8D3X: PDB entry 8D3X

Human alpha3 Na+/K+-ATPase in its K+-occluded state. Determined by electron microscopy at 4.1 Å resolution. Released 21 Sept 2022.

Method: Electron microscopy
Resolution: 4.1 Å
Organism: Homo sapiens
Chains: 3
Atoms: 10,219
Mol. weight: 157.93 kDa
Ligands: MF4
Released: 21 Sept 2022

Explore 8D3X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8D3X contains 55 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: 49 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	38-44	7
β-strand	48	1	6
β-strand	52	1	6
α-helix	55-65	11
α-helix	70-73	4
α-helix	80-87	8
α-helix	92-108	17
α-helix	120-137	18
α-helix	147-150	4
β-strand	158-163	6	7
β-strand	166-171	6	7
β-strand	180-183	4	7
β-strand	188	1	8
β-strand	192-202	11	7
β-strand	203	1	9
β-strand	215	1	9
β-strand	232-233	2	7
β-strand	238	1	8
β-strand	241-250	10	7
α-helix	256-267	12
α-helix	270-272	3
α-helix	273-303	31
α-helix	307-321	15
α-helix	327-342	16
β-strand	346-348	3	10
α-helix	353-359	7
β-strand	362-365	4	10
β-strand	372	1	11
β-strand	380-383	4	12
β-strand	386-389	4	12
α-helix	406-417	12
β-strand	422-423	2	13
α-helix	424	1
α-helix	432-434	3
β-strand	437-438	2	13
α-helix	441-453	13
α-helix	457-463	7
β-strand	468-470	3	12
β-strand	478-483	6	12
β-strand	494-499	6	12
α-helix	501-507	7
β-strand	508-513	6	12
β-strand	516-519	4	12
α-helix	522-536	15
β-strand	543-549	7	12
β-strand	573-580	8	12
α-helix	582-584	3
β-strand	585	1	11
α-helix	586	1
α-helix	589-598	10
β-strand	602-606	5	10
α-helix	611-621	11
α-helix	631-637	7
α-helix	642-644	3
α-helix	647-649	3
β-strand	652-655	4	10
α-helix	660-662	3
α-helix	665-674	10
β-strand	677-680	4	10
α-helix	685-697	13
β-strand	702-706	5	10
α-helix	712-717	6
β-strand	720-724	5	10
α-helix	730-734	5
β-strand	738-740	3	10
α-helix	745-771	27
α-helix	774-785	12
α-helix	795-803	9
α-helix	807-811	5
α-helix	819-823	5
α-helix	825-828	4
α-helix	837-840	4
α-helix	841-847	7
α-helix	848-864	17
α-helix	877-880	4
β-strand	888-889	2	14
β-strand	895-896	2	14
α-helix	898-927	30
α-helix	934-937	4
α-helix	942-958	17
α-helix	965-968	4
α-helix	975-979	5
α-helix	982-1001	20
α-helix	1006-1011	6

Chain B: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	34-59	26
β-strand	77-79	3	1
β-strand	87-90	4	2
α-helix	99-109	11
α-helix	153-155	3
β-strand	178-180	3	1
α-helix	181-182	2
β-strand	184	1	3
β-strand	210	1	4
β-strand	211-213	3	2
β-strand	227-230	4	5
β-strand	237	1	4
α-helix	243-244	2
β-strand	245	1	3
β-strand	259	1	1
β-strand	260-263	4	5
β-strand	272-278	7	2
β-strand	294-301	8	2

Chain G: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	37-57	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sodium/potassium-transporting ATPase subunit beta-1	B	protein	303	Homo sapiens	P05026 (AlphaFold model)
FXYD domain-containing ion transport regulator 6	G	protein	98	Homo sapiens	Q9H0Q3 (AlphaFold model)
Sodium/potassium-transporting ATPase subunit alpha-3	A	protein	1013	Homo sapiens	P13637 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>8D3X_1 Sodium/potassium-transporting ATPase subunit beta-1 (chains B)
MARGKAKEEGSWKKFIWNSEKKEFLGRTGGSWFKILLFYVIFYGCLAGIFIGTIQVMLLT
ISEFKPTYQDRVAPPGLTQIPQIQKTEISFRPNDPKSYEAYVLNIVRFLEKYKDSAQRDD
MIFEDCGDVPSEPKERGDFNHERGERKVCRFKLEWLGNCSGLNDETYGYKEGKPCIIIKL
NRVLGFKPKPPKNESLETYPVMKYNPNVLPVQCTGKRDEDKDKVGNVEYFGLGNSPGFPL
QYYPYYGKLLQPKYLQPLLAVQFTNLTMDTEIRIECKAYGENIGYSEKDRFQGRFDVKIE
VKS

Sequence of entity 2 (G), FASTA

>8D3X_2 FXYD domain-containing ion transport regulator 6 (chains G)
MATMELVLVFLCSLLAPMVLASAAEKEKEMDPFHYDYQTLRIGGLVFAVVLFSVGILLIL
SRRCKCSFNQKPRAPGDEEAQVENLITANATEPQKAEN

Sequence of entity 3 (A), FASTA

>8D3X_3 Sodium/potassium-transporting ATPase subunit alpha-3 (chains A)
MGDKKDDKDSPKKNKGKERRDLDDLKKEVAMTEHKMSVEEVCRKYNTDCVQGLTHSKAQE
ILARDGPNALTPPPTTPEWVKFCRQLFGGFSILLWIGAILCFLAYGIQAGTEDDPSGDNL
YLGIVLAAVVIITGCFSYYQEAKSSKIMESFKNMVPQQALVIREGEKMQVNAEEVVVGDL
VEIKGGDRVPADLRIISAHGCKVDNSSLTGESEPQTRSPDCTHDNPLETRNITFFSTNCV
EGTARGVVVATGDRTVMGRIATLASGLEVGKTPIAIEIEHFIQLITGVAVFLGVSFFILS
LILGYTWLEAVIFLIGIIVANVPEGLLATVTVCLTLTAKRMARKNCLVKNLEAVETLGST
STICSDKTGTLTQNRMTVAHMWFDNQIHEADTTEDQSGTSFDKSSHTWVALSHIAGLCNR
AVFKGGQDNIPVLKRDVAGDASESALLKCIELSSGSVKLMRERNKKVAEIPFNSTNKYQL
SIHETEDPNDNRYLLVMKGAPERILDRCSTILLQGKEQPLDEEMKEAFQNAYLELGGLGE
RVLGFCHYYLPEEQFPKGFAFDCDDVNFTTDNLCFVGLMSMIDPPRAAVPDAVGKCRSAG
IKVIMVTGDHPITAKAIAKGVGIISEGNETVEDIAARLNIPVSQVNPRDAKACVIHGTDL
KDFTSEQIDEILQNHTEIVFARTSPQQKLIIVEGCQRQGAIVAVTGDGVNDSPALKKADI
GVAMGIAGSDVSKQAADMILLDDNFASIVTGVEEGRLIFDNLKKSIAYTLTSNIPEITPF
LLFIMANIPLPLGTITILCIDLGTDMVPAISLAYEAAESDIMKRQPRNPRTDKLVNERLI
SMAYGQIGMIQALGGFFSYFVILAENGFLPGNLVGIRLNWDDRTVNDLEDSYGQQWTYEQ
RKVVEFTCHTAFFVSIVVVQWADLIICKTRRNSVFQQGMKNKILIFGLFEETALAAFLSY
CPGMDVALRMYPLKPSWWFCAFPYSFLIFVYDEIRKLILRRNPGGWVEKETYY

Ligands and cofactors

ID	Name	Formula	Copies
MF4	TETRAFLUOROMAGNESATE(2-)	F4 Mg	1

Primary citation

Structural basis for gating mechanism of the human sodium-potassium pump. Nguyen, P.T., Deisl, C., Fine, M. et al. Nat Commun (2022) 13:5293-5293. DOI 10.1038/s41467-022-32990-x · PubMed

Other PDB entries of the same protein (UniProt P05026 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8ZYJ 2.37 Å, Cryo-EM structure of human testis-specific Na+,K+-ATPase alpha4 in ouabain-bound form
9WAJ 2.39 Å, Cryo-EM structure of a human sodium pump wildtype in ouabain-bound E2P state
7E20 2.7 Å, Cryo EM structure of a K+-bound Na+,K+-ATPase in the E2 state
9ROG 2.8 Å, Human alpha3 Na+,K+-ATPase in the Na+-occluded E1P-ADP state obtained under turnover…
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
9ROH 2.92 Å, Human alpha3 Na+,K+-ATPase in the Na+-occluded E2P state obtained under turnover…
9ROE 2.94 Å, Human alpha3 Na+,K+-ATPase in the outward open E2P state
9ROI 2.94 Å, Human alpha3 Na+,K+-ATPase in the K+-occluded E2P state obtained under turnover conditions
9ROA 3.08 Å, Human alpha3 Na+,K+-ATPase in the Na+-occluded E1P-ADP state
9ROD 3.12 Å, Human alpha3 Na+,K+-ATPase in the Na+-occluded E2P state
7E1Z 3.2 Å, Cryo EM structure of a Na+-bound Na+,K+-ATPase in the E1 state

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