SMTL ID : 7e1z.1

Cryo EM structure of a Na+-bound Na+,K+-ATPase in the E1 state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain B: N.158, E.228, F.230 No protein-ligand interaction detected (PLIP)

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

NA.2: 5 residues within 4Å: Chain A: A.330, T.779, S.782, N.783, D.815 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.782 NA.3: 4 residues within 4Å: Chain A: V.329, V.332, E.334, D.811 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.332, A:E.334 Water bridges: A:G.335 NA.4: 5 residues within 4Å: Chain A: T.781, S.782, T.814, D.815, Q.930 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.782, A:T.814, A:T.814 NA.5: 3 residues within 4Å: Chain A: K.726, A.745, D.747 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.747

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 2 residues within 4Å: Chain A: D.376, D.717 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.717

6 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.7: 8 residues within 4Å: Chain A: W.931, V.944, F.945, G.948, M.949, S.995, F.999 Ligands: Y01.14 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.931, A:F.945, A:F.999 Y01.8: 8 residues within 4Å: Chain A: S.943, F.945, Q.946, E.1003, V.1004, L.1007, R.1010, R.1011 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.945, A:E.1003, A:V.1004, A:L.1007 Salt bridges: A:R.1010, A:R.1010 Y01.9: 9 residues within 4Å: Chain A: I.141, I.142, C.145, F.146, Y.149, Q.150, F.956 Chain C: L.45, R.48 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:I.142, A:I.142, A:F.146, A:Y.149, A:F.956, C:L.45 Salt bridges: A:K.153 Hydrogen bonds: C:R.48 Y01.10: 11 residues within 4Å: Chain A: I.792, L.863, F.870, P.880, I.881, L.884 Chain B: F.50, I.51, I.54, Q.55 Ligands: Y01.12 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.792, A:L.863, A:F.870, A:F.870, A:P.880, A:I.881, A:L.884, B:F.50, B:I.51 Hydrogen bonds: B:Q.55 Y01.12: 4 residues within 4Å: Chain A: L.884 Chain B: A.47, F.50 Ligands: Y01.10 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.884, B:A.47, B:F.50 Y01.14: 11 residues within 4Å: Chain A: W.931, F.959, T.962, Y.970, P.985, W.988 Chain C: V.26, G.29, G.30, F.33 Ligands: Y01.7 9 PLIP interactions: 3 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:F.33, C:F.33, A:W.931, A:W.931, A:W.931, A:T.962, A:P.985, A:W.988 Hydrogen bonds: C:V.26

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

PC1.11: 12 residues within 4Å: Chain A: V.1000, Y.1001, V.1004, I.1008, R.1012, G.1015, W.1016, V.1017 Chain B: F.38, I.41, F.42, L.46 13 PLIP interactions: 5 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:F.38, B:F.42, B:F.42, B:L.46, A:V.1000, A:Y.1001, A:V.1004, A:I.1008, A:V.1017 Salt bridges: B:K.34, A:R.1012 Hydrogen bonds: A:G.1014, A:W.1016

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

NAG.13: 3 residues within 4Å: Chain B: G.225, N.265, T.267 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.265

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, Y. et al., Cryo-EM structures of recombinant human sodium-potassium pump determined in three different states. Nat Commun (2022)

Release Date

2022-06-15

Peptides

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

Sodium/potassium-transporting ATPase subunit gamma

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