9KCL: Human sodium pump E1003K

Cryo-EM structure of human sodium pump E1003K complexed with NDRG3 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

3

Atoms

11,654

Mol. weight

173.79 kDa

Ligands

ACP

Released

12 Nov 2025

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

Secondary structure: helices and β-sheets

9KCL contains 69 α-helices and 56 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: 45 helices, 32 β-strands

Molecules and chains

>9KCL_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

>9KCL_2 Sodium/potassium-transporting ATPase subunit beta-3 (chains B)
MTKNEKKSLNQSLAEWKLFIYNPTTGEFLGRTAKSWGLILLFYLVFYGFLAALFSFTMWV
MLQTLNDEVPKYRDQIPSPGLMVFPKPVTALEYTFSRSDPTSYAGYIEDLKKFLKPYTLE
EQKNLTVCPDGALFEQKGPVYVACQFPISLLQACSGMNDPDFGYSQGNPCILVKMNRIIG
LKPEGVPRIDCVSKNEDIPNVAVYPHNGMIDLKYFPYYGKKLHVGYLQPLVAVQVSFAPN
NTGKEVTVECKIDGSANLKSQDDRDKFLGRVMFKITARA

>9KCL_3 Protein NDRG3 (chains N)
CQEHDIETTHGVVHVTIRGLPKGNRPVILTYHDIGLNHKSCFNAFFNFEDMQEITQHFAV
CHVDAPGQQEGAPSFPTGYQYPTMDELAEMLPPVLTHLSLKSIIGIGVGAGAYILSRFAL
NHPELVEGLVLINVDPCAKGWIDWAASKLSGLTTNVVDIILAHHFGQEELQANLDLIQTY
RMHIAQDINQDNLQLFLNSYNGRRDLEIERPILGQNDNKSKTLKCSTLLVVGDNSPAVEA
VVECNSRLNPINTTLLKMADCGGLPQVVQPGKLTEAFKYFLQGMGYIPSASMTRLARS

Ligands and cofactors

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.

Related structures

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
• 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
• 9KCR 3.2 Å, Cryo-EM structure of human sodium pump E1003K complexed with NDRG3 in (2Na+)E1 state

Browse structure collections

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