4RES: PDB entry 4RES

Crystal structure of the Na,K-ATPase E2P-bufalin complex with bound potassium. Determined by X-ray diffraction at 3.41 Å resolution. Released 28 Jan 2015.

Method: X-ray diffraction
Resolution: 3.41 Å
Organism: Sus scrofa
Chains: 6
Atoms: 20,881
Mol. weight: 314.3 kDa
Ligands: BUF, CLR, MG, NAG
Released: 28 Jan 2015

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

Secondary structure: helices and β-sheets

4RES contains 130 α-helices and 107 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: 54 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	22-29	8
α-helix	41-47	7
β-strand	51	1	1
β-strand	55-56	2	1
α-helix	58-67	10
α-helix	73-76	4
α-helix	82-89	8
α-helix	93-111	19
α-helix	122-153	32
β-strand	161-166	6	1
β-strand	169-174	6	1
β-strand	183-186	4	1
β-strand	191	1	1
β-strand	195-207	13	1
α-helix	209-212	4
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	276-306	31
α-helix	310-323	14
α-helix	327-346	20
β-strand	349-351	3	2
α-helix	359-362	4
β-strand	365-368	4	3
β-strand	371	1	4
β-strand	375	1	4
β-strand	380-386	7	5
β-strand	389-392	4	5
α-helix	409-420	12
β-strand	425-426	2	6
β-strand	440-441	2	6
α-helix	444-456	13
α-helix	460-466	7
β-strand	469-473	5	5
α-helix	474-476	3
β-strand	482-486	5	5
α-helix	495	1
β-strand	496-502	7	5
α-helix	506-509	4
β-strand	513-514	2	5
β-strand	516	1	7
β-strand	519	1	7
α-helix	525-539	15
β-strand	544-553	10	5
β-strand	577-585	9	5
β-strand	588	1	4
α-helix	592-602	11
α-helix	604	1
β-strand	605-609	5	3
α-helix	614-624	11
α-helix	634-641	8
α-helix	650-652	3
β-strand	656-658	3	3
α-helix	660-665	6
α-helix	668-677	10
β-strand	681-683	3	3
α-helix	688-700	13
β-strand	705-708	4	3
α-helix	712-714	3
α-helix	715-720	6
β-strand	723-725	3	3
β-strand	726-727	2	2
α-helix	734-737	4
β-strand	741-743	3	2
α-helix	749-789	41
α-helix	791-793	3
α-helix	797-801	5
α-helix	802-807	6
α-helix	809-814	6
α-helix	815-817	3
α-helix	828-830	3
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	8
β-strand	898	1	8
α-helix	901-909	9
α-helix	913-930	18
α-helix	937-940	4
α-helix	945-963	19
α-helix	967-970	4
α-helix	978-982	5
α-helix	985-1004	20
α-helix	1009-1013	5

Chains B and D: 10 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	20-21	2	9
β-strand	24-25	2	9
α-helix	32-59	28
α-helix	70-72	3
α-helix	75	1
β-strand	76	1	10
β-strand	77-79	3	11
β-strand	87-90	4	12
α-helix	99-108	10
β-strand	123-124	2	13
α-helix	146-147	2
β-strand	148-149	2	13
α-helix	153-155	3
β-strand	175-180	6	11
α-helix	181-182	2
β-strand	184	1	14
α-helix	190-192	3
β-strand	208-210	3	15
β-strand	211-214	4	12
β-strand	226-230	5	11
β-strand	237-239	3	15
α-helix	240-242	3
β-strand	245	1	14
α-helix	247-250	4
β-strand	258-265	8	11
β-strand	272-278	7	12
β-strand	292	1	10
β-strand	294-301	8	12

Chain C: 54 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	22-29	8
α-helix	41-47	7
β-strand	51	1	16
β-strand	55-56	2	16
α-helix	58-67	10
α-helix	73-76	4
α-helix	82-89	8
α-helix	93-111	19
α-helix	122-154	33
β-strand	161-166	6	16
β-strand	169-174	6	16
β-strand	183-186	4	16
β-strand	191	1	16
β-strand	195-207	13	16
α-helix	209-212	4
α-helix	217	1
β-strand	218-219	2	16
β-strand	235-236	2	16
α-helix	240	1
β-strand	241-253	13	16
α-helix	255-257	3
α-helix	259-268	10
α-helix	276-306	31
α-helix	310-323	14
α-helix	327-346	20
β-strand	349-351	3	17
α-helix	359-362	4
β-strand	365-368	4	18
α-helix	370-374	5
β-strand	375	1	19
β-strand	380-386	7	20
β-strand	389-392	4	20
α-helix	409-420	12
β-strand	425-426	2	21
β-strand	440-441	2	21
α-helix	444-456	13
α-helix	460-466	7
β-strand	469-473	5	20
α-helix	474-476	3
β-strand	482-486	5	20
α-helix	495	1
β-strand	496-502	7	20
α-helix	506-509	4
β-strand	513-514	2	20
β-strand	516	1	22
β-strand	519	1	22
α-helix	525-539	15
β-strand	544-553	10	20
β-strand	577-585	9	20
β-strand	588	1	19
α-helix	592-602	11
β-strand	605-609	5	18
α-helix	614-624	11
α-helix	634-641	8
α-helix	650-652	3
β-strand	656-658	3	18
α-helix	660-665	6
α-helix	668-677	10
β-strand	681-683	3	18
α-helix	688-700	13
β-strand	705-708	4	18
α-helix	712-714	3
α-helix	715-720	6
β-strand	723-725	3	18
β-strand	726-727	2	17
α-helix	734-737	4
β-strand	741-743	3	17
α-helix	749-789	41
α-helix	791-793	3
α-helix	797-801	5
α-helix	802-807	6
α-helix	809-814	6
α-helix	815-817	3
α-helix	828-830	3
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	23
β-strand	898	1	23
α-helix	901-909	9
α-helix	913-930	18
α-helix	937-940	4
α-helix	945-963	19
α-helix	967-970	4
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	24-45	22

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

>4RES_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

>4RES_2 Sodium/potassium-transporting ATPase subunit beta-1 (chains B, D)
MARGKAKEEGSWKKFIWNSEKKEFLGRTGGSWFKILLFYVIFYGCLAGIFIGTIQVMLLT
ISEFKPTYQDRVAPPGLTQIPQSQKTEISFRPNDPQSYESYVVSIVRFLEKYKDLAQKDD
MIFEDCGNVPSELKERGEYNNERGERKVCRFRLEWLGNCSGLNDETYGYKDGKPCVIIKL
NRVLGFKPKPPKNESLETYPVMKYNPYVLPVHCTGKRDEDKEKVGTMEYFGLGGYPGFPL
QYYPYYGKLLQPKYLQPLMAVQFTNLTMDTEIRIECKAYGENIGYSEKDRFQGRFDVKIE
VKS

Sequence of entity 3 (E, G), FASTA

>4RES_3 Na+/K+ ATPase gamma subunit transcript variant a (chains E, G)
MAGLSTDDGGSPKGDVDPFYYDYETVRNGGLIFAALAFIVGLIIILSKRLRCGGKKHRPI
NEDEL

Ligands and cofactors

ID	Name	Formula	Copies
BUF	bufalin	C24 H34 O4	2
CLR	Cholesterol	C27 H46 O	2
MG	Magnesium ion	Mg	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
17F	O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L…	C42 H78 N O10 P	1

Water and common crystallization additives (K) are not listed.

Primary citation

Structures and characterization of digoxin- and bufalin-bound Na+,K+-ATPase compared with the ouabain-bound complex. Laursen, M., Gregersen, J.L., Yatime, L. et al. Proc Natl Acad Sci U S A (2015) 112:1755-1760. DOI 10.1073/pnas.1422997112 · 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…
4HYT 3.4 Å, Na,K-ATPase in the E2P state with bound ouabain and Mg2+ in the cation-binding site
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

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