7D92: PDB entry 7D92

Crystal Structure of the Na+,K+-ATPase in the E2P state with bound Mg2+ and anthroylouabain (P4(3)2(1)2 symmetry). Determined by X-ray diffraction at 3.9 Å resolution. Released 27 Jan 2021.

Method: X-ray diffraction
Resolution: 3.9 Å
Organism: Sus scrofa
Chains: 3
Atoms: 10,740
Mol. weight: 163.65 kDa
Ligands: H0C, NAG, BEF, PCW
Released: 27 Jan 2021

Explore 7D92 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7D92 contains 66 α-helices and 56 β-strands across 3 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	22-30	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	73-78	6
α-helix	81-90	10
α-helix	93-112	20
α-helix	121-152	32
β-strand	162-166	5	2
β-strand	169-173	5	2
α-helix	175-177	3
β-strand	184-186	3	2
β-strand	191-192	2	3
β-strand	195-201	7	2
β-strand	204-207	4	3
α-helix	217	1
β-strand	218-220	3	3
β-strand	235-236	2	2
β-strand	240-244	5	3
β-strand	247-253	7	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	390-392	3	6
α-helix	409-420	12
β-strand	426	1	7
β-strand	440	1	7
α-helix	444-456	13
α-helix	461-465	5
β-strand	469-473	5	6
β-strand	482-486	5	6
β-strand	497-502	6	6
α-helix	504-509	6
β-strand	513-516	4	6
β-strand	519-521	3	6
α-helix	525-540	16
β-strand	544	1	6
β-strand	547-551	5	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
α-helix	634-641	8
α-helix	650-652	3
β-strand	655-659	5	4
α-helix	660-663	4
α-helix	668-676	9
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	733-738	6
β-strand	741-743	3	4
α-helix	749-774	26
α-helix	777-788	12
α-helix	797-802	6
α-helix	803-807	5
α-helix	809-814	6
α-helix	824-826	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	8
β-strand	898-899	2	8
α-helix	901-930	30
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	1009-1012	4

Chain B: 11 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	24	1	9
β-strand	27	1	9
α-helix	29-60	32
α-helix	70-72	3
β-strand	76	1	10
β-strand	77-79	3	11
β-strand	87-90	4	12
α-helix	99-108	10
α-helix	109-112	4
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	1	14
β-strand	178-180	3	11
β-strand	184	1	15
β-strand	208-210	3	16
β-strand	211-214	4	12
α-helix	220-223	4
β-strand	227-230	4	14
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	258-259	2	11
β-strand	260-263	4	14
β-strand	272-278	7	12
α-helix	279	1
β-strand	292	1	10
β-strand	296-301	6	12

Chain 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	protein	1016	Sus scrofa	P05024 (AlphaFold model)
Sodium/potassium-transporting ATPase subunit beta-1	B	protein	303	Sus scrofa	P05027 (AlphaFold model)
FXYD domain-containing ion transport regulator	G	protein	65	Sus scrofa	Q58K79 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7D92_1 Sodium/potassium-transporting ATPase subunit alpha-1 (chains A)
GRDKYEPAAVSEHGDKKKAKKERDMDELKKEVSMDDHKLSLDELHRKYGTDLSRGLTPAR
AAEILARDGPNALTPPPTTPEWVKFCRQLFGGFSMLLWIGAILCFLAYGIQAATEEEPQN
DNLYLGVVLSAVVIITGCFSYYQEAKSSKIMESFKNMVPQQALVIRNGEKMSINAEEVVV
GDLVEVKGGDRIPADLRIISANGCKVDNSSLTGESEPQTRSPDFTNENPLETRNIAFFST
NCVEGTARGIVVYTGDRTVMGRIATLASGLEGGQTPIAAEIEHFIHIITGVAVFLGVSFF
ILSLILEYTWLEAVIFLIGIIVANVPEGLLATVTVCLTLTAKRMARKNCLVKNLEAVETL
GSTSTICSDKTGTLTQNRMTVAHMWSDNQIHEADTTENQSGVSFDKTSATWLALSRIAGL
CNRAVFQANQENLPILKRAVAGDASESALLKCIELCCGSVKEMRERYTKIVEIPFNSTNK
YQLSIHKNPNTAEPRHLLVMKGAPERILDRCSSILIHGKEQPLDEELKDAFQNAYLELGG
LGERVLGFCHLFLPDEQFPEGFQFDTDDVNFPLDNLCFVGLISMIDPPRAAVPDAVGKCR
SAGIKVIMVTGDHPITAKAIAKGVGIISEGNETVEDIAARLNIPVSQVNPRDAKACVVHG
SDLKDMTSEQLDDILKYHTEIVFARTSPQQKLIIVEGCQRQGAIVAVTGDGVNDSPASKK
ADIGVAMGIAGSDVSKQAADMILLDDNFASIVTGVEEGRLIFDNLKKSIAYTLTSNIPEI
TPFLIFIIANIPLPLGTVTILCIDLGTDMVPAISLAYEQAESDIMKRQPRNPKTDKLVNE
QLISMAYGQIGMIQALGGFFTYFVILAENGFLPIHLLGLRVNWDDRWINDVEDSYGQQWT
YEQRKIVEFTCHTPFFVTIVVVQWADLVICKTRRNSVFQQGMKNKILIFGLFEETALAAF
LSYCPGMGVALRMYPLKPTWWFCAFPYSLLIFVYDEVRKLIIRRRPGGWVEKETYY

Sequence of entity 2 (B), FASTA

>7D92_2 Sodium/potassium-transporting ATPase subunit beta-1 (chains B)
MARGKAKEEGSWKKFIWNSEKKEFLGRTGGSWFKILLFYVIFYGCLAGIFIGTIQVMLLT
ISEFKPTYQDRVAPPGLTQIPQSQKTEISFRPNDPQSYESYVVSIVRFLEKYKDLAQKDD
MIFEDCGNVPSELKERGEYNNERGERKVCRFRLEWLGNCSGLNDETYGYKDGKPCVIIKL
NRVLGFKPKPPKNESLETYPVMKYNPYVLPVHCTGKRDEDKEKVGTMEYFGLGGYPGFPL
QYYPYYGKLLQPKYLQPLMAVQFTNLTMDTEIRIECKAYGENIGYSEKDRFQGRFDVKIE
VKS

Sequence of entity 3 (G), FASTA

>7D92_3 FXYD domain-containing ion transport regulator (chains G)
MAGLSTDDGGSPKGDVDPFYYDYETVRNGGLIFAALAFIVGLIIILSKRLRCGGKKHRPI
NEDEL

Ligands and cofactors

ID	Name	Formula	Copies
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	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
BEF	Beryllium trifluoride ion	Be F3	1
PCW	1,2-dioleoyl-sn-glycero-3-phosphocholine	C44 H85 N O8 P	8
CLR	Cholesterol	C27 H46 O	3
MG	Magnesium ion	Mg	3

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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