3WGU: PDB entry 3WGU

Crystal structure of a Na+-bound Na+,K+-ATPase preceding the E1P state without oligomycin. Determined by X-ray diffraction at 2.8 Å resolution. Released 9 Oct 2013.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Sus scrofa
Chains: 6
Atoms: 21,807
Mol. weight: 321.4 kDa
Ligands: CLR, PC1, NAG, ADP
Released: 9 Oct 2013

Explore 3WGU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3WGU contains 129 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: 55 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	41-48	8
β-strand	51	1	1
β-strand	55	1	1
α-helix	58-68	11
α-helix	73-75	3
α-helix	81-89	9
α-helix	93-114	22
α-helix	121-150	30
α-helix	152-154	3
β-strand	161-164	4	2
β-strand	171-174	4	2
α-helix	175-177	3
β-strand	183-186	4	2
β-strand	190-191	2	2
β-strand	195-207	13	2
α-helix	209-212	4
β-strand	218-220	3	2
β-strand	235-236	2	2
α-helix	237	1
β-strand	241-253	13	2
α-helix	255-257	3
α-helix	259-262	4
α-helix	276-305	30
α-helix	310-323	14
α-helix	328-345	18
β-strand	349-351	3	3
α-helix	356-361	6
β-strand	365-368	4	3
α-helix	370-374	5
β-strand	375	1	4
β-strand	380-386	7	5
β-strand	389-392	4	5
α-helix	409-420	12
α-helix	444-456	13
α-helix	460-466	7
β-strand	469-473	5	5
β-strand	481-487	7	5
β-strand	496-502	7	5
α-helix	504-509	6
β-strand	511-516	6	5
β-strand	519-522	4	5
α-helix	525-540	16
β-strand	543-553	11	5
β-strand	576-585	10	5
α-helix	587	1
β-strand	588	1	4
α-helix	589	1
α-helix	592-600	9
β-strand	605-609	5	3
α-helix	614-624	11
β-strand	629	1	6
β-strand	631	1	6
α-helix	634-641	8
α-helix	645-647	3
α-helix	650-652	3
β-strand	655-659	5	3
α-helix	660-663	4
α-helix	668-676	9
β-strand	680-684	5	3
α-helix	688-700	13
β-strand	705-709	5	3
α-helix	715-720	6
β-strand	723-727	5	3
α-helix	733-738	6
β-strand	741-743	3	3
α-helix	750-774	25
α-helix	776-788	13
α-helix	797-807	11
α-helix	810-814	5
α-helix	818-820	3
α-helix	824-826	3
α-helix	828-831	4
α-helix	840-843	4
α-helix	844-849	6
α-helix	850-868	19
α-helix	873-876	4
α-helix	880-883	4
β-strand	891-892	2	7
β-strand	898-899	2	7
α-helix	901-929	29
α-helix	937-940	4
α-helix	945-963	19
α-helix	967-970	4
α-helix	975-977	3
α-helix	978-983	6
α-helix	985-1004	20
α-helix	1011-1014	4

Chain B: 10 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	12-15	4
α-helix	31-58	28
β-strand	77-79	3	8
β-strand	87-89	3	9
α-helix	96-98	3
α-helix	99-109	11
β-strand	123-124	2	10
α-helix	146-147	2
β-strand	148-149	2	10
β-strand	175-180	6	8
β-strand	184	1	11
β-strand	208-210	3	12
β-strand	211-213	3	13
β-strand	229-230	2	8
α-helix	232-234	3
β-strand	237-239	3	12
α-helix	240-242	3
α-helix	243	1
β-strand	245	1	11
α-helix	247-250	4
α-helix	254-257	4
β-strand	258-262	5	8
β-strand	271-274	4	9
β-strand	276-278	3	13
β-strand	294	1	13
β-strand	297-300	4	9

Chain C: 53 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	27-30	4
α-helix	41-48	8
β-strand	51	1	14
β-strand	55	1	14
α-helix	58-68	11
α-helix	73-75	3
α-helix	81-89	9
α-helix	93-113	21
α-helix	121-152	32
α-helix	155-157	3
β-strand	161-165	5	15
β-strand	170-174	5	15
α-helix	175-177	3
β-strand	181-187	7	15
β-strand	190-191	2	15
β-strand	195-207	13	15
α-helix	209-212	4
β-strand	218-220	3	15
β-strand	235-236	2	15
α-helix	237	1
β-strand	241-253	13	15
α-helix	255-257	3
α-helix	276-305	30
α-helix	310-323	14
α-helix	329-346	18
β-strand	349-351	3	16
α-helix	355-361	7
β-strand	365-368	4	16
α-helix	370-374	5
β-strand	375	1	17
β-strand	380-386	7	18
β-strand	389-392	4	18
α-helix	409-420	12
β-strand	425-426	2	19
β-strand	440-441	2	19
α-helix	444-454	11
α-helix	460-466	7
β-strand	469-473	5	18
β-strand	481-486	6	18
β-strand	497-502	6	18
α-helix	504-509	6
β-strand	511-516	6	18
β-strand	519-522	4	18
α-helix	525-538	14
α-helix	539-541	3
β-strand	544-552	9	18
β-strand	576-585	10	18
α-helix	587	1
β-strand	588	1	17
α-helix	589	1
α-helix	592-601	10
β-strand	605-609	5	16
α-helix	614-624	11
β-strand	629	1	20
β-strand	631	1	20
α-helix	634-640	7
α-helix	645-647	3
β-strand	655-659	5	16
α-helix	660-663	4
α-helix	668-676	9
β-strand	680-684	5	16
α-helix	688-701	14
β-strand	705-709	5	16
α-helix	712-714	3
α-helix	715-720	6
β-strand	723-727	5	16
α-helix	733-738	6
β-strand	741-743	3	16
α-helix	749-774	26
α-helix	776-788	13
α-helix	791-793	3
α-helix	797-807	11
α-helix	810-817	8
α-helix	828-831	4
α-helix	840-843	4
α-helix	844-850	7
α-helix	851-868	18
α-helix	873-875	3
α-helix	880-884	5
β-strand	891-892	2	21
β-strand	898-899	2	21
α-helix	901-929	29
α-helix	937-940	4
α-helix	945-963	19
α-helix	967-970	4
α-helix	978-983	6
α-helix	985-1004	20
α-helix	1009-1014	6

Chain D: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	12-15	4
α-helix	31-58	28
β-strand	62	1	22
β-strand	65	1	22
β-strand	76	1	23
β-strand	77-79	3	24
β-strand	87-89	3	25
α-helix	99-109	11
β-strand	123-124	2	26
β-strand	148-149	2	26
α-helix	153-155	3
β-strand	175-180	6	24
α-helix	181-182	2
β-strand	184	1	27
β-strand	208-210	3	28
β-strand	211-214	4	25
β-strand	230	1	24
α-helix	232-234	3
β-strand	237-239	3	28
α-helix	240-242	3
α-helix	243-244	2
β-strand	245	1	27
α-helix	254-257	4
β-strand	258-262	5	24
β-strand	271-278	8	25
β-strand	292	1	23
β-strand	296-300	5	25

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	1016	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

>3WGU_1 Sodium/potassium-transporting ATPase subunit alpha-1 (chains A, C)
GRDKYEPAAVSEHGDKKKAKKERDMDELKKEVSMDDHKLSLDELHRKYGTDLSRGLTPAR
AAEILARDGPNALTPPPTTPEWVKFCRQLFGGFSMLLWIGAILCFLAYGIQAATEEEPQN
DNLYLGVVLSAVVIITGCFSYYQEAKSSKIMESFKNMVPQQALVIRNGEKMSINAEEVVV
GDLVEVKGGDRIPADLRIISANGCKVDNSSLTGESEPQTRSPDFTNENPLETRNIAFFST
NCVEGTARGIVVYTGDRTVMGRIATLASGLEGGQTPIAAEIEHFIHIITGVAVFLGVSFF
ILSLILEYTWLEAVIFLIGIIVANVPEGLLATVTVCLTLTAKRMARKNCLVKNLEAVETL
GSTSTICSDKTGTLTQNRMTVAHMWFDNQIHEADTTENQSGVSFDKTSATWLALSRIAGL
CNRAVFQANQENLPILKRAVAGDASESALLKCIELCCGSVKEMRERYTKIVEIPFNSTNK
YQLSIHKNPNTAEPRHLLVMKGAPERILDRCSSILIHGKEQPLDEELKDAFQNAYLELGG
LGERVLGFCHLFLPDEQFPEGFQFDTDDVNFPLDNLCFVGLISMIDPPRAAVPDAVGKCR
SAGIKVIMVTGDHPITAKAIAKGVGIISEGNETVEDIAARLNIPVSQVNPRDAKACVVHG
SDLKDMTSEQLDDILKYHTEIVFARTSPQQKLIIVEGCQRQGAIVAVTGDGVNDSPALKK
ADIGVAMGIAGSDVSKQAADMILLDDNFASIVTGVEEGRLIFDNLKKSIAYTLTSNIPEI
TPFLIFIIANIPLPLGTVTILCIDLGTDMVPAISLAYEQAESDIMKRQPRNPKTDKLVNE
RLISMAYGQIGMIQALGGFFTYFVILAENGFLPIHLLGLRVNWDDRWINDVEDSYGQQWT
YEQRKIVEFTCHTAFFVSIVVVQWADLVICKTRRNSVFQQGMKNKILIFGLFEETALAAF
LSYCPGMGVALRMYPLKPTWWFCAFPYSLLIFVYDEVRKLIIRRRPGGWVEKETYY

Sequence of entity 2 (B, D), FASTA

>3WGU_2 Sodium/potassium-transporting ATPase subunit beta-1 (chains B, D)
MARGKAKEEGSWKKFIWNSEKKEFLGRTGGSWFKILLFYVIFYGCLAGIFIGTIQVMLLT
ISEFKPTYQDRVAPPGLTQIPQSQKTEISFRPNDPQSYESYVVSIVRFLEKYKDLAQKDD
MIFEDCGNVPSELKERGEYNNERGERKVCRFRLEWLGNCSGLNDETYGYKDGKPCVIIKL
NRVLGFKPKPPKNESLETYPVMKYNPYVLPVHCTGKRDEDKEKVGTMEYFGLGGYPGFPL
QYYPYYGKLLQPKYLQPLMAVQFTNLTMDTEIRIECKAYGENIGYSEKDRFQGRFDVKIE
VKS

Sequence of entity 3 (E, G), FASTA

>3WGU_3 Na+/K+ ATPase gamma subunit transcript variant a (chains E, G)
MAGLSTDDGGSPKGDVDPFYYDYETVRNGGLIFAALAFIVGLIIILSKRLRCGGKKHRPI
NEDEL

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	6
PC1	1,2-diacyl-sn-glycero-3-phosphocholine	C44 H88 N O8 P	10
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2
ALF	Tetrafluoroaluminate ion	Al F4	2
MG	Magnesium ion	Mg	4

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

Primary citation

Crystal structure of a Na1-bound Na1,K1-ATPase preceding the E1P state. Kanai, R., Ogawa, H., Vilsen, B. et al. Nature (2013) 502:201-206.

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

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
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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