8D3U: PDB entry 8D3U

Human alpha3 Na+/K+-ATPase in its Na+-occluded state. Determined by electron microscopy at 3.7 Å resolution. Released 21 Sept 2022.

Method: Electron microscopy
Resolution: 3.7 Å
Organism: Homo sapiens
Chains: 3
Atoms: 10,121
Mol. weight: 158.36 kDa
Ligands: ADP, ALF
Released: 21 Sept 2022

Explore 8D3U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8D3U contains 64 α-helices and 50 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, 34 β-strands

Element	Residues	Length	Sheet
α-helix	38-44	7
β-strand	48	1	1
β-strand	52	1	1
α-helix	55-65	11
α-helix	80-87	8
α-helix	92-109	18
α-helix	120-152	33
β-strand	158-162	5	2
β-strand	167-171	5	2
α-helix	175-176	2
β-strand	180-183	4	2
β-strand	187-188	2	2
β-strand	193-203	11	2
β-strand	215-216	2	2
β-strand	232-233	2	2
β-strand	238-248	11	2
α-helix	256-259	4
α-helix	273-303	31
α-helix	307-320	14
α-helix	326-342	17
β-strand	346-348	3	3
α-helix	353-358	6
β-strand	362-365	4	3
β-strand	368	1	4
β-strand	372	1	4
β-strand	377-382	6	5
β-strand	387-389	3	5
α-helix	406-418	13
β-strand	422-423	2	6
β-strand	437-438	2	6
α-helix	441-453	13
α-helix	457-463	7
β-strand	466-470	5	5
β-strand	478-483	6	5
β-strand	494-499	6	5
α-helix	501-507	7
β-strand	508-511	4	5
β-strand	518-519	2	5
α-helix	522-537	16
β-strand	540-549	10	5
α-helix	550-551	2
β-strand	573-582	10	5
α-helix	584	1
β-strand	585	1	4
α-helix	586	1
α-helix	589-598	10
β-strand	602-605	4	3
α-helix	611-621	11
α-helix	631-638	8
α-helix	642-644	3
β-strand	652-653	2	7
α-helix	659-661	3
α-helix	665-674	10
β-strand	677-678	2	7
α-helix	685-696	12
β-strand	702-706	5	3
α-helix	709-711	3
α-helix	712-717	6
β-strand	720-724	5	3
α-helix	730-735	6
β-strand	738-740	3	3
α-helix	747-769	23
α-helix	771-773	3
α-helix	774-786	13
α-helix	788-790	3
α-helix	794-804	11
α-helix	807-811	5
α-helix	812-814	3
α-helix	825-827	3
α-helix	837-841	5
α-helix	842-848	7
α-helix	849-866	18
α-helix	870-872	3
α-helix	877-880	4
β-strand	888	1	8
β-strand	896	1	8
α-helix	898-926	29
α-helix	934-937	4
α-helix	942-960	19
α-helix	964-967	4
α-helix	975-979	5
α-helix	982-1001	20
α-helix	1006-1010	5

Chain B: 14 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	35-60	26
α-helix	70-72	3
α-helix	75-76	2
β-strand	77-79	3	9
β-strand	87-90	4	10
α-helix	95-98	4
α-helix	99-109	11
α-helix	110-112	3
β-strand	124	1	11
α-helix	132-135	4
α-helix	146-147	2
β-strand	149	1	11
α-helix	153-156	4
α-helix	173-174	2
β-strand	177-180	4	9
α-helix	181-182	2
β-strand	184	1	12
α-helix	190-191	2
β-strand	208-210	3	13
β-strand	211-215	5	10
α-helix	218-221	4
β-strand	228-230	3	9
β-strand	232	1	14
β-strand	235	1	14
β-strand	237-239	3	13
α-helix	243-244	2
β-strand	245	1	12
β-strand	258-262	5	9
β-strand	272-278	7	10
β-strand	296-301	6	10

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 alpha-3	A	protein	1013	Homo sapiens	P13637 (AlphaFold model)
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)

Sequence of entity 1 (A), FASTA

>8D3U_1 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

Sequence of entity 2 (B), FASTA

>8D3U_2 Sodium/potassium-transporting ATPase subunit beta-1 (chains B)
MARGKAKEEGSWKKFIWNSEKKEFLGRTGGSWFKILLFYVIFYGCLAGIFIGTIQVMLLT
ISEFKPTYQDRVAPPGLTQIPQIQKTEISFRPNDPKSYEAYVLNIVRFLEKYKDSAQRDD
MIFEDCGDVPSEPKERGDFNHERGERKVCRFKLEWLGNCSGLNDETYGYKEGKPCIIIKL
NRVLGFKPKPPKNESLETYPVMKYNPNVLPVQCTGKRDEDKDKVGNVEYFGLGNSPGFPL
QYYPYYGKLLQPKYLQPLLAVQFTNLTMDTEIRIECKAYGENIGYSEKDRFQGRFDVKIE
VKS

Sequence of entity 3 (G), FASTA

>8D3U_3 FXYD domain-containing ion transport regulator 6 (chains G)
MATMELVLVFLCSLLAPMVLASAAEKEKEMDPFHYDYQTLRIGGLVFAVVLFSVGILLIL
SRRCKCSFNQKPRAPGDEEAQVENLITANATEPQKAEN

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
ALF	Tetrafluoroaluminate ion	Al F4	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 P13637 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9ROG 2.8 Å, Human alpha3 Na+,K+-ATPase in the Na+-occluded E1P-ADP state obtained under turnover…
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
9RO9 3.27 Å, Human alpha3 Na+,K+-ATPase in the Na+-bound E1-ATP state
9ROF 3.27 Å, Human alpha3 Na+,K+-ATPase in the Na+-bound E1-ATP state obtained under turnover…
8D3V 3.4 Å, Human alpha3 Na+/K+-ATPase in its cytoplasmic side-open state
8D3W 3.5 Å, Human alpha3 Na+/K+-ATPase in its AMPPCP-bound cytoplasmic side-open state
9ROL 3.54 Å, Human alpha3 Q140L Na+,K+-ATPase in the Na+-occluded E2P state
9ROJ 3.58 Å, Human alpha3 Q140L Na+,K+-ATPase in the Na+-bound E1 state

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