3B8E: Sodium-potassium pump

Crystal structure of the sodium-potassium pump. Determined by X-ray diffraction at 3.5 Å resolution. Released 18 Dec 2007.

Method: X-ray diffraction
Resolution: 3.5 Å
Organism: Sus scrofa
Chains: 6
Atoms: 16,718
Mol. weight: 239.88 kDa
Ligands: MG, RB, MF4, PC1
Released: 18 Dec 2007

Explore 3B8E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3B8E contains 108 α-helices and 76 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: 51 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	22-25	4
α-helix	41-48	8
β-strand	51	1	1
β-strand	55	1	1
β-strand	56	1	2
α-helix	58-68	11
α-helix	94-103	10
α-helix	117-119	3
α-helix	123-138	16
α-helix	151-154	4
β-strand	163-165	3	3
β-strand	166	1	2
β-strand	170-172	3	3
α-helix	175-177	3
β-strand	183-187	5	3
β-strand	191	1	3
β-strand	195-207	13	3
α-helix	209-212	4
β-strand	218-220	3	3
β-strand	235-236	2	3
β-strand	241-253	13	3
α-helix	255-257	3
α-helix	259-269	11
α-helix	276-294	19
α-helix	296-301	6
α-helix	310-322	13
α-helix	330-341	12
α-helix	345-347	3
β-strand	350-351	2	4
α-helix	354-358	5
β-strand	365-368	4	4
α-helix	370-374	5
β-strand	375	1	5
β-strand	380-384	5	6
β-strand	391-392	2	6
α-helix	409-420	12
α-helix	435-437	3
α-helix	444-455	12
α-helix	460-466	7
β-strand	468-473	6	6
β-strand	482-487	6	6
β-strand	491	1	7
β-strand	493	1	7
β-strand	496-502	7	6
α-helix	504-508	5
β-strand	511-514	4	6
β-strand	516	1	8
β-strand	519	1	8
α-helix	521	1
β-strand	522	1	6
α-helix	523	1
α-helix	526-539	14
β-strand	544-553	10	6
α-helix	555-557	3
β-strand	576-585	10	6
α-helix	587	1
β-strand	588	1	5
α-helix	589	1
α-helix	592-601	10
β-strand	605-609	5	4
α-helix	614-623	10
β-strand	631	1	9
α-helix	632-635	4
β-strand	655	1	9
β-strand	657-659	3	4
α-helix	660-663	4
α-helix	668-675	8
β-strand	682-684	3	4
α-helix	688-699	12
β-strand	705-708	4	4
α-helix	717-720	4
β-strand	723-725	3	4
α-helix	735-738	4
β-strand	741-742	2	4
α-helix	752-774	23
α-helix	777-788	12
α-helix	797-800	4
α-helix	809-817	9
α-helix	824-826	3
α-helix	840-844	5
α-helix	850-870	21
α-helix	898-901	4
α-helix	907-912	6
α-helix	913-929	17
α-helix	945-963	19
α-helix	967-969	3
α-helix	985-1004	20
α-helix	1010-1013	4

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	34-58	25

Chain C: 52 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	22-25	4
α-helix	41-48	8
β-strand	51	1	10
β-strand	55	1	10
β-strand	56	1	11
α-helix	58-68	11
α-helix	82-85	4
α-helix	94-103	10
α-helix	117-119	3
α-helix	123-138	16
α-helix	151-155	5
β-strand	163-165	3	3
β-strand	166	1	11
β-strand	170-172	3	3
α-helix	175-177	3
β-strand	183-187	5	3
β-strand	191	1	3
β-strand	195-207	13	3
α-helix	209-212	4
β-strand	218-220	3	3
β-strand	235-236	2	3
β-strand	241-253	13	3
α-helix	255-257	3
α-helix	259-269	11
α-helix	276-301	26
α-helix	311-315	5
α-helix	317-321	5
α-helix	330-344	15
α-helix	345-347	3
β-strand	350-351	2	12
α-helix	354-358	5
β-strand	365-368	4	12
α-helix	370-374	5
β-strand	375	1	13
β-strand	380-384	5	14
β-strand	391-392	2	14
α-helix	409-420	12
α-helix	435-437	3
α-helix	444-455	12
α-helix	460-466	7
β-strand	468-473	6	14
β-strand	482-487	6	14
β-strand	491	1	15
β-strand	493	1	15
β-strand	497-502	6	14
α-helix	504-508	5
β-strand	511-514	4	14
β-strand	516	1	16
β-strand	519	1	16
α-helix	521	1
β-strand	522	1	14
α-helix	523	1
α-helix	526-539	14
β-strand	544-552	9	14
α-helix	555-557	3
β-strand	576-585	10	14
α-helix	587	1
β-strand	588	1	13
α-helix	589	1
α-helix	592-601	10
β-strand	605-609	5	12
α-helix	614-623	10
β-strand	631	1	17
α-helix	632-635	4
β-strand	655	1	17
β-strand	657-659	3	12
α-helix	660-663	4
α-helix	668-675	8
β-strand	682-684	3	12
α-helix	688-699	12
β-strand	705-708	4	12
α-helix	712-714	3
α-helix	717-720	4
β-strand	723-725	3	12
α-helix	735-738	4
β-strand	741-742	2	12
α-helix	752-773	22
α-helix	777-779	3
α-helix	781-788	8
α-helix	797-800	4
α-helix	803-808	6
α-helix	809-817	9
α-helix	840-844	5
α-helix	850-867	18
β-strand	896	1	18
β-strand	899	1	18
α-helix	907-912	6
α-helix	913-927	15
α-helix	945-962	18
α-helix	982-984	3
α-helix	985-1004	20

Chain D: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	32-36	5
α-helix	39-58	20

Chain G: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	32-35	4

Chain H: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	38-40	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sodium/potassium-transporting ATPase subunit alpha-1	A, C	protein	998	Sus scrofa	P05024 (AlphaFold model)
Sodium/potassium-transporting ATPase subunit beta-1	B, D	protein	46	Sus scrofa	P05027 (AlphaFold model)
Na+/K+ ATPase gamma subunit transcript variant a	G, H	protein	29	Sus scrofa	Q58K79 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>3B8E_1 Sodium/potassium-transporting ATPase subunit alpha-1 (chains A, C)
AKKERDMDELKKEVSMDDHKLSLDELHRKYGTDLSRGLTPARAAEILARDGPNALTPPPT
TPEWVKFCRQLFGGFSMLLWIGAILCFLAYGIQAATEEEPQNDNLYLGVVLSAVVIITGC
FSYYQEAKSSKIMESFKNMVPQQALVIRNGEKMSINAEEVVVGDLVEVKGGDRIPADLRI
ISANGCKVDNSSLTGESEPQTRSPDFTNENPLETRNIAFFSTNCVEGTARGIVVYTGDRT
VMGRIATLASGLEGGQTPIAAEIEHFIHIITGVAVFLGVSFFILSLILEYTWLEAVIFLI
GIIVANVPEGLLATVTVCLTLTAKRMARKNCLVKNLEAVETLGSTSTICSDKTGTLTQNR
MTVAHMWSDNQIHEADTTENQSGVSFDKTSATWLALSRIAGLCNRAVFQANQENLPILKR
AVAGDASESALLKCIELCCGSVKEMRERYTKIVEIPFNSTNKYQLSIHKNPNTAEPRHLL
VMKGAPERILDRCSSILIHGKEQPLDEELKDAFQNAYLELGGLGERVLGFCHLFLPDEQF
PEGFQFDTDDVNFPLDNLCFVGLISMIDPPRAAVPDAVGKCRSAGIKVIMVTGDHPITAK
AIAKGVGIISEGNETVEDIAARLNIPVSQVNPRDAKACVVHGSDLKDMTSEQLDDILKYH
TEIVFARTSPQQKLIIVEGCQRQGAIVAVTGDGVNDSPASKKADIGVAMGIAGSDVSKQA
ADMILLDDNFASIVTGVEEGRLIFDNLKKSIAYTLTSNIPEITPFLIFIIANIPLPLGTV
TILCIDLGTDMVPAISLAYEQAESDIMKRQPRNPKTDKLVNEQLISMAYGQIGMIQALGG
FFTYFVILAENGFLPIHLLGLRVNWDDRWINDVEDSYGQQWTYEQRKIVEFTCHTPFFVT
IVVVQWADLVICKTRRNSVFQQGMKNKILIFGLFEETALAAFLSYCPGMGVALRMYPLKP
TWWFCAFPYSLLIFVYDEVRKLIIRRRPGGWVEKETYY

Sequence of entity 2 (B, D), FASTA

>3B8E_2 Sodium/potassium-transporting ATPase subunit beta-1 (chains B, D)
TGGSWFKILLFYVIFYGCLAGIFIGTIQVMLLTISEFKPTYQDRVA

Sequence of entity 3 (G, H), FASTA

>3B8E_3 Na+/K+ ATPase gamma subunit transcript variant a (chains G, H)
YETVRNGGLIFAALAFIVGLIIILSKRLR

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
RB	Rubidium ion	Rb	6
MF4	TETRAFLUOROMAGNESATE(2-)	F4 Mg	2
PC1	1,2-diacyl-sn-glycero-3-phosphocholine	C44 H88 N O8 P	2

Primary citation

Crystal structure of the sodium-potassium pump. Morth, J.P., Pedersen, B.P., Toustrup-Jensen, M.S. et al. Nature (2007) 450:1043-1049. DOI 10.1038/nature06419 · 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
3KDP 3.5 Å, Crystal structure of the sodium-potassium pump

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3B8E is part of these collections:

Membrane proteins and transporters

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