8JBM: Na+,K+-ATPase in the E1.Mn2+ state

Crystal structure of Na+,K+-ATPase in the E1.Mn2+ state. Determined by X-ray diffraction at 2.9 Å resolution. Released 9 Aug 2023.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Sus scrofa
Chains: 6
Atoms: 21,682
Mol. weight: 329.49 kDa
Ligands: MN, CLR, PC1, PCW
Released: 9 Aug 2023

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

Secondary structure: helices and β-sheets

8JBM contains 145 α-helices and 98 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: 56 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	41-48	8
α-helix	58-68	11
α-helix	73-79	7
α-helix	81-89	9
α-helix	92-113	22
α-helix	121-152	32
α-helix	153-156	4
α-helix	159-160	2
β-strand	161-166	6	1
β-strand	169-174	6	1
α-helix	175-177	3
β-strand	183-187	5	1
α-helix	190	1
β-strand	191	1	1
α-helix	192	1
β-strand	195-207	13	1
α-helix	216	1
β-strand	217-220	4	1
β-strand	235-236	2	1
β-strand	241-253	13	1
α-helix	255-257	3
α-helix	259-266	8
α-helix	276-305	30
α-helix	310-324	15
α-helix	329-346	18
β-strand	349-351	3	2
α-helix	356-359	4
α-helix	360-362	3
β-strand	365-369	5	2
α-helix	370-374	5
β-strand	375	1	3
β-strand	380-386	7	4
β-strand	389-392	4	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	460-466	7
β-strand	468-473	6	4
β-strand	481	1	4
β-strand	483-487	5	4
β-strand	497-502	6	4
α-helix	504-509	6
β-strand	511-516	6	4
β-strand	519-522	4	4
α-helix	525-539	15
β-strand	543-552	10	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
β-strand	605-609	5	2
α-helix	614-624	11
α-helix	634-641	8
α-helix	645-647	3
α-helix	650-652	3
β-strand	655-658	4	2
α-helix	660-664	5
α-helix	668-676	9
β-strand	680-683	4	2
α-helix	688-690	3
α-helix	691-700	10
β-strand	705-709	5	2
α-helix	715-720	6
β-strand	723-727	5	2
α-helix	733-738	6
β-strand	741-743	3	2
α-helix	748-772	25
α-helix	776-788	13
α-helix	797-801	5
α-helix	802-807	6
α-helix	811-814	4
α-helix	815-817	3
α-helix	828-831	4
α-helix	840-845	6
α-helix	846-850	5
α-helix	851-869	19
α-helix	880-884	5
β-strand	891-892	2	6
β-strand	898-899	2	6
α-helix	901-930	30
α-helix	937-940	4
α-helix	945-963	19
α-helix	967-970	4
α-helix	978-981	4
α-helix	985-1004	20
α-helix	1009-1014	6

Chain B: 14 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	17-18	2	7
β-strand	23-24	2	7
β-strand	27-28	2	7
α-helix	29-58	30
β-strand	77-80	4	8
α-helix	84-86	3
β-strand	87-90	4	9
α-helix	99-109	11
α-helix	110-112	3
β-strand	123-124	2	10
β-strand	148-149	2	10
α-helix	153-155	3
α-helix	169-171	3
β-strand	175	1	8
β-strand	177-180	4	8
α-helix	181-182	2
β-strand	184	1	11
α-helix	190-192	3
α-helix	193-195	3
α-helix	200-201	2
β-strand	208-210	3	12
β-strand	211-214	4	9
α-helix	218-223	6
β-strand	226-231	6	8
α-helix	232-234	3
β-strand	237-239	3	12
α-helix	240-242	3
β-strand	245	1	11
α-helix	247-250	4
β-strand	258-264	7	8
β-strand	272-278	7	9
β-strand	294-301	8	9

Chain C: 59 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	41-44	4
α-helix	45-49	5
α-helix	58-68	11
α-helix	73-80	8
α-helix	81-89	9
α-helix	94-113	20
α-helix	121-155	35
α-helix	159-160	2
β-strand	161-166	6	13
β-strand	169-174	6	13
α-helix	175-177	3
α-helix	178-179	2
β-strand	183-187	5	13
α-helix	190	1
β-strand	191	1	13
α-helix	192	1
β-strand	195-207	13	13
α-helix	208-210	3
α-helix	216	1
β-strand	217-220	4	13
β-strand	235-236	2	13
α-helix	237	1
β-strand	241-253	13	13
α-helix	255-257	3
α-helix	261-267	7
α-helix	273-275	3
α-helix	276-305	30
α-helix	310-324	15
α-helix	329-346	18
β-strand	349-351	3	14
α-helix	355-359	5
β-strand	365-368	4	14
α-helix	370-374	5
β-strand	375	1	15
β-strand	380-386	7	16
β-strand	389-392	4	16
α-helix	409-420	12
β-strand	425-426	2	17
α-helix	427	1
β-strand	440-441	2	17
α-helix	444-456	13
α-helix	460-466	7
β-strand	469-473	5	16
β-strand	481-486	6	16
β-strand	497-502	6	16
α-helix	504-510	7
β-strand	511-516	6	16
β-strand	519-522	4	16
α-helix	525-539	15
β-strand	543-551	9	16
β-strand	576-585	10	16
α-helix	587	1
β-strand	588	1	15
α-helix	589	1
α-helix	592-601	10
β-strand	605-609	5	14
α-helix	614-624	11
α-helix	634-641	8
α-helix	650-652	3
β-strand	655-659	5	14
α-helix	660-664	5
α-helix	668-676	9
β-strand	680-684	5	14
α-helix	688-690	3
α-helix	691-700	10
β-strand	705-709	5	14
α-helix	715-720	6
β-strand	723-727	5	14
α-helix	733-738	6
β-strand	741-743	3	14
α-helix	748-774	27
α-helix	776-788	13
α-helix	797-802	6
α-helix	803-807	5
α-helix	809-814	6
α-helix	815-817	3
α-helix	828-830	3
α-helix	840-846	7
α-helix	850-869	20
α-helix	874-876	3
α-helix	879-883	5
β-strand	891-892	2	18
β-strand	898-899	2	18
α-helix	901-930	30
α-helix	937-940	4
α-helix	945-963	19
α-helix	967-970	4
α-helix	978-980	3
α-helix	985-1003	19
α-helix	1009-1014	6

Chain D: 14 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	17-18	2	19
β-strand	23-24	2	19
β-strand	27-28	2	19
α-helix	29-58	30
α-helix	70-72	3
β-strand	77-80	4	20
α-helix	84-86	3
β-strand	87-90	4	21
α-helix	99-109	11
α-helix	110-112	3
β-strand	123-124	2	22
α-helix	141-143	3
β-strand	148-149	2	22
α-helix	153-155	3
β-strand	175-180	6	20
β-strand	184	1	23
α-helix	190-192	3
α-helix	193-195	3
α-helix	200-201	2
β-strand	208-210	3	24
β-strand	211-215	5	21
α-helix	218-224	7
β-strand	226-230	5	20
α-helix	232-234	3
β-strand	237-239	3	24
α-helix	240-242	3
β-strand	245	1	23
α-helix	247-250	4
β-strand	258-264	7	20
β-strand	271-278	8	21
β-strand	294-301	8	21

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	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)
FXYD domain-containing ion transport regulator	E, G	protein	65	Sus scrofa	Q58K79 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>8JBM_1 Sodium/potassium-transporting ATPase subunit alpha (chains A, C)
MGKGVGRDKYEPAAVSEHGDKKKAKKERDMDELKKEVSMDDHKLSLDELHRKYGTDLSRG
LTPARAAEILARDGPNALTPPPTTPEWVKFCRQLFGGFSMLLWIGAILCFLAYGIQAATE
EEPQNDNLYLGVVLSAVVIITGCFSYYQEAKSSKIMESFKNMVPQQALVIRNGEKMSINA
EEVVVGDLVEVKGGDRIPADLRIISANGCKVDNSSLTGESEPQTRSPDFTNENPLETRNI
AFFSTNCVEGTARGIVVYTGDRTVMGRIATLASGLEGGQTPIAAEIEHFIHIITGVAVFL
GVSFFILSLILEYTWLEAVIFLIGIIVANVPEGLLATVTVCLTLTAKRMARKNCLVKNLE
AVETLGSTSTICSDKTGTLTQNRMTVAHMWFDNQIHEADTTENQSGVSFDKTSATWLALS
RIAGLCNRAVFQANQENLPILKRAVAGDASESALLKCIELCCGSVKEMRERYTKIVEIPF
NSTNKYQLSIHKNPNTAEPRHLLVMKGAPERILDRCSSILIHGKEQPLDEELKDAFQNAY
LELGGLGERVLGFCHLFLPDEQFPEGFQFDTDDVNFPLDNLCFVGLISMIDPPRAAVPDA
VGKCRSAGIKVIMVTGDHPITAKAIAKGVGIISEGNETVEDIAARLNIPVSQVNPRDAKA
CVVHGSDLKDMTSEQLDDILKYHTEIVFARTSPQQKLIIVEGCQRQGAIVAVTGDGVNDS
PALKKADIGVAMGIAGSDVSKQAADMILLDDNFASIVTGVEEGRLIFDNLKKSIAYTLTS
NIPEITPFLIFIIANIPLPLGTVTILCIDLGTDMVPAISLAYEQAESDIMKRQPRNPKTD
KLVNERLISMAYGQIGMIQALGGFFTYFVILAENGFLPIHLLGLRVNWDDRWINDVEDSY
GQQWTYEQRKIVEFTCHTAFFVSIVVVQWADLVICKTRRNSVFQQGMKNKILIFGLFEET
ALAAFLSYCPGMGVALRMYPLKPTWWFCAFPYSLLIFVYDEVRKLIIRRRPGGWVEKETY
Y

Sequence of entity 2 (B, D), FASTA

>8JBM_2 Sodium/potassium-transporting ATPase subunit beta-1 (chains B, D)
MARGKAKEEGSWKKFIWNSEKKEFLGRTGGSWFKILLFYVIFYGCLAGIFIGTIQVMLLT
ISEFKPTYQDRVAPPGLTQIPQSQKTEISFRPNDPQSYESYVVSIVRFLEKYKDLAQKDD
MIFEDCGNVPSELKERGEYNNERGERKVCRFRLEWLGNCSGLNDETYGYKDGKPCVIIKL
NRVLGFKPKPPKNESLETYPVMKYNPYVLPVHCTGKRDEDKEKVGTMEYFGLGGYPGFPL
QYYPYYGKLLQPKYLQPLMAVQFTNLTMDTEIRIECKAYGENIGYSEKDRFQGRFDVKIE
VKS

Sequence of entity 3 (E, G), FASTA

>8JBM_3 FXYD domain-containing ion transport regulator (chains E, G)
MAGLSTDDGGSPKGDVDPFYYDYETVRNGGLIFAALAFIVGLIIILSKRLRCGGKKHRPI
NEDEL

Ligands and cofactors

ID	Name	Formula	Copies
MN	Manganese (II) ion	Mn	6
CLR	Cholesterol	C27 H46 O	6
PC1	1,2-diacyl-sn-glycero-3-phosphocholine	C44 H88 N O8 P	3
PCW	1,2-dioleoyl-sn-glycero-3-phosphocholine	C44 H85 N O8 P	14
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
DMU	Decyl-beta-D-maltopyranoside	C22 H42 O11	1

Primary citation

Crystal structures of Na + ,K + -ATPase reveal the mechanism that converts the K + -bound form to Na + -bound form and opens and closes the cytoplasmic gate. Kanai, R., Vilsen, B., Cornelius, F. et al. FEBS Lett (2023) 597:1957-1976. DOI 10.1002/1873-3468.14689 · 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
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
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

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