8D3W: PDB entry 8D3W

Human alpha3 Na+/K+-ATPase in its AMPPCP-bound cytoplasmic side-open state. Determined by electron microscopy at 3.5 Å resolution. Released 21 Sept 2022.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 3
Atoms: 10,046
Mol. weight: 158.33 kDa
Ligands: ACP
Released: 21 Sept 2022

Explore 8D3W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8D3W contains 63 α-helices and 51 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, 38 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	70-76	7
α-helix	80-86	7
α-helix	89-91	3
α-helix	92-107	16
α-helix	120-149	30
α-helix	151-154	4
β-strand	158-162	5	2
β-strand	167-171	5	2
α-helix	172-174	3
β-strand	180-184	5	2
β-strand	188	1	3
β-strand	192-198	7	2
β-strand	202-204	3	3
α-helix	214	1
β-strand	215-216	2	3
β-strand	232-233	2	2
β-strand	238-241	4	3
β-strand	243-250	8	2
α-helix	273-303	31
α-helix	309-321	13
α-helix	326-343	18
β-strand	347-348	2	4
α-helix	352-355	4
β-strand	362-365	4	4
β-strand	372	1	5
β-strand	380-383	4	6
β-strand	386-389	4	6
α-helix	406-415	10
β-strand	422	1	7
β-strand	438	1	7
α-helix	442-451	10
α-helix	459-463	5
β-strand	466-470	5	8
β-strand	480-484	5	8
β-strand	493-495	3	8
α-helix	501-505	5
β-strand	508	1	9
β-strand	510-513	4	10
β-strand	516-519	4	10
α-helix	522-536	15
β-strand	542-545	4	6
β-strand	548-550	3	8
α-helix	551	1
β-strand	573	1	9
β-strand	577-580	4	6
α-helix	584	1
β-strand	585	1	5
α-helix	586	1
α-helix	589-598	10
β-strand	602-606	5	4
α-helix	611-621	11
α-helix	631-638	8
α-helix	642-644	3
α-helix	647-649	3
β-strand	652-656	5	4
α-helix	657-660	4
α-helix	665-673	9
β-strand	677-681	5	4
α-helix	685-695	11
β-strand	702-705	4	4
α-helix	709-711	3
α-helix	712-717	6
β-strand	720-724	5	4
α-helix	730-734	5
β-strand	738-740	3	4
α-helix	746-771	26
α-helix	778-785	8
α-helix	794-799	6
α-helix	800-805	6
α-helix	808-814	7
α-helix	815-818	4
α-helix	825-827	3
α-helix	837-841	5
α-helix	842-847	6
α-helix	848-865	18
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	934-936	3
α-helix	942-960	19
α-helix	975-979	5
α-helix	982-1001	20
α-helix	1006-1010	5

Chain B: 11 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	33-59	27
β-strand	77-79	3	12
β-strand	87-90	4	13
α-helix	95-97	3
α-helix	99-109	11
α-helix	110-112	3
α-helix	114-116	3
β-strand	123-124	2	14
α-helix	146-147	2
β-strand	148-149	2	14
α-helix	153-155	3
β-strand	176-180	5	12
α-helix	181-182	2
β-strand	184	1	15
β-strand	211-215	5	13
α-helix	218-221	4
β-strand	227-230	4	12
α-helix	232-234	3
α-helix	240-242	3
β-strand	245	1	15
β-strand	258-263	6	12
β-strand	268	1	13
β-strand	272-278	7	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

>8D3W_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

>8D3W_2 Sodium/potassium-transporting ATPase subunit beta-1 (chains B)
MARGKAKEEGSWKKFIWNSEKKEFLGRTGGSWFKILLFYVIFYGCLAGIFIGTIQVMLLT
ISEFKPTYQDRVAPPGLTQIPQIQKTEISFRPNDPKSYEAYVLNIVRFLEKYKDSAQRDD
MIFEDCGDVPSEPKERGDFNHERGERKVCRFKLEWLGNCSGLNDETYGYKEGKPCIIIKL
NRVLGFKPKPPKNESLETYPVMKYNPNVLPVQCTGKRDEDKDKVGNVEYFGLGNSPGFPL
QYYPYYGKLLQPKYLQPLLAVQFTNLTMDTEIRIECKAYGENIGYSEKDRFQGRFDVKIE
VKS

Sequence of entity 3 (G), FASTA

>8D3W_3 FXYD domain-containing ion transport regulator 6 (chains G)
MATMELVLVFLCSLLAPMVLASAAEKEKEMDPFHYDYQTLRIGGLVFAVVLFSVGILLIL
SRRCKCSFNQKPRAPGDEEAQVENLITANATEPQKAEN

Ligands and cofactors

ID	Name	Formula	Copies
ACP	Phosphomethylphosphonic acid adenylate ester	C11 H18 N5 O12 P3	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
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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