SMTL ID : 8ijl.1

Cyo-EM structure of wildtype non-gastric proton pump in the presence of Na+, AlF and ADP

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-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: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.338, H2O.1

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: 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

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.3: 12 residues within 4Å: Chain A: D.412, S.414, E.415, F.444, S.446, K.449, Q.451, K.470, G.471, A.472, V.514, L.515 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.412, A:S.414, A:E.415, A:S.446, A:Q.451, A:K.470, A:V.514 pi-Stacking: A:F.444, A:F.444

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

PCW.4: 14 residues within 4Å: Chain A: I.893, A.894, I.906, F.907, G.910, L.911, W.918, I.921, A.922, V.925, A.958, I.959, W.962 Ligands: Q7G.13 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.893, A:A.894, A:W.918, A:W.918, A:A.922, A:V.925, A:A.958, A:I.959 Hydrogen bonds: A:L.911 PCW.5: 20 residues within 4Å: Chain A: M.822, L.960, V.963, Y.964, M.967, F.971, Y.975, P.976, G.977, S.978, W.979, W.980 Chain B: K.54, F.58, I.61, F.62, C.65, L.66, I.69 Ligands: Q7G.17 25 PLIP interactions: 14 interactions with chain A, 11 interactions with chain B Hydrophobic interactions: A:V.963, A:Y.964, A:M.967, A:F.971, A:F.971, A:F.971, A:F.971, A:Y.975, A:W.979, A:W.979, A:W.980, A:W.980, A:W.980, B:K.54, B:K.54, B:F.58, B:F.58, B:F.58, B:I.61, B:I.61, B:F.62, B:L.66, B:I.69 Hydrogen bonds: A:W.979 Salt bridges: B:K.54 PCW.6: 15 residues within 4Å: Chain A: H.252, I.256, I.746, K.803, D.804, R.805, N.808, T.809, A.812, Y.816, L.817 Chain B: Y.63 Ligands: PCW.7, CLR.9, CLR.15 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.256, A:A.812, A:L.817 Hydrogen bonds: A:T.809, A:T.809, A:T.809 Salt bridges: A:H.252, A:D.804 PCW.7: 19 residues within 4Å: Chain A: C.750, I.754, L.825, F.828, F.832, W.841, P.842, T.843, I.846 Chain B: Y.63, A.67, F.70, I.71, Q.75, L.78, I.81 Ligands: PCW.6, Q7G.12, Q7G.17 15 PLIP interactions: 11 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.754, A:L.825, A:L.825, A:F.828, A:F.832, A:P.842, A:I.846, B:A.67, B:F.70, B:I.71, B:I.71 Hydrogen bonds: A:T.843, A:T.843 pi-Cation interactions: A:W.841, A:W.841 PCW.8: 11 residues within 4Å: Chain A: Q.837, V.948, Q.949, F.952, V.953, P.956 Chain B: V.76, K.85, T.87, Y.88 Ligands: Q7G.16 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.948, A:V.948, A:F.952, A:F.952

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.9: 7 residues within 4Å: Chain A: H.255, G.259, V.260, S.263, I.264, I.267 Ligands: PCW.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.260, A:I.264, A:I.267 CLR.15: 8 residues within 4Å: Chain A: T.809, Q.810, I.813 Chain B: W.52, L.56, Y.59, Y.63 Ligands: PCW.6 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:W.52, B:W.52, B:L.56, B:Y.59, B:Y.59, B:Y.59, B:Y.63, B:Y.63, A:T.809, A:I.813

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

NA.10: 7 residues within 4Å: Chain A: V.291, A.292, V.294, E.296, N.745, E.748, D.773 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.748 NA.11: 6 residues within 4Å: Chain A: L.687, K.688, A.690, D.691, G.693, D.709 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.691, A:G.693 Water bridges: A:K.688

4 x Q7G: 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside(Non-covalent)

Q7G.12: 5 residues within 4Å: Chain A: I.754, V.757, T.843, I.846 Ligands: PCW.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.757, A:T.843, A:I.846 Q7G.13: 13 residues within 4Å: Chain A: R.903, N.904, S.905, F.907, Q.908, W.962, V.963, E.966, M.967, L.970, R.973, L.974 Ligands: PCW.4 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.907, A:W.962, A:V.963, A:V.963, A:E.966 Hydrogen bonds: A:R.903, A:N.904, A:S.905, A:Q.908, A:R.973 Salt bridges: A:R.973 Q7G.16: 6 residues within 4Å: Chain A: L.960 Chain B: I.69, G.72, L.79 Ligands: PCW.8, Q7G.17 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.69, B:L.79, A:L.960 Q7G.17: 7 residues within 4Å: Chain B: C.65, G.68, I.69, Q.75 Ligands: PCW.5, PCW.7, Q7G.16 No protein-ligand interaction detected (PLIP)

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.14: 3 residues within 4Å: Chain B: N.178, E.191, Q.283 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abe, K. et al., An unusual conformation from Na + -sensitive non-gastric proton pump mutants reveals molecular mechanisms of cooperative Na + -binding. Biochim Biophys Acta Mol Cell Res (2023)

Release Date

2023-10-18

Peptides

Sodium/potassium-transporting ATPase subunit alpha: A
Sodium/potassium-transporting ATPase subunit beta-1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

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

Sodium/potassium-transporting ATPase subunit beta-1

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