SMTL ID : 8zyj.1

Cryo-EM structure of human testis-specific Na+,K+-ATPase alpha4 in ouabain-bound form

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: D.339, T.341, T.343, D.678, G.679, D.682 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.341, A:D.678, H2O.1, H2O.3

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

NA.2: 5 residues within 4Å: Chain A: L.686, K.687, A.689, G.692, D.708 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.692, A:D.708

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.3: 4 residues within 4Å: Chain A: Y.931, I.946, W.949, I.953 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.931, A:W.949, A:W.949, A:W.949, A:I.953

1 x OBN: OUABAIN(Non-covalent)

OBN.4: 18 residues within 4Å: Chain A: Q.81, T.89, D.91, N.92, L.95, E.282, I.285, F.286, G.289, V.292, A.293, F.751, F.754, L.761, T.765, I.768, R.848 Ligands: Q7G.5 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:L.95, A:I.285, A:F.286, A:F.751, A:F.751, A:F.751, A:L.761, A:I.768 Hydrogen bonds: A:Q.81, A:T.89, A:T.89, A:N.92, A:E.282, A:T.765 Water bridges: A:N.85, A:N.85, A:N.92, A:E.282, A:R.848, A:E.852

3 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.5: 21 residues within 4Å: Chain A: T.89, D.91, Y.94, L.761, G.764, T.765, I.766, L.773, E.870, K.873, E.876, F.877, Q.880, V.937, A.938, L.939, R.940 Chain B: E.287, K.288 Ligands: OBN.4, Q7G.7 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.766, A:L.939 Hydrogen bonds: A:D.91, A:T.765, A:T.765, A:E.870, A:E.870, A:E.876, A:Q.880, A:V.937, A:R.940 Water bridges: A:K.873, A:D.936, A:R.940 Q7G.7: 6 residues within 4Å: Chain A: L.925, F.928, M.935, A.938, L.939 Ligands: Q7G.5 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.939 Q7G.8: 15 residues within 4Å: Chain A: L.265, I.745, K.801, H.808, Y.815, G.816, M.820 Chain B: K.13, I.16, L.25, G.26, R.27, W.32, Y.39, Y.43 17 PLIP interactions: 9 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:R.27, B:W.32, B:Y.39, A:L.265 Hydrogen bonds: B:K.13, B:G.26, B:R.27, A:K.801, A:H.808 Water bridges: B:K.13, B:S.31, A:N.804, A:H.808, A:R.809 Salt bridges: B:K.13, A:H.808, A:H.808

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

PCW.6: 16 residues within 4Å: Chain A: L.958, V.961, Y.962, I.965, R.966, L.969, H.973, G.976, W.977, V.978, R.980 Chain B: K.34, F.38, F.42, C.45, L.46 15 PLIP interactions: 7 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:K.34, B:F.38, B:F.38, B:F.38, B:F.42, B:F.42, B:L.46, A:V.961, A:Y.962, A:Y.962, A:I.965, A:R.966, A:L.969, A:W.977 Hydrogen bonds: A:W.977

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.9: 3 residues within 4Å: Chain B: N.158, E.228, F.230 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.158, B:N.158, B:E.228 NAG.10: 2 residues within 4Å: Chain B: N.226, N.265 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:N.226 Hydrogen bonds: B:N.265

Links

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Citation

Abe, K. et al., Molecular Structure of the Na + ,K + -ATPase alpha 4 beta 1 Isoform in Its Ouabain-Bound Conformation. Int J Mol Sci (2024)

Release Date

2024-12-04

Peptides

Sodium/potassium-transporting ATPase subunit alpha-4: 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-4

Sodium/potassium-transporting ATPase subunit beta-1

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