7E21: PDB entry 7E21

Cryo EM structure of a Na+-bound Na+,K+-ATPase in the E1 state with ATP-gamma-S. Determined by electron microscopy at 2.9 Å resolution. Released 15 Jun 2022.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 3
Atoms: 10,636
Mol. weight: 161.2 kDa
Ligands: AGS, Y01, PC1, MG
Released: 15 Jun 2022

Explore 7E21 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7E21 contains 56 α-helices and 49 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: 45 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	48-52	5
α-helix	65-74	10
α-helix	88-96	9
α-helix	102-121	20
α-helix	130-158	29
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	202-213	12	1
β-strand	225-226	2	1
β-strand	248	1	2
β-strand	249-260	12	1
α-helix	266-269	4
α-helix	285-310	26
α-helix	318-331	14
α-helix	336-351	16
α-helix	352-354	3
β-strand	356-358	3	3
α-helix	362-367	6
β-strand	372-375	4	3
β-strand	382	1	4
β-strand	387-392	6	5
β-strand	397	1	5
α-helix	416-427	12
β-strand	433	1	6
β-strand	447	1	6
α-helix	451-457	7
α-helix	468-473	6
β-strand	478-479	2	5
β-strand	488-493	6	5
β-strand	503-509	7	5
α-helix	511-514	4
β-strand	521	1	7
β-strand	528	1	7
α-helix	532-546	15
β-strand	550-560	11	5
β-strand	584-592	9	5
α-helix	594	1
β-strand	595	1	4
α-helix	596	1
α-helix	599-608	10
β-strand	612-616	5	3
α-helix	623-631	9
β-strand	636	1	8
β-strand	638	1	8
α-helix	641-647	7
β-strand	662-666	5	3
α-helix	675-679	5
α-helix	681-684	4
β-strand	687-691	5	3
α-helix	698-706	9
β-strand	712-716	5	3
α-helix	722-725	4
β-strand	730-734	5	3
β-strand	748-750	3	3
α-helix	755-779	25
α-helix	780-782	3
α-helix	784-795	12
α-helix	798-800	3
α-helix	804-821	18
α-helix	831-833	3
α-helix	835-837	3
α-helix	847-850	4
α-helix	851-857	7
α-helix	858-876	19
α-helix	887-890	4
β-strand	898-899	2	9
β-strand	905-906	2	9
α-helix	908-936	29
α-helix	952-970	19
α-helix	974-977	4
α-helix	982-984	3
α-helix	985-987	3
α-helix	992-1011	20
α-helix	1016-1021	6

Chain B: 10 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	23-24	2	10
β-strand	27-28	2	10
α-helix	29-57	29
β-strand	76	1	11
β-strand	77-79	3	12
β-strand	87-90	4	13
α-helix	99-108	10
α-helix	114-116	3
β-strand	123-124	2	14
α-helix	146-147	2
β-strand	148-149	2	14
α-helix	150-152	3
α-helix	153-156	4
α-helix	169-171	3
β-strand	175-180	6	12
α-helix	181-182	2
β-strand	208-210	3	15
β-strand	211-215	5	13
β-strand	227-230	4	12
β-strand	237-239	3	15
α-helix	247-250	4
β-strand	259-263	5	12
α-helix	266-267	2
β-strand	272-278	7	13
β-strand	292	1	11
β-strand	294-301	8	13

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

>7E21_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

>7E21_2 Sodium/potassium-transporting ATPase subunit beta-1 (chains B)
MARGKAKEEGSWKKFIWNSEKKEFLGRTGGSWFKILLFYVIFYGCLAGIFIGTIQVMLLT
ISEFKPTYQDRVAPPGLTQIPQIQKTEISFRPNDPKSYEAYVLNIVRFLEKYKDSAQRDD
MIFEDCGDVPSEPKERGDFNHERGERKVCRFKLEWLGNCSGLNDETYGYKEGKPCIIIKL
NRVLGFKPKPPKNESLETYPVMKYNPNVLPVQCTGKRDEDKDKVGNVEYFGLGNSPGFPL
QYYPYYGKLLQPKYLQPLLAVQFTNLTMDTEIRIECKAYGENIGYSEKDRFQGRFDVKIE
VKS

Sequence of entity 3 (C), FASTA

>7E21_3 Sodium/potassium-transporting ATPase subunit gamma (chains C)
MTGLSMDGGGSPKGDVDPFYYDYETVRNGGLIFAGLAFIVGLLILLSRRFRCGGNKKRRQ
INEDEP

Ligands and cofactors

ID	Name	Formula	Copies
AGS	Phosphothiophosphoric acid-adenylate ester	C10 H16 N5 O12 P3 S	1
Y01	Cholesterol hemisuccinate	C31 H50 O4	6
PC1	1,2-diacyl-sn-glycero-3-phosphocholine	C44 H88 N O8 P	2
MG	Magnesium ion	Mg	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	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
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
7E1Z 3.2 Å, Cryo EM structure of a Na+-bound Na+,K+-ATPase in the E1 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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