7D93: PDB entry 7D93

Crystal Structure of the Na+,K+-ATPase in the E2P state with bound Mg2+ and anthroylouabain (P2(1)2(1)2(1) symmetry). Determined by X-ray diffraction at 3.65 Å resolution. Released 27 Jan 2021.

Method: X-ray diffraction
Resolution: 3.65 Å
Organism: Sus scrofa
Chains: 6
Atoms: 21,396
Mol. weight: 323.86 kDa
Ligands: MG, CLR, PCW, H0C
Released: 27 Jan 2021

Explore 7D93 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7D93 contains 138 α-helices and 110 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: 57 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	22-30	9
α-helix	32-33	2
α-helix	41-48	8
β-strand	51	1	1
β-strand	55	1	1
α-helix	58-68	11
α-helix	73-76	4
α-helix	81-88	8
α-helix	93-114	22
α-helix	121-152	32
β-strand	161-166	6	2
β-strand	169-174	6	2
α-helix	175-177	3
β-strand	183-187	5	2
β-strand	188	1	3
β-strand	190	1	3
β-strand	191	1	2
α-helix	192	1
β-strand	195-207	13	2
α-helix	209-212	4
β-strand	218-219	2	2
β-strand	235-236	2	2
β-strand	241-253	13	2
α-helix	255-257	3
α-helix	259-268	10
α-helix	276-306	31
α-helix	310-323	14
α-helix	329-346	18
β-strand	349-351	3	4
α-helix	356-362	7
β-strand	365-368	4	4
α-helix	370-374	5
β-strand	375	1	5
β-strand	380-386	7	6
β-strand	389-392	4	6
α-helix	393-394	2
α-helix	409-420	12
β-strand	425-426	2	7
β-strand	440-441	2	7
α-helix	444-456	13
α-helix	461-465	5
β-strand	469-473	5	6
β-strand	481-486	6	6
β-strand	496-502	7	6
α-helix	504-507	4
α-helix	508-510	3
β-strand	513-516	4	6
β-strand	519-521	3	6
α-helix	525-540	16
β-strand	544-553	10	6
β-strand	577-585	9	6
α-helix	587	1
β-strand	588	1	5
α-helix	589	1
α-helix	592-601	10
α-helix	604	1
β-strand	605-609	5	4
α-helix	614-624	11
β-strand	629	1	8
β-strand	631	1	8
α-helix	634-640	7
α-helix	650-652	3
β-strand	655-659	5	4
α-helix	660-663	4
α-helix	668-677	10
β-strand	680-684	5	4
α-helix	688-700	13
β-strand	705-709	5	4
α-helix	712-714	3
α-helix	715-720	6
β-strand	723-727	5	4
α-helix	733-737	5
β-strand	741-743	3	4
α-helix	750-774	25
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	828-831	4
α-helix	840-845	6
α-helix	846-850	5
α-helix	851-868	18
α-helix	874-876	3
α-helix	880-883	4
β-strand	891-892	2	9
β-strand	898-899	2	9
α-helix	901-931	31
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

Chain B: 12 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	24	1	10
β-strand	27	1	10
α-helix	29-59	31
α-helix	70-72	3
β-strand	76	1	11
β-strand	77-79	3	12
β-strand	87-90	4	13
α-helix	99-108	10
α-helix	109-111	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	175-180	6	12
α-helix	181-182	2
β-strand	184	1	15
α-helix	190-192	3
β-strand	208-210	3	16
β-strand	211-214	4	13
α-helix	220-223	4
β-strand	227-230	4	12
α-helix	232-234	3
β-strand	237-239	3	16
α-helix	240-242	3
β-strand	245	1	15
α-helix	247-250	4
β-strand	258-263	6	12
β-strand	272-278	7	13
β-strand	292	1	11
β-strand	296-301	6	13

Chain C: 55 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	22-30	9
α-helix	32-33	2
α-helix	41-48	8
β-strand	51	1	17
β-strand	55	1	17
α-helix	58-68	11
α-helix	73-76	4
α-helix	81-88	8
α-helix	93-114	22
α-helix	121-152	32
β-strand	161-166	6	18
β-strand	169-174	6	18
α-helix	175-177	3
β-strand	183-187	5	18
β-strand	188	1	19
β-strand	190	1	19
β-strand	191	1	18
β-strand	195-207	13	18
α-helix	209-212	4
β-strand	218-219	2	18
β-strand	235-236	2	18
β-strand	241-253	13	18
α-helix	255-257	3
α-helix	259-268	10
α-helix	276-306	31
α-helix	310-323	14
α-helix	329-346	18
β-strand	349-351	3	20
α-helix	356-362	7
β-strand	365-368	4	20
α-helix	370-374	5
β-strand	375	1	21
β-strand	380-386	7	22
β-strand	389-392	4	22
α-helix	393-394	2
α-helix	409-420	12
β-strand	425-426	2	23
β-strand	440-441	2	23
α-helix	444-456	13
α-helix	461-465	5
β-strand	469-473	5	22
β-strand	481-486	6	22
β-strand	496-502	7	22
α-helix	504-508	5
β-strand	513-517	5	22
β-strand	519-521	3	22
α-helix	525-540	16
β-strand	544-553	10	22
β-strand	577-585	9	22
α-helix	587	1
β-strand	588	1	21
α-helix	589	1
α-helix	592-601	10
α-helix	604	1
β-strand	605-609	5	20
α-helix	614-624	11
α-helix	634-640	7
α-helix	650-652	3
β-strand	655-659	5	20
α-helix	660-663	4
α-helix	668-677	10
β-strand	680-684	5	20
α-helix	688-700	13
β-strand	705-709	5	20
α-helix	712-714	3
α-helix	715-720	6
β-strand	723-727	5	20
α-helix	733-737	5
β-strand	741-743	3	20
α-helix	750-774	25
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	828-831	4
α-helix	840-843	4
α-helix	844-850	7
α-helix	851-868	18
α-helix	874-876	3
α-helix	880-883	4
β-strand	891-892	2	24
β-strand	898-899	2	24
α-helix	901-931	31
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

Chain D: 12 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	24	1	25
β-strand	27	1	25
α-helix	29-60	32
α-helix	70-72	3
β-strand	76	1	26
β-strand	77-79	3	27
β-strand	87-90	4	28
α-helix	99-108	10
α-helix	109-111	3
β-strand	123-124	2	29
α-helix	146-147	2
β-strand	148-149	2	29
α-helix	153-155	3
β-strand	175	1	30
β-strand	178-180	3	27
α-helix	181-182	2
β-strand	184	1	31
α-helix	190-192	3
β-strand	208-210	3	32
β-strand	211-214	4	28
α-helix	220-223	4
β-strand	227-230	4	30
α-helix	232-234	3
β-strand	237-239	3	32
α-helix	240-242	3
β-strand	245	1	31
α-helix	247-250	4
β-strand	258-259	2	27
β-strand	260-263	4	30
β-strand	272-278	7	28
β-strand	292	1	26
β-strand	296-301	6	28

Chain E: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	23-45	23

Chain G: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	23-44	22

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

Sequence of entity 1 (A, C), FASTA

>7D93_1 Sodium/potassium-transporting ATPase subunit alpha-1 (chains A, C)
GRDKYEPAAVSEHGDKKKAKKERDMDELKKEVSMDDHKLSLDELHRKYGTDLSRGLTPAR
AAEILARDGPNALTPPPTTPEWVKFCRQLFGGFSMLLWIGAILCFLAYGIQAATEEEPQN
DNLYLGVVLSAVVIITGCFSYYQEAKSSKIMESFKNMVPQQALVIRNGEKMSINAEEVVV
GDLVEVKGGDRIPADLRIISANGCKVDNSSLTGESEPQTRSPDFTNENPLETRNIAFFST
NCVEGTARGIVVYTGDRTVMGRIATLASGLEGGQTPIAAEIEHFIHIITGVAVFLGVSFF
ILSLILEYTWLEAVIFLIGIIVANVPEGLLATVTVCLTLTAKRMARKNCLVKNLEAVETL
GSTSTICSDKTGTLTQNRMTVAHMWSDNQIHEADTTENQSGVSFDKTSATWLALSRIAGL
CNRAVFQANQENLPILKRAVAGDASESALLKCIELCCGSVKEMRERYTKIVEIPFNSTNK
YQLSIHKNPNTAEPRHLLVMKGAPERILDRCSSILIHGKEQPLDEELKDAFQNAYLELGG
LGERVLGFCHLFLPDEQFPEGFQFDTDDVNFPLDNLCFVGLISMIDPPRAAVPDAVGKCR
SAGIKVIMVTGDHPITAKAIAKGVGIISEGNETVEDIAARLNIPVSQVNPRDAKACVVHG
SDLKDMTSEQLDDILKYHTEIVFARTSPQQKLIIVEGCQRQGAIVAVTGDGVNDSPASKK
ADIGVAMGIAGSDVSKQAADMILLDDNFASIVTGVEEGRLIFDNLKKSIAYTLTSNIPEI
TPFLIFIIANIPLPLGTVTILCIDLGTDMVPAISLAYEQAESDIMKRQPRNPKTDKLVNE
QLISMAYGQIGMIQALGGFFTYFVILAENGFLPIHLLGLRVNWDDRWINDVEDSYGQQWT
YEQRKIVEFTCHTPFFVTIVVVQWADLVICKTRRNSVFQQGMKNKILIFGLFEETALAAF
LSYCPGMGVALRMYPLKPTWWFCAFPYSLLIFVYDEVRKLIIRRRPGGWVEKETYY

Sequence of entity 2 (B, D), FASTA

>7D93_2 Sodium/potassium-transporting ATPase subunit beta-1 (chains B, D)
MARGKAKEEGSWKKFIWNSEKKEFLGRTGGSWFKILLFYVIFYGCLAGIFIGTIQVMLLT
ISEFKPTYQDRVAPPGLTQIPQSQKTEISFRPNDPQSYESYVVSIVRFLEKYKDLAQKDD
MIFEDCGNVPSELKERGEYNNERGERKVCRFRLEWLGNCSGLNDETYGYKDGKPCVIIKL
NRVLGFKPKPPKNESLETYPVMKYNPYVLPVHCTGKRDEDKEKVGTMEYFGLGGYPGFPL
QYYPYYGKLLQPKYLQPLMAVQFTNLTMDTEIRIECKAYGENIGYSEKDRFQGRFDVKIE
VKS

Sequence of entity 3 (E, G), FASTA

>7D93_3 FXYD domain-containing ion transport regulator (chains E, G)
MAGLSTDDGGSPKGDVDPFYYDYETVRNGGLIFAALAFIVGLIIILSKRLRCGGKKHRPI
NEDEL

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	4
CLR	Cholesterol	C27 H46 O	5
PCW	1,2-dioleoyl-sn-glycero-3-phosphocholine	C44 H85 N O8 P	11
H0C	[(2~{R},3~{R},4~{R},5~{S},6~{S})-2-[[(1~{R},3~{S},5~{S},8~{R},9~{S},10~{R},11~{…	C44 H52 O13	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

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

Primary citation

Binding of cardiotonic steroids to Na + ,K + -ATPase in the E2P state. Kanai, R., Cornelius, F., Ogawa, H. et al. Proc Natl Acad Sci U S A (2021) 118. DOI 10.1073/pnas.2020438118 · 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
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

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