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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