9KCR: Human sodium pump E1003K

Cryo-EM structure of human sodium pump E1003K complexed with NDRG3 in (2Na+)E1 state. Determined by electron microscopy at 3.2 Å resolution. Released 12 Nov 2025.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 3
Atoms: 11,486
Mol. weight: 173.26 kDa
Released: 12 Nov 2025

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

Secondary structure: helices and β-sheets

9KCR contains 76 α-helices and 68 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: 52 helices, 43 β-strands

Element	Residues	Length	Sheet
α-helix	48-54	7
α-helix	65-75	11
α-helix	89-97	9
α-helix	101-121	21
α-helix	129-157	29
β-strand	168	1	1
β-strand	171	1	2
α-helix	173-175	3
β-strand	178	1	2
β-strand	181	1	1
α-helix	182-184	3
β-strand	190-193	4	2
β-strand	197-198	2	3
α-helix	199	1
β-strand	202-208	7	2
β-strand	212-214	3	3
α-helix	215-217	3
β-strand	224-226	3	3
α-helix	236-238	3
β-strand	242-243	2	2
β-strand	248-251	4	3
β-strand	254-260	7	2
α-helix	266-269	4
α-helix	283-312	30
α-helix	317-331	15
α-helix	337-352	16
β-strand	356-358	3	4
α-helix	362-367	6
β-strand	372	1	5
β-strand	375	1	6
β-strand	378	1	7
β-strand	382	1	7
β-strand	387-393	7	8
β-strand	396-399	4	8
α-helix	416-427	12
β-strand	432-433	2	9
α-helix	434	1
α-helix	442-444	3
β-strand	447-448	2	9
α-helix	451-463	13
α-helix	467-473	7
β-strand	475-479	5	10
α-helix	480-482	3
β-strand	488	1	8
β-strand	491-494	4	10
β-strand	504	1	11
β-strand	506	1	10
β-strand	507-509	3	8
α-helix	511-514	4
β-strand	520-523	4	8
β-strand	526-528	3	8
α-helix	532-546	15
β-strand	550-557	8	8
β-strand	559	1	11
β-strand	584-592	9	8
α-helix	594	1
β-strand	595	1	7
α-helix	596	1
α-helix	599-608	10
β-strand	612	1	5
β-strand	614-617	4	6
α-helix	621-631	11
α-helix	641-647	7
α-helix	652-654	3
α-helix	657-659	3
β-strand	662-666	5	6
α-helix	667-670	4
α-helix	675-684	10
β-strand	687-691	5	6
α-helix	695-697	3
α-helix	698-706	9
β-strand	712	1	5
β-strand	713-715	3	4
α-helix	722-727	6
β-strand	730-734	5	4
α-helix	740-745	6
β-strand	748-750	3	4
α-helix	755-766	12
α-helix	768-780	13
α-helix	784-796	13
α-helix	804-813	10
α-helix	817-823	7
α-helix	827-828	2
α-helix	831-833	3
α-helix	835-837	3
α-helix	847-851	5
α-helix	852-857	6
α-helix	858-875	18
α-helix	880-882	3
α-helix	887-890	4
β-strand	898-899	2	12
β-strand	905-906	2	12
α-helix	908-940	33
α-helix	988-990	3
α-helix	992-1008	17

Chain B: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	33-63	31
β-strand	80	1	13
β-strand	81-84	4	14
β-strand	92-96	5	15
α-helix	104-114	11
α-helix	115-117	3
α-helix	126-127	2
α-helix	148-154	7
β-strand	170-175	6	14
β-strand	188	1	16
β-strand	189-192	4	17
β-strand	201-203	3	14
β-strand	209	1	16
α-helix	212-214	3
β-strand	232-235	4	14
β-strand	243	1	15
β-strand	249-252	4	17
β-strand	268	1	13
β-strand	270-272	3	17
β-strand	274-278	5	15

Chain N: 18 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	31	1	18
β-strand	34-37	4	18
β-strand	40-46	7	18
α-helix	54-55	2
β-strand	56-60	5	19
α-helix	67-70	4
α-helix	71-73	3
α-helix	80-86	7
β-strand	89	1	19
β-strand	90-93	4	18
α-helix	113-118	6
α-helix	120-126	7
β-strand	132-137	6	19
α-helix	139-150	12
β-strand	155-158	4	19
β-strand	161	1	19
α-helix	171-179	9
α-helix	185-193	9
α-helix	196-201	6
α-helix	204-214	11
α-helix	219-230	12
α-helix	233-235	3
α-helix	248-250	3
β-strand	255-261	7	19
α-helix	267-274	8
β-strand	282-287	6	19
α-helix	294-297	4
α-helix	299-313	15
α-helix	322-325	4

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)
Protein NDRG3	N	protein	298	Homo sapiens	Q9UGV2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9KCR_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

>9KCR_2 Sodium/potassium-transporting ATPase subunit beta-3 (chains B)
MTKNEKKSLNQSLAEWKLFIYNPTTGEFLGRTAKSWGLILLFYLVFYGFLAALFSFTMWV
MLQTLNDEVPKYRDQIPSPGLMVFPKPVTALEYTFSRSDPTSYAGYIEDLKKFLKPYTLE
EQKNLTVCPDGALFEQKGPVYVACQFPISLLQACSGMNDPDFGYSQGNPCILVKMNRIIG
LKPEGVPRIDCVSKNEDIPNVAVYPHNGMIDLKYFPYYGKKLHVGYLQPLVAVQVSFAPN
NTGKEVTVECKIDGSANLKSQDDRDKFLGRVMFKITARA

Sequence of entity 3 (N), FASTA

>9KCR_3 Protein NDRG3 (chains N)
CQEHDIETTHGVVHVTIRGLPKGNRPVILTYHDIGLNHKSCFNAFFNFEDMQEITQHFAV
CHVDAPGQQEGAPSFPTGYQYPTMDELAEMLPPVLTHLSLKSIIGIGVGAGAYILSRFAL
NHPELVEGLVLINVDPCAKGWIDWAASKLSGLTTNVVDIILAHHFGQEELQANLDLIQTY
RMHIAQDINQDNLQLFLNSYNGRRDLEIERPILGQNDNKSKTLKCSTLLVVGDNSPAVEA
VVECNSRLNPINTTLLKMADCGGLPQVVQPGKLTEAFKYFLQGMGYIPSASMTRLARS

Primary citation

Structural basis of a sodium pump quaternary complex leading phospholipid scrambling in the living cell. Dou, Y., Matsui, R., Abe, K. et al. 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
9KCJ 3.1 Å, Cryo-EM structure of human sodium pump E1003 in (3Na+)E1-AMPPCP state
7E1Z 3.2 Å, Cryo EM structure of a Na+-bound Na+,K+-ATPase in the E1 state

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