SMTL ID : 9kcj.1

Cryo-EM structure of human sodium pump E1003 in (3Na+)E1-AMPPCP state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.1: 18 residues within 4Å: Chain A: D.338, K.339, T.340, S.414, E.415, F.444, S.446, K.449, Q.451, K.470, G.471, R.513, V.514, L.515, T.579, G.580, D.581, R.654 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:K.339, A:K.339, A:T.340, A:T.340, A:S.414, A:S.446, A:Q.451, A:K.470, A:R.513, A:R.513, A:T.579, A:G.580, A:G.580, A:R.654, A:R.654, A:K.660 Salt bridges: A:K.449 pi-Stacking: A:F.444, A:F.444

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

PCW.2: 14 residues within 4Å: Chain A: I.104, T.105, F.108, Y.111, Q.112, K.115, K.311, L.774, M.778, V.779, I.782, Y.786, I.915 Ligands: PCW.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.104, A:F.108, A:I.782, A:I.782, A:I.915, A:I.915 Hydrogen bonds: A:Q.112 Salt bridges: A:K.115 PCW.3: 9 residues within 4Å: Chain A: Y.93, V.97, L.926, L.930, P.934, G.935, M.936 Ligands: PCW.2, PCW.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.93, A:V.97, A:L.926, A:L.930 PCW.4: 11 residues within 4Å: Chain A: E.922, A.925, L.926, F.929, P.934 Chain C: H.140, R.143, L.147, A.151, F.154 Ligands: PCW.3 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:A.925, A:L.926, A:F.929, A:F.929, A:F.929, C:L.147, C:A.151, C:F.154 PCW.10: 14 residues within 4Å: Chain A: L.959, Y.963, V.966, R.967, R.974, W.978, V.979 Chain B: L.38, L.41, F.42, V.45, F.46, F.49, L.50 12 PLIP interactions: 6 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:L.41, B:F.42, B:V.45, B:F.46, B:F.49, B:L.50, A:L.959, A:Y.963, A:Y.963, A:R.967, A:W.978, A:V.979 PCW.11: 19 residues within 4Å: Chain A: T.750, M.821, A.824, L.825, F.828, P.842, I.843, L.846 Chain B: A.51, F.54, S.55, M.58, W.59, L.62, Q.63, L.65, D.67 Ligands: PCW.12, CLR.13 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:T.750, A:A.824, A:L.825, A:F.828, A:L.846, B:F.54, B:F.54, B:M.58 PCW.12: 6 residues within 4Å: Chain A: I.843, L.846 Chain B: Y.47, G.48, S.55 Ligands: PCW.11 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.47, A:L.846 PCW.14: 15 residues within 4Å: Chain A: W.893, A.894, T.924, Y.932, P.947, W.950, F.951, S.957 Chain C: L.142, R.145, G.146, V.149, V.152, L.153, T.156 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:V.152, C:T.156, A:W.893, A:A.894 Hydrogen bonds: C:R.145, A:T.924

2 x NA: SODIUM ION(Non-functional Binders)

NA.5: 6 residues within 4Å: Chain A: V.294, P.295, E.296, D.773, D.777 Ligands: NA.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.294, A:E.296, A:E.296, A:D.777 NA.6: 7 residues within 4Å: Chain A: A.292, S.744, N.745, E.748, D.773, D.777 Ligands: NA.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.292, A:D.777

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.7: 10 residues within 4Å: Chain A: F.829, E.837, T.948, F.951, C.952, P.955 Chain B: L.53, T.57, V.60, M.61 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.829, A:P.955, B:L.53, B:T.57, B:M.61 CLR.13: 9 residues within 4Å: Chain A: T.750, L.753, E.809, S.813, Y.816 Chain B: Y.43, Y.47 Ligands: PC1.8, PCW.11 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.43, A:L.753, A:Y.816 Hydrogen bonds: A:E.809

2 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.8: 10 residues within 4Å: Chain A: I.256, V.260, K.805, V.807, N.808, E.809, I.812 Chain B: L.29 Ligands: PC1.9, CLR.13 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.256, A:V.260, A:I.812 Hydrogen bonds: A:E.809 Salt bridges: A:E.809 PC1.9: 10 residues within 4Å: Chain A: E.249, H.252, F.253, I.256, K.805, L.806, V.807, E.809 Chain B: L.29 Ligands: PC1.8 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.256, B:L.29 Salt bridges: A:H.252, A:K.805

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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