4HYT: PDB entry 4HYT

Na,K-ATPase in the E2P state with bound ouabain and Mg2+ in the cation-binding site. Determined by X-ray diffraction at 3.4 Å resolution. Released 26 Jun 2013.

Method: X-ray diffraction
Resolution: 3.4 Å
Organism: Sus scrofa
Chains: 6
Atoms: 21,220
Mol. weight: 320.76 kDa
Ligands: MG, 1DS, 17F, 1AT
Released: 26 Jun 2013

Explore 4HYT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4HYT contains 153 α-helices and 102 β-strands across 6 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: 64 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	22-29	8
α-helix	41-48	8
β-strand	51	1	1
β-strand	55-56	2	1
α-helix	58-65	8
α-helix	73-76	4
α-helix	82-84	3
α-helix	85-88	4
α-helix	93-110	18
α-helix	111-113	3
α-helix	117-119	3
α-helix	122-152	31
β-strand	162-166	5	1
β-strand	169-173	5	1
α-helix	175-177	3
β-strand	183-186	4	1
β-strand	191	1	1
β-strand	195-207	13	1
α-helix	217	1
β-strand	218-219	2	1
β-strand	235-236	2	1
α-helix	240	1
β-strand	241-253	13	1
α-helix	255-257	3
α-helix	259-268	10
α-helix	276-304	29
α-helix	310-324	15
α-helix	328-346	19
β-strand	349-351	3	2
α-helix	355-357	3
α-helix	359-362	4
β-strand	365-368	4	2
α-helix	370-374	5
β-strand	375	1	3
β-strand	380-385	6	4
β-strand	390-392	3	4
α-helix	409-420	12
β-strand	425-426	2	5
β-strand	440-441	2	5
α-helix	444-456	13
α-helix	461-466	6
α-helix	468	1
β-strand	469-473	5	4
α-helix	474-476	3
β-strand	482-486	5	4
α-helix	495-496	2
β-strand	497-502	6	4
α-helix	504-510	7
β-strand	511-516	6	4
β-strand	519-521	3	4
α-helix	525-540	16
β-strand	544-552	9	4
β-strand	576-585	10	4
α-helix	587	1
β-strand	588	1	3
α-helix	589	1
α-helix	592-601	10
α-helix	604	1
β-strand	605-609	5	2
α-helix	614-624	11
α-helix	631-633	3
α-helix	634-640	7
α-helix	650-652	3
β-strand	655-659	5	2
α-helix	660-664	5
α-helix	668-677	10
β-strand	680-684	5	2
α-helix	688-700	13
β-strand	705-708	4	2
α-helix	712-714	3
α-helix	715-720	6
β-strand	723-727	5	2
α-helix	733-738	6
β-strand	741-743	3	2
α-helix	749-774	26
α-helix	776-789	14
α-helix	797-801	5
α-helix	802-807	6
α-helix	809-814	6
α-helix	815-817	3
α-helix	828-831	4
α-helix	840-845	6
α-helix	846-850	5
α-helix	851-868	18
α-helix	873-876	4
α-helix	880-883	4
β-strand	892	1	6
β-strand	898	1	6
α-helix	901-909	9
α-helix	912-930	19
α-helix	937-940	4
α-helix	945-963	19
α-helix	967-970	4
α-helix	975-977	3
α-helix	978-982	5
α-helix	985-1004	20
α-helix	1009-1013	5

Chains B and D: 12 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	20-21	2	7
β-strand	24-25	2	7
α-helix	32-59	28
α-helix	75	1
β-strand	76	1	8
β-strand	77-79	3	9
β-strand	87-90	4	10
α-helix	99-108	10
α-helix	109-111	3
β-strand	123-124	2	11
α-helix	146-147	2
β-strand	148-149	2	11
α-helix	153-155	3
β-strand	175-180	6	9
α-helix	181-182	2
β-strand	184	1	12
α-helix	190-192	3
β-strand	208-210	3	13
β-strand	211-214	4	10
β-strand	227-230	4	9
α-helix	232-234	3
β-strand	237-239	3	13
α-helix	240-242	3
β-strand	245	1	12
α-helix	247-250	4
α-helix	254-257	4
β-strand	258-263	6	9
β-strand	272-278	7	10
β-strand	292	1	8
β-strand	296-301	6	10

Chain C: 63 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	22-29	8
α-helix	41-48	8
β-strand	51	1	14
β-strand	55-56	2	14
α-helix	58-65	8
α-helix	73-76	4
α-helix	82-84	3
α-helix	85-88	4
α-helix	93-110	18
α-helix	111-113	3
α-helix	117-119	3
α-helix	122-152	31
β-strand	162-166	5	14
β-strand	169-173	5	14
α-helix	175-177	3
β-strand	183-186	4	14
β-strand	191	1	14
β-strand	195-207	13	14
α-helix	217	1
β-strand	218-219	2	14
β-strand	235-236	2	14
α-helix	240	1
β-strand	241-253	13	14
α-helix	255-257	3
α-helix	259-268	10
α-helix	276-304	29
α-helix	310-324	15
α-helix	328-346	19
β-strand	349-351	3	15
α-helix	355-357	3
α-helix	359-362	4
β-strand	365-368	4	15
α-helix	370-374	5
β-strand	375	1	16
β-strand	380-385	6	17
β-strand	390-392	3	17
α-helix	409-420	12
β-strand	425-426	2	18
β-strand	440-441	2	18
α-helix	444-456	13
α-helix	461-466	6
α-helix	468	1
β-strand	469-473	5	17
β-strand	481-486	6	17
α-helix	495-496	2
β-strand	497-502	6	17
α-helix	504-510	7
β-strand	511-516	6	17
β-strand	519-521	3	17
α-helix	525-540	16
β-strand	544-552	9	17
β-strand	576-585	10	17
α-helix	586-587	2
β-strand	588	1	16
α-helix	589	1
α-helix	592-601	10
α-helix	604	1
β-strand	605-609	5	15
α-helix	614-624	11
α-helix	631-633	3
α-helix	634-640	7
α-helix	650-652	3
β-strand	655-659	5	15
α-helix	660-664	5
α-helix	668-677	10
β-strand	680-684	5	15
α-helix	688-700	13
β-strand	705-708	4	15
α-helix	712-714	3
α-helix	715-720	6
β-strand	723-727	5	15
α-helix	733-738	6
β-strand	741-743	3	15
α-helix	749-774	26
α-helix	776-789	14
α-helix	797-801	5
α-helix	802-807	6
α-helix	809-814	6
α-helix	815-817	3
α-helix	828-831	4
α-helix	840-845	6
α-helix	846-850	5
α-helix	851-868	18
α-helix	873-876	4
α-helix	880-883	4
β-strand	892	1	19
β-strand	898	1	19
α-helix	901-909	9
α-helix	912-930	19
α-helix	937-940	4
α-helix	945-963	19
α-helix	967-970	4
α-helix	975-977	3
α-helix	978-982	5
α-helix	985-1004	20
α-helix	1009-1013	5

Chains E and G: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	23-45	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sodium/potassium-transporting ATPase subunit alpha-1	A, C	protein	1021	Sus scrofa	P05024 (AlphaFold model)
Sodium/potassium-transporting ATPase subunit beta-1	B, D	protein	303	Sus scrofa	P05027 (AlphaFold model)
Na+/K+ ATPase gamma subunit transcript variant a	E, G	protein	65	Sus scrofa	Q58K79 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4HYT_1 Sodium/potassium-transporting ATPase subunit alpha-1 (chains A, C)
MGKGVGRDKYEPAAVSEHGDKKKAKKERDMDELKKEVSMDDHKLSLDELHRKYGTDLSRG
LTPARAAEILARDGPNALTPPPTTPEWVKFCRQLFGGFSMLLWIGAILCFLAYGIQAATE
EEPQNDNLYLGVVLSAVVIITGCFSYYQEAKSSKIMESFKNMVPQQALVIRNGEKMSINA
EEVVVGDLVEVKGGDRIPADLRIISANGCKVDNSSLTGESEPQTRSPDFTNENPLETRNI
AFFSTNCVEGTARGIVVYTGDRTVMGRIATLASGLEGGQTPIAAEIEHFIHIITGVAVFL
GVSFFILSLILEYTWLEAVIFLIGIIVANVPEGLLATVTVCLTLTAKRMARKNCLVKNLE
AVETLGSTSTICSDKTGTLTQNRMTVAHMWSDNQIHEADTTENQSGVSFDKTSATWLALS
RIAGLCNRAVFQANQENLPILKRAVAGDASESALLKCIELCCGSVKEMRERYTKIVEIPF
NSTNKYQLSIHKNPNTAEPRHLLVMKGAPERILDRCSSILIHGKEQPLDEELKDAFQNAY
LELGGLGERVLGFCHLFLPDEQFPEGFQFDTDDVNFPLDNLCFVGLISMIDPPRAAVPDA
VGKCRSAGIKVIMVTGDHPITAKAIAKGVGIISEGNETVEDIAARLNIPVSQVNPRDAKA
CVVHGSDLKDMTSEQLDDILKYHTEIVFARTSPQQKLIIVEGCQRQGAIVAVTGDGVNDS
PASKKADIGVAMGIAGSDVSKQAADMILLDDNFASIVTGVEEGRLIFDNLKKSIAYTLTS
NIPEITPFLIFIIANIPLPLGTVTILCIDLGTDMVPAISLAYEQAESDIMKRQPRNPKTD
KLVNEQLISMAYGQIGMIQALGGFFTYFVILAENGFLPIHLLGLRVNWDDRWINDVEDSY
GQQWTYEQRKIVEFTCHTPFFVTIVVVQWADLVICKTRRNSVFQQGMKNKILIFGLFEET
ALAAFLSYCPGMGVALRMYPLKPTWWFCAFPYSLLIFVYDEVRKLIIRRRPGGWVEKETY
Y

Sequence of entity 2 (B, D), FASTA

>4HYT_2 Sodium/potassium-transporting ATPase subunit beta-1 (chains B, D)
MARGKAKEEGSWKKFIWNSEKKEFLGRTGGSWFKILLFYVIFYGCLAGIFIGTIQVMLLT
ISEFKPTYQDRVAPPGLTQIPQSQKTEISFRPNDPQSYESYVVSIVRFLEKYKDLAQKDD
MIFEDCGNVPSELKERGEYNNERGERKVCRFRLEWLGNCSGLNDETYGYKDGKPCVIIKL
NRVLGFKPKPPKNESLETYPVMKYNPYVLPVHCTGKRDEDKEKVGTMEYFGLGGYPGFPL
QYYPYYGKLLQPKYLQPLMAVQFTNLTMDTEIRIECKAYGENIGYSEKDRFQGRFDVKIE
VKS

Sequence of entity 3 (E, G), FASTA

>4HYT_3 Na+/K+ ATPase gamma subunit transcript variant a (chains E, G)
MAGLSTDDGGSPKGDVDPFYYDYETVRNGGLIFAALAFIVGLIIILSKRLRCGGKKHRPI
NEDEL

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	6
1DS	1-O-decanoyl-beta-D-tagatofuranosyl beta-D-allopyranoside	C22 H40 O12	1
17F	O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L…	C42 H78 N O10 P	5
1AT	beta-D-fructofuranosyl 6-O-decanoyl-alpha-D-glucopyranoside	C22 H40 O12	1
CLR	Cholesterol	C27 H46 O	4
OBN	Ouabain	C29 H44 O12	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5
CE1	O-dodecanyl octaethylene glycol	C28 H58 O9	2

Primary citation

Crystal structure of the high-affinity Na+,K+-ATPase-ouabain complex with Mg2+ bound in the cation binding site. Laursen, M., Yatime, L., Nissen, P. et al. Proc Natl Acad Sci U S A (2013) 110:10958-10963. DOI 10.1073/pnas.1222308110 · PubMed

Other PDB entries of the same protein (UniProt P05024 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3WGU 2.8 Å, Crystal structure of a Na+-bound Na+,K+-ATPase preceding the E1P state without oligomycin
3WGV 2.8 Å, Crystal structure of a Na+-bound Na+,K+-ATPase preceding the E1P state with oligomycin
8JBK 2.8 Å, Crystal structure of Na+,K+-ATPase in the E1.3Na+ state
7WYT 2.9 Å, Crystal structures of Na+,K+-ATPase in complex with ouabain
8JBM 2.9 Å, Crystal structure of Na+,K+-ATPase in the E1.Mn2+ state
8JBL 3.0 Å, Crystal structure of Na+,K+-ATPase in the E1.Mg2+ state
7DDL 3.2 Å, Crystal structures of Na+,K+-ATPase in complex with bufalin
7D91 3.35 Å, Crystal Structure of the Na+,K+-ATPase in the E2P state with bound Mg2+ (P4(3)2(1)2…
4RES 3.41 Å, Crystal structure of the Na,K-ATPase E2P-bufalin complex with bound potassium
7DDH 3.46 Å, Crystal structures of Na+,K+-ATPase in complex with digoxin
3B8E 3.5 Å, Crystal structure of the sodium-potassium pump
3KDP 3.5 Å, Crystal structure of the sodium-potassium pump

Browse structure collections

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