9KCM: Human sodium pump E1003K

Cryo-EM structure of human sodium pump E1003K complexed with NDRG3 and TMX2 in (2Na+)E1-AMPPCP state. Determined by electron microscopy at 2.9 Å resolution. Released 12 Nov 2025.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 4
Atoms: 12,419
Mol. weight: 207.86 kDa
Ligands: ACP
Released: 12 Nov 2025

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

Secondary structure: helices and β-sheets

9KCM contains 78 α-helices and 62 β-strands across 4 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: 45 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	48-55	8
α-helix	65-75	11
α-helix	82-84	3
α-helix	89-95	7
α-helix	101-121	21
α-helix	129-160	32
α-helix	161-163	3
β-strand	168-169	2	5
β-strand	171	1	6
β-strand	172-173	2	7
β-strand	176-177	2	7
β-strand	180-181	2	5
α-helix	182-184	3
β-strand	190-193	4	6
β-strand	197-198	2	6
β-strand	202-214	13	6
α-helix	224	1
β-strand	225-227	3	6
β-strand	242-243	2	6
β-strand	248-260	13	6
α-helix	283-312	30
α-helix	317-331	15
α-helix	336-350	15
β-strand	357-358	2	8
α-helix	362-366	5
β-strand	372-376	5	8
β-strand	378	1	9
β-strand	382	1	9
β-strand	387-392	6	10
β-strand	398-399	2	10
α-helix	405-407	3
α-helix	416-428	13
β-strand	432-433	2	11
β-strand	447-448	2	11
α-helix	451-463	13
α-helix	467-473	7
β-strand	476-480	5	10
β-strand	488-493	6	10
β-strand	504-509	6	10
α-helix	511-515	5
β-strand	518-521	4	10
β-strand	523	1	12
β-strand	526	1	12
β-strand	529	1	10
α-helix	532-546	15
β-strand	550-557	8	10
β-strand	583-592	10	10
α-helix	594	1
β-strand	595	1	9
α-helix	596	1
α-helix	599-608	10
β-strand	612-616	5	8
α-helix	623-631	9
α-helix	641-647	7
α-helix	652-654	3
α-helix	657-659	3
β-strand	662-666	5	8
α-helix	667-670	4
α-helix	675-682	8
β-strand	687-691	5	8
α-helix	695-697	3
α-helix	698-706	9
β-strand	712-716	5	8
α-helix	722-727	6
β-strand	730-734	5	8
α-helix	742-745	4
β-strand	748-750	3	8
α-helix	755-766	12
α-helix	769-776	8
α-helix	783-792	10
α-helix	793-797	5
α-helix	804-813	10
α-helix	817-823	7
α-helix	835-837	3
α-helix	847-855	9
α-helix	859-875	17
α-helix	887-890	4
β-strand	898-899	2	13
α-helix	900	1
β-strand	905-906	2	13
α-helix	908-940	33
α-helix	992-1009	18

Chain B: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	42-62	21
β-strand	81-84	4	1
α-helix	86-87	2
β-strand	92-95	4	2
α-helix	100-113	14
α-helix	119-121	3
α-helix	128-129	2
α-helix	148-150	3
β-strand	170-175	6	1
β-strand	188-189	2	3
β-strand	192	1	2
β-strand	201-203	3	1
α-helix	228-230	3
β-strand	231-235	5	1
β-strand	245-251	7	2
β-strand	252-253	2	3
β-strand	270-277	8	2

Chain N: 18 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	31-36	6	4
β-strand	41-47	7	4
β-strand	56-60	5	4
α-helix	67-70	4
α-helix	79-82	4
β-strand	89-93	5	4
α-helix	101-105	5
α-helix	110-112	3
α-helix	113-116	4
α-helix	117-119	3
α-helix	120-126	7
β-strand	132-137	6	4
α-helix	139-150	12
α-helix	152-154	3
β-strand	155-161	7	4
α-helix	171-182	12
α-helix	185-193	9
α-helix	203-216	14
α-helix	219-230	12
α-helix	239-241	3
β-strand	255-261	7	4
α-helix	267-274	8
β-strand	282-287	6	4
α-helix	294-297	4
α-helix	299-311	13
α-helix	320-321	2

Chain T: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	138-141	4	14
α-helix	145-151	7
β-strand	157-163	7	14
α-helix	168-181	14
β-strand	189-195	7	14
α-helix	202-205	4
β-strand	219-222	4	14
α-helix	224-226	3
β-strand	230-232	3	14
α-helix	234	1
β-strand	235	1	15
β-strand	241	1	15
α-helix	242-243	2
α-helix	248-255	8
α-helix	257-271	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
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)
Sodium/potassium-transporting ATPase subunit alpha-1	A	protein	985	Homo sapiens	P05023 (AlphaFold model)
Thioredoxin-related transmembrane protein 2	T	protein	296	Homo sapiens	Q9Y320 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>9KCM_1 Sodium/potassium-transporting ATPase subunit beta-3 (chains B)
MTKNEKKSLNQSLAEWKLFIYNPTTGEFLGRTAKSWGLILLFYLVFYGFLAALFSFTMWV
MLQTLNDEVPKYRDQIPSPGLMVFPKPVTALEYTFSRSDPTSYAGYIEDLKKFLKPYTLE
EQKNLTVCPDGALFEQKGPVYVACQFPISLLQACSGMNDPDFGYSQGNPCILVKMNRIIG
LKPEGVPRIDCVSKNEDIPNVAVYPHNGMIDLKYFPYYGKKLHVGYLQPLVAVQVSFAPN
NTGKEVTVECKIDGSANLKSQDDRDKFLGRVMFKITARA

Sequence of entity 2 (N), FASTA

>9KCM_2 Protein NDRG3 (chains N)
CQEHDIETTHGVVHVTIRGLPKGNRPVILTYHDIGLNHKSCFNAFFNFEDMQEITQHFAV
CHVDAPGQQEGAPSFPTGYQYPTMDELAEMLPPVLTHLSLKSIIGIGVGAGAYILSRFAL
NHPELVEGLVLINVDPCAKGWIDWAASKLSGLTTNVVDIILAHHFGQEELQANLDLIQTY
RMHIAQDINQDNLQLFLNSYNGRRDLEIERPILGQNDNKSKTLKCSTLLVVGDNSPAVEA
VVECNSRLNPINTTLLKMADCGGLPQVVQPGKLTEAFKYFLQGMGYIPSASMTRLARS

Sequence of entity 3 (A), FASTA

>9KCM_3 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 4 (T), FASTA

>9KCM_4 Thioredoxin-related transmembrane protein 2 (chains T)
MAVLAPLIALVYSVPRLSRWLAQPYYLLSALLSAAFLLVRKLPPLCHGLPTQREDGNPCD
FDWREVEILMFLSAIVMMKNRRSITVEQHIGNIFMFSKVANTILFFRLDIRMGLLYITLC
IVFLMTCKPPLYMGPEYIKYFNDKTIDEELERDKRVTWIVEFFANWSNDCQSFAPIYADL
SLKYNCTGLNFGKVDVGRYTDVSTRYKVSTSPLTKQLPTLILFQGGKEAMRRPQIDKKGR
AVSWTFSEENVIREFNLNELYQRAKKLSKAGDNIPEEQPVASTPTTVSDGENKKDK

Ligands and cofactors

ID	Name	Formula	Copies
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. Matsui, R., Dou, Y., Abe, K. et al. To be published.

Other PDB entries of the same protein (UniProt P54709 (AlphaFold model), which also has an AlphaFold model), best resolution first:

24RC 2.61 Å, Cryo-EM structure of human sodium pump W931R mutant in K+-occluded E2-Pi state
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…
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
9KCR 3.2 Å, Cryo-EM structure of human sodium pump E1003K complexed with NDRG3 in (2Na+)E1 state

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