SMTL ID : 9kci.1

Cryo-EM structure of human sodium pump WT in (2K+)E2-AlF state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.1: 13 residues within 4Å: Chain A: T.181, G.182, E.183, D.338, K.339, T.340, T.579, G.580, K.660, D.679, N.682, D.683 Ligands: MG.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.338, A:D.338

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: G.182, D.338, T.340, D.679 Ligands: ALF.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.338, A:T.340, A:D.679

3 x K: POTASSIUM ION(Non-covalent)

K.3: 5 residues within 4Å: Chain A: T.741, S.744, N.745, E.748, D.773 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.741, A:S.744, A:D.773, H2O.1 K.4: 7 residues within 4Å: Chain A: V.291, A.292, V.294, E.296, N.745, E.748, D.773 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:A.292, A:V.294, A:E.748, A:D.773 K.5: 4 residues within 4Å: Chain A: L.687, K.688, A.690, D.709 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:L.687, A:A.690, A:D.709

6 x PCW: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PCW.6: 19 residues within 4Å: Chain A: W.893, A.894, V.897, V.906, F.907, Q.908, Q.909, G.910, M.911, K.912, L.920, F.921, T.924, F.954, S.957, L.958, F.961 Chain C: L.153 Ligands: CLR.14 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:W.893, A:W.893, A:A.894, A:V.897, A:M.911, A:L.920, A:L.920, A:F.921, A:F.954, A:L.958, A:F.961, A:F.961, A:F.961, C:L.153 PCW.7: 15 residues within 4Å: Chain A: L.959, V.962, Y.963, V.966, R.967, R.974, W.978, V.979, K.981 Chain B: L.38, L.41, F.42, V.45, F.46, F.49 14 PLIP interactions: 8 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:V.962, A:Y.963, A:Y.963, A:V.966, A:R.967, A:W.978, B:F.42, B:F.42, B:F.46, B:F.46, B:F.49, B:F.49 Hydrogen bonds: A:W.978 Salt bridges: A:R.974 PCW.9: 15 residues within 4Å: Chain A: H.252, I.256, V.260, I.746, I.749, T.750, L.753, N.808, E.809, Y.816 Chain B: F.19, L.29, G.30, W.36 Ligands: CLR.13 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.256, A:V.260, A:I.746, A:I.749, A:T.750, A:L.753, A:Y.816, B:F.19, B:W.36 Salt bridges: A:H.252 PCW.10: 12 residues within 4Å: Chain A: L.65, I.71, L.72, F.74, S.78, I.79, A.82, T.83, V.266, W.279, L.286, I.290 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.65, A:I.71, A:L.72, A:F.74, A:F.74, A:A.82, A:W.279, A:L.286, A:I.290 Hydrogen bonds: A:W.279 PCW.11: 16 residues within 4Å: Chain A: Y.93, V.97, A.100, V.101, I.104, A.300, V.767, L.770, C.771, L.774, G.775, L.926, L.930, V.938, A.939, L.940 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.97, A:V.97, A:A.100, A:V.101, A:I.104, A:A.300, A:V.767, A:V.767, A:L.770, A:L.774, A:L.926, A:L.930 PCW.12: 15 residues within 4Å: Chain A: I.754, A.824, L.825, F.828, F.832, P.842, I.843 Chain B: Y.47, L.50, A.51, F.54, S.55, M.58, W.59, Q.63 14 PLIP interactions: 5 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:Y.47, B:L.50, B:A.51, B:F.54, A:I.754, A:A.824, A:L.825, A:F.828, A:F.828, A:F.832, A:F.832, A:P.842, A:I.843 Hydrogen bonds: B:Q.63

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.8: 11 residues within 4Å: Chain A: F.829, E.837, T.948, F.951, C.952, P.955 Chain B: L.53, F.56, T.57, V.60, M.61 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.53, B:F.56, B:T.57, B:V.60, B:M.61, A:F.829, A:T.948, A:P.955 Hydrogen bonds: B:K.71, B:K.71, A:E.837 CLR.13: 9 residues within 4Å: Chain A: E.809, S.813, M.821 Chain B: R.31, W.36, I.39, Y.43, Y.47 Ligands: PCW.9 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.36, B:I.39, B:Y.43, B:Y.43, B:Y.47 Hydrogen bonds: B:R.31 CLR.14: 11 residues within 4Å: Chain A: W.893, T.924, Y.932, P.947, W.950, F.951 Chain C: L.142, R.145, G.146, V.149 Ligands: PCW.6 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.893, A:T.924, A:Y.932, A:P.947, A:W.950, A:W.950, A:F.951

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dou, Y. et al., Structural basis of a sodium pump quaternary complex leading phospholipid scrambling in the living cell. To Be Published

Release Date

2025-11-12

Peptides

Sodium/potassium-transporting ATPase subunit alpha-1: A
Sodium/potassium-transporting ATPase subunit beta-3: B
FXYD domain-containing ion transport regulator 5: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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Sodium/potassium-transporting ATPase subunit alpha-1

Sodium/potassium-transporting ATPase subunit beta-3

FXYD domain-containing ion transport regulator 5

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