8D3V: PDB entry 8D3V

Human alpha3 Na+/K+-ATPase in its cytoplasmic side-open state. Determined by electron microscopy at 3.4 Å resolution. Released 21 Sept 2022.

Method: Electron microscopy
Resolution: 3.4 Å
Organism: Homo sapiens
Chains: 3
Atoms: 10,011
Mol. weight: 157.83 kDa
Released: 21 Sept 2022

Explore 8D3V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8D3V contains 65 α-helices and 47 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: 55 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	38-42	5
α-helix	43-45	3
α-helix	57-65	9
α-helix	72-76	5
α-helix	80-86	7
α-helix	89-91	3
α-helix	92-106	15
α-helix	120-139	20
α-helix	142-148	7
α-helix	149-152	4
β-strand	158-162	5	1
β-strand	167-171	5	1
β-strand	180-184	5	1
β-strand	187-188	2	2
β-strand	192-198	7	1
β-strand	201-204	4	2
α-helix	214	1
β-strand	215-217	3	2
α-helix	226-228	3
β-strand	232-233	2	1
β-strand	238-241	4	2
β-strand	243-250	8	1
α-helix	273-303	31
α-helix	309-321	13
α-helix	326-343	18
β-strand	347-348	2	3
α-helix	352-355	4
β-strand	362-366	5	3
α-helix	367-371	5
β-strand	372	1	4
β-strand	377-383	7	5
β-strand	386-389	4	5
α-helix	406-415	10
α-helix	422-424	3
α-helix	441-451	11
α-helix	457-463	7
β-strand	482-484	3	6
β-strand	493-495	3	6
β-strand	498-499	2	7
α-helix	501-507	7
β-strand	508-513	6	8
β-strand	516-519	4	8
α-helix	520	1
α-helix	522-536	15
β-strand	540-543	4	5
β-strand	544-545	2	7
β-strand	573-575	3	8
β-strand	577-582	6	5
α-helix	584	1
β-strand	585	1	4
α-helix	586	1
α-helix	589-598	10
β-strand	602-606	5	3
α-helix	611-621	11
α-helix	631-638	8
α-helix	642-644	3
β-strand	652-656	5	3
α-helix	657-660	4
α-helix	665-674	10
β-strand	677-681	5	3
α-helix	685-695	11
α-helix	696-698	3
β-strand	702-705	4	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	746-771	26
α-helix	774-785	12
α-helix	794-801	8
α-helix	808-814	7
α-helix	815-817	3
α-helix	825-828	4
α-helix	837-842	6
α-helix	843-847	5
α-helix	848-865	18
α-helix	870-872	3
α-helix	877-880	4
β-strand	888-889	2	9
β-strand	895-896	2	9
α-helix	898-926	29
α-helix	934-936	3
α-helix	942-958	17
α-helix	964-967	4
α-helix	975-979	5
α-helix	982-1001	20
α-helix	1006-1010	5

Chain B: 9 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	34-59	26
β-strand	76	1	10
β-strand	77-79	3	11
β-strand	87-90	4	12
α-helix	95-98	4
α-helix	99-109	11
α-helix	114-116	3
β-strand	123-124	2	13
α-helix	132-134	3
β-strand	148-149	2	13
α-helix	153-155	3
β-strand	176-180	5	11
β-strand	184	1	14
β-strand	211-215	5	12
α-helix	218-221	4
β-strand	227-230	4	11
α-helix	232-234	3
α-helix	240-242	3
β-strand	245	1	14
β-strand	259-263	5	11
β-strand	272-278	7	12
β-strand	292	1	10
β-strand	295-301	7	12

Chain G: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	37-56	20

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

>8D3V_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

>8D3V_2 Sodium/potassium-transporting ATPase subunit beta-1 (chains B)
MARGKAKEEGSWKKFIWNSEKKEFLGRTGGSWFKILLFYVIFYGCLAGIFIGTIQVMLLT
ISEFKPTYQDRVAPPGLTQIPQIQKTEISFRPNDPKSYEAYVLNIVRFLEKYKDSAQRDD
MIFEDCGDVPSEPKERGDFNHERGERKVCRFKLEWLGNCSGLNDETYGYKEGKPCIIIKL
NRVLGFKPKPPKNESLETYPVMKYNPNVLPVQCTGKRDEDKDKVGNVEYFGLGNSPGFPL
QYYPYYGKLLQPKYLQPLLAVQFTNLTMDTEIRIECKAYGENIGYSEKDRFQGRFDVKIE
VKS

Sequence of entity 3 (G), FASTA

>8D3V_3 FXYD domain-containing ion transport regulator 6 (chains G)
MATMELVLVFLCSLLAPMVLASAAEKEKEMDPFHYDYQTLRIGGLVFAVVLFSVGILLIL
SRRCKCSFNQKPRAPGDEEAQVENLITANATEPQKAEN

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…
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
9ROM 3.6 Å, Human alpha3 Q140L Na+,K+-ATPase in the outward open E2P state

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