7E1Z: PDB entry 7E1Z

Cryo EM structure of a Na+-bound Na+,K+-ATPase in the E1 state. Determined by electron microscopy at 3.2 Å resolution. Released 15 Jun 2022.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 3
Atoms: 10,550
Mol. weight: 159.89 kDa
Ligands: MG, Y01, NAG, PC1
Released: 15 Jun 2022

Explore 7E1Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7E1Z contains 62 α-helices and 53 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: 51 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	48-52	5
α-helix	65-74	10
α-helix	76-77	2
α-helix	79-84	6
α-helix	90-96	7
α-helix	103-118	16
α-helix	129-158	30
α-helix	159-161	3
β-strand	169-171	3	1
β-strand	178-180	3	1
β-strand	190-193	4	1
α-helix	197	1
β-strand	198	1	2
α-helix	199	1
β-strand	202-209	8	1
β-strand	212-214	3	3
β-strand	224-226	3	3
β-strand	242-243	2	1
β-strand	248	1	2
β-strand	249	1	3
β-strand	253-260	8	1
α-helix	262-264	3
α-helix	285-310	26
α-helix	311-313	3
α-helix	318-330	13
α-helix	336-353	18
β-strand	357-358	2	4
α-helix	361-363	3
α-helix	364-367	4
β-strand	372-376	5	4
β-strand	382	1	5
β-strand	387-388	2	6
β-strand	392	1	6
β-strand	397	1	6
α-helix	416-424	9
β-strand	432-433	2	7
β-strand	447-448	2	7
α-helix	451-463	13
α-helix	468-473	6
β-strand	478-479	2	8
α-helix	481-483	3
β-strand	489	1	6
β-strand	491-492	2	8
β-strand	503-509	7	6
β-strand	518-520	3	6
β-strand	521-522	2	9
β-strand	527-528	2	9
α-helix	532-546	15
β-strand	550-560	11	6
β-strand	583-592	10	6
β-strand	595	1	5
α-helix	599-608	10
β-strand	612-616	5	4
α-helix	623-631	9
α-helix	641-648	8
α-helix	652-654	3
β-strand	662-666	5	4
α-helix	675-684	10
β-strand	687-691	5	4
α-helix	695-698	4
α-helix	699-706	8
β-strand	712-715	4	4
α-helix	722-725	4
β-strand	730-734	5	4
α-helix	740-744	5
β-strand	748-750	3	4
α-helix	756-779	24
α-helix	784-795	12
α-helix	798-800	3
α-helix	804-814	11
α-helix	821-824	4
α-helix	825-828	4
α-helix	835-838	4
α-helix	847-852	6
α-helix	853-857	5
α-helix	858-876	19
α-helix	880-883	4
α-helix	887-890	4
β-strand	898-899	2	10
β-strand	905-906	2	10
α-helix	908-936	29
α-helix	944-946	3
α-helix	952-969	18
α-helix	974-977	4
α-helix	982-984	3
α-helix	985-987	3
α-helix	992-1010	19
α-helix	1016-1021	6

Chain B: 10 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	13-16	4
β-strand	23-24	2	11
β-strand	27-28	2	11
α-helix	29-57	29
β-strand	76	1	12
β-strand	77-79	3	13
β-strand	87-90	4	14
α-helix	99-108	10
α-helix	114-116	3
β-strand	123-124	2	15
α-helix	146-147	2
β-strand	148-149	2	15
α-helix	150-152	3
α-helix	153-156	4
α-helix	169-171	3
β-strand	175-180	6	13
α-helix	181-182	2
β-strand	208-210	3	16
β-strand	211-215	5	14
β-strand	227-230	4	13
β-strand	237-239	3	16
β-strand	259-263	5	13
α-helix	266-267	2
β-strand	272-278	7	14
β-strand	292	1	12
β-strand	294-301	8	14

Chain C: 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	protein	1023	Homo sapiens	P05023 (AlphaFold model)
Sodium/potassium-transporting ATPase subunit beta-1	B	protein	303	Homo sapiens	P05026 (AlphaFold model)
Sodium/potassium-transporting ATPase subunit gamma	C	protein	66	Homo sapiens	P54710 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7E1Z_1 Sodium/potassium-transporting ATPase subunit alpha-1 (chains A)
MGKGVGRDKYEPAAVSEQGDKKGKKGKKDRDMDELKKEVSMDDHKLSLDELHRKYGTDLS
RGLTSARAAEILARDGPNALTPPPTTPEWIKFCRQLFGGFSMLLWIGAILCFLAYSIQAA
TEEEPQNDNLYLGVVLSAVVIITGCFSYYQEAKSSKIMESFKNMVPQQALVIRNGEKMSI
NAEEVVVGDLVEVKGGDRIPADLRIISANGCKVDNSSLTGESEPQTRSPDFTNENPLETR
NIAFFSTNCVEGTARGIVVYTGDRTVMGRIATLASGLEGGQTPIAAEIEHFIHIITGVAV
FLGVSFFILSLILEYTWLEAVIFLIGIIVANVPEGLLATVTVCLTLTAKRMARKNCLVKN
LEAVETLGSTSTICSDKTGTLTQNRMTVAHMWFDNQIHEADTTENQSGVSFDKTSATWLA
LSRIAGLCNRAVFQANQENLPILKRAVAGDASESALLKCIELCCGSVKEMRERYAKIVEI
PFNSTNKYQLSIHKNPNTSEPQHLLVMKGAPERILDRCSSILLHGKEQPLDEELKDAFQN
AYLELGGLGERVLGFCHLFLPDEQFPEGFQFDTDDVNFPIDNLCFVGLISMIDPPRAAVP
DAVGKCRSAGIKVIMVTGDHPITAKAIAKGVGIISEGNETVEDIAARLNIPVSQVNPRDA
KACVVHGSDLKDMTSEQLDDILKYHTEIVFARTSPQQKLIIVEGCQRQGAIVAVTGDGVN
DSPALKKADIGVAMGIAGSDVSKQAADMILLDDNFASIVTGVEEGRLIFDNLKKSIAYTL
TSNIPEITPFLIFIIANIPLPLGTVTILCIDLGTDMVPAISLAYEQAESDIMKRQPRNPK
TDKLVNERLISMAYGQIGMIQALGGFFTYFVILAENGFLPIHLLGLRVDWDDRWINDVED
SYGQQWTYEQRKIVEFTCHTAFFVSIVVVQWADLVICKTRRNSVFQQGMKNKILIFGLFE
ETALAAFLSYCPGMGVALRMYPLKPTWWFCAFPYSLLIFVYDEVRKLIIRRRPGGWVEKE
TYY

Sequence of entity 2 (B), FASTA

>7E1Z_2 Sodium/potassium-transporting ATPase subunit beta-1 (chains B)
MARGKAKEEGSWKKFIWNSEKKEFLGRTGGSWFKILLFYVIFYGCLAGIFIGTIQVMLLT
ISEFKPTYQDRVAPPGLTQIPQIQKTEISFRPNDPKSYEAYVLNIVRFLEKYKDSAQRDD
MIFEDCGDVPSEPKERGDFNHERGERKVCRFKLEWLGNCSGLNDETYGYKEGKPCIIIKL
NRVLGFKPKPPKNESLETYPVMKYNPNVLPVQCTGKRDEDKDKVGNVEYFGLGNSPGFPL
QYYPYYGKLLQPKYLQPLLAVQFTNLTMDTEIRIECKAYGENIGYSEKDRFQGRFDVKIE
VKS

Sequence of entity 3 (C), FASTA

>7E1Z_3 Sodium/potassium-transporting ATPase subunit gamma (chains C)
MTGLSMDGGGSPKGDVDPFYYDYETVRNGGLIFAGLAFIVGLLILLSRRFRCGGNKKRRQ
INEDEP

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
Y01	Cholesterol hemisuccinate	C31 H50 O4	6
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
PC1	1,2-diacyl-sn-glycero-3-phosphocholine	C44 H88 N O8 P	1

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

Primary citation

Cryo-EM structures of recombinant human sodium-potassium pump determined in three different states. Guo, Y., Zhang, Y., Yan, R. et al. Nat Commun (2022) 13:3957-3957. DOI 10.1038/s41467-022-31602-y · PubMed

Other PDB entries of the same protein (UniProt P05023 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9WAJ 2.39 Å, Cryo-EM structure of a human sodium pump wildtype in ouabain-bound E2P state
24RC 2.61 Å, Cryo-EM structure of human sodium pump W931R mutant in K+-occluded E2-Pi state
7E20 2.7 Å, Cryo EM structure of a K+-bound Na+,K+-ATPase in the E2 state
9WAK 2.86 Å, Cryo-EM structure of a human sodium pump W931R mutant in ouabain-bound E2P state
7E21 2.9 Å, Cryo EM structure of a Na+-bound Na+,K+-ATPase in the E1 state with ATP-gamma-S
9KCI 2.9 Å, Cryo-EM structure of human sodium pump WT in (2K+)E2-AlF state
9KCK 2.9 Å, Cryo-EM structure of human sodium pump E1003K in (2K+)E2-AlF state
9KCL 2.9 Å, Cryo-EM structure of human sodium pump E1003K complexed with NDRG3 in (2Na+)E1-AMPPCP…
9KCM 2.9 Å, Cryo-EM structure of human sodium pump E1003K complexed with NDRG3 and TMX2 in…
9KCG 3.1 Å, Cryo-EM structure of human sodium pump WT in (3Na+)E1-AMPPCP state
9KCJ 3.1 Å, Cryo-EM structure of human sodium pump E1003 in (3Na+)E1-AMPPCP state
9KCR 3.2 Å, Cryo-EM structure of human sodium pump E1003K complexed with NDRG3 in (2Na+)E1 state

Browse structure collections

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