8D3Y: PDB entry 8D3Y

Human alpha3 Na+/K+-ATPase in its exoplasmic side-open state. Determined by electron microscopy at 3.9 Å resolution. Released 21 Sept 2022.

Method: Electron microscopy
Resolution: 3.9 Å
Organism: Homo sapiens
Chains: 3
Atoms: 9,898
Mol. weight: 157.69 kDa
Ligands: BEF
Released: 21 Sept 2022

Explore 8D3Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8D3Y contains 60 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: 51 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	38-44	7
β-strand	48	1	1
β-strand	52	1	1
α-helix	55-64	10
α-helix	70-75	6
α-helix	78-83	6
α-helix	91-110	20
α-helix	118-142	25
α-helix	148-151	4
β-strand	159-163	5	2
β-strand	166-170	5	2
α-helix	172-174	3
β-strand	180-183	4	2
β-strand	193-203	11	2
β-strand	215-217	3	2
β-strand	232-233	2	2
β-strand	239-248	10	2
α-helix	252-254	3
α-helix	256-260	5
α-helix	273-283	11
α-helix	287-303	17
α-helix	307-319	13
α-helix	327-343	17
β-strand	346-348	3	3
α-helix	353-359	7
β-strand	362-364	3	4
β-strand	368	1	5
β-strand	372	1	5
β-strand	380-383	4	6
β-strand	386-389	4	6
α-helix	406-418	13
β-strand	422-423	2	7
α-helix	424	1
α-helix	432-434	3
β-strand	437-438	2	7
α-helix	441-453	13
α-helix	457-463	7
β-strand	466-469	4	8
β-strand	479-483	5	8
β-strand	493-499	7	8
α-helix	501-504	4
α-helix	505-507	3
β-strand	508-511	4	8
β-strand	512-513	2	9
β-strand	516-517	2	9
α-helix	524-536	13
β-strand	544-550	7	8
β-strand	573-577	5	8
α-helix	582-584	3
β-strand	585	1	5
α-helix	586	1
α-helix	589-598	10
α-helix	601	1
β-strand	602-604	3	4
β-strand	605-606	2	10
α-helix	611-621	11
α-helix	625	1
α-helix	631-638	8
α-helix	647-649	3
β-strand	654-656	3	10
α-helix	657-660	4
α-helix	665-674	10
β-strand	679-681	3	10
α-helix	685-697	13
β-strand	702-704	3	4
α-helix	712-717	6
β-strand	720-721	2	4
β-strand	722-724	3	3
β-strand	738-740	3	3
α-helix	746-770	25
α-helix	774-785	12
α-helix	794-802	9
α-helix	807-811	5
α-helix	824-828	5
α-helix	837-841	5
α-helix	842-847	6
α-helix	848-864	17
α-helix	870-872	3
α-helix	877-880	4
β-strand	888-889	2	11
β-strand	895-896	2	11
α-helix	898-926	29
α-helix	934-937	4
α-helix	942-958	17
α-helix	975-981	7
α-helix	982-1001	20
α-helix	1006-1011	6

Chain B: 8 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	34-58	25
β-strand	79	1	12
β-strand	87-90	4	13
α-helix	95-97	3
α-helix	99-109	11
α-helix	110-112	3
β-strand	176-179	4	12
α-helix	180-182	3
β-strand	184	1	14
β-strand	208	1	15
β-strand	211-213	3	13
β-strand	227-230	4	12
β-strand	239	1	15
α-helix	240-242	3
α-helix	243-244	2
β-strand	245	1	14
β-strand	258-263	6	12
α-helix	266-267	2
β-strand	270-278	9	13
β-strand	294-301	8	13

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

>8D3Y_1 Sodium/potassium-transporting ATPase subunit alpha-3 (chains A)
MGDKKDDKDSPKKNKGKERRDLDDLKKEVAMTEHKMSVEEVCRKYNTDCVQGLTHSKAQE
ILARDGPNALTPPPTTPEWVKFCRQLFGGFSILLWIGAILCFLAYGIQAGTEDDPSGDNL
YLGIVLAAVVIITGCFSYYQEAKSSKIMESFKNMVPQQALVIREGEKMQVNAEEVVVGDL
VEIKGGDRVPADLRIISAHGCKVDNSSLTGESEPQTRSPDCTHDNPLETRNITFFSTNCV
EGTARGVVVATGDRTVMGRIATLASGLEVGKTPIAIEIEHFIQLITGVAVFLGVSFFILS
LILGYTWLEAVIFLIGIIVANVPAGLLATVTVCLTLTAKRMARKNCLVKNLEAVETLGST
STICSDKTGTLTQNRMTVAHMWFDNQIHEADTTEDQSGTSFDKSSHTWVALSHIAGLCNR
AVFKGGQDNIPVLKRDVAGDASESALLKCIELSSGSVKLMRERNKKVAEIPFNSTNKYQL
SIHETEDPNDNRYLLVMKGAPERILDRCSTILLQGKEQPLDEEMKEAFQNAYLELGGLGE
RVLGFCHYYLPEEQFPKGFAFDCDDVNFTTDNLCFVGLMSMIDPPRAAVPDAVGKCRSAG
IKVIMVTGDHPITAKAIAKGVGIISEGNETVEDIAARLNIPVSQVNPRDAKACVIHGTDL
KDFTSEQIDEILQNHTEIVFARTSPQQKLIIVEGCQRQGAIVAVTGDGVNDSPALKKADI
GVAMGIAGSDVSKQAADMILLDDNFASIVTGVEEGRLIFDNLKKSIAYTLTSNIPAITPF
LLFIMANIPLPLGTITILCIALGTAMVPAISLAYEAAESDIMKRQPRNPRTDKLVNERLI
SMAYGQIGMIQALGGFFSYFVILAENGFLPGNLVGIRLNWDDRTVNDLEDSYGQQWTYEQ
RKVVEFTCHTAFFVSIVVVQWADLIICKTRRNSVFQQGMKNKILIFGLFEETALAAFLSY
CPGMDVALRMYPLKPSWWFCAFPYSFLIFVYDEIRKLILRRNPGGWVEKETYY

Sequence of entity 2 (B), FASTA

>8D3Y_2 Sodium/potassium-transporting ATPase subunit beta-1 (chains B)
MARGKAKEEGSWKKFIWNSEKKEFLGRTGGSWFKILLFYVIFYGCLAGIFIGTIQVMLLT
ISEFKPTYQDRVAPPGLTQIPQIQKTEISFRPNDPKSYEAYVLNIVRFLEKYKDSAQRDD
MIFEDCGDVPSEPKERGDFNHERGERKVCRFKLEWLGNCSGLNDETYGYKEGKPCIIIKL
NRVLGFKPKPPKNESLETYPVMKYNPNVLPVQCTGKRDEDKDKVGNVEYFGLGNSPGFPL
QYYPYYGKLLQPKYLQPLLAVQFTNLTMDTEIRIECKAYGENIGYSEKDRFQGRFDVKIE
VKS

Sequence of entity 3 (G), FASTA

>8D3Y_3 FXYD domain-containing ion transport regulator 6 (chains G)
MATMELVLVFLCSLLAPMVLASAAEKEKEMDPFHYDYQTLRIGGLVFAVVLFSVGILLIL
SRRCKCSFNQKPRAPGDEEAQVENLITANATEPQKAEN

Ligands and cofactors

ID	Name	Formula	Copies
BEF	Beryllium trifluoride ion	Be F3	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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