGKEVTVECKIDGSANLKSQDDRDKFLGRVMFKITARA

Sequence of entity 3 (C), FASTA

>9KCJ_3 FXYD domain-containing ion transport regulator 5 (chains C)
MSPSGRLCLLTIVGLILPTRGQTLKDTTSSSSADSTIMDIQVPTRAPDAVYTELQPTSPT
PTWPADETPQPQTQTQQLEGTDGPLVTDPETHKSTKAAHPTDDTTTLSERPSPSTDVQTD
PQTLKPSGFHEDDPFFYDEHTLRKRGLLVAAVLFITGIIILTSGKCRQLSRLCRNRCR

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	2
PC1	1,2-diacyl-sn-glycero-3-phosphocholine	C44 H88 N O8 P	2
PCW	1,2-dioleoyl-sn-glycero-3-phosphocholine	C44 H85 N O8 P	7
ACP	Phosphomethylphosphonic acid adenylate ester	C11 H18 N5 O12 P3	1

Water and common crystallization additives (NA) are not listed.

Primary citation

Structural basis of a sodium pump quaternary complex leading phospholipid scrambling in the living cell. Dou, Y., Abe, K., Suzuki, J. To be published.

Other PDB entries of the same protein (UniProt P05023 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9WAJ 2.39 Å, Cryo-EM structure of a human sodium pump wildtype in ouabain-bound E2P state
24RC 2.61 Å, Cryo-EM structure of human sodium pump W931R mutant in K+-occluded E2-Pi state
7E20 2.7 Å, Cryo EM structure of a K+-bound Na+,K+-ATPase in the E2 state
9WAK 2.86 Å, Cryo-EM structure of a human sodium pump W931R mutant in ouabain-bound E2P state
7E21 2.9 Å, Cryo EM structure of a Na+-bound Na+,K+-ATPase in the E1 state with ATP-gamma-S
9KCI 2.9 Å, Cryo-EM structure of human sodium pump WT in (2K+)E2-AlF state
9KCK 2.9 Å, Cryo-EM structure of human sodium pump E1003K in (2K+)E2-AlF state
9KCL 2.9 Å, Cryo-EM structure of human sodium pump E1003K complexed with NDRG3 in (2Na+)E1-AMPPCP…
9KCM 2.9 Å, Cryo-EM structure of human sodium pump E1003K complexed with NDRG3 and TMX2 in…
9KCG 3.1 Å, Cryo-EM structure of human sodium pump WT in (3Na+)E1-AMPPCP state
7E1Z 3.2 Å, Cryo EM structure of a Na+-bound Na+,K+-ATPase in the E1 state
9KCR 3.2 Å, Cryo-EM structure of human sodium pump E1003K complexed with NDRG3 in (2Na+)E1 state

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