SMTL ID : 7wyz.2 (1 other biounit)

Cryo-EM structure of Na+,K+-ATPase in the E2P state formed by ATP with ouabain

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-FUC.1: 7 residues within 4Å: Chain B: H.107, D.111, N.114, S.116, R.154, L.163, T.166 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.163

1 x NAG- NAG- BMA- MAN- NAG- MAN: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-NAG-MAN.2: 3 residues within 4Å: Chain B: N.159, E.230, Q.264 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-FUC.3: 3 residues within 4Å: Chain B: N.194, T.196, Y.206 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.196

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.4: 1 residues within 4Å: Chain B: N.267 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 5 residues within 4Å: Chain A: D.381, T.383, D.722, G.723, D.726 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.383, A:D.722, H2O.1, H2O.1

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

NA.6: 4 residues within 4Å: Chain A: L.730, K.731, A.733, D.752 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.730 NA.7: 4 residues within 4Å: Chain A: A.335, N.788, E.791, D.816 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.788

1 x OBN: OUABAIN(Non-covalent)

OBN.8: 16 residues within 4Å: Chain A: Q.123, E.127, N.134, L.137, E.324, I.327, F.328, G.331, A.335, F.795, F.798, L.805, T.809, I.812, R.892, D.896 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.328, A:F.795, A:L.805, A:T.809, A:I.812 Hydrogen bonds: A:Q.123, A:E.127, A:E.324, A:T.809, A:D.896, A:D.896

4 x CLR: CHOLESTEROL(Non-covalent)

CLR.9: 9 residues within 4Å: Chain A: F.872, E.880, S.991, F.994, C.995 Chain B: V.57, L.58, T.61, K.68 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.57, B:V.57, B:L.58, B:T.61, A:F.872 Hydrogen bonds: B:K.68, B:K.68, A:S.991 CLR.20: 5 residues within 4Å: Chain A: E.852 Chain B: I.36, Y.40, Y.44 Ligands: PCW.19 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.36, B:Y.40, B:Y.44 Hydrogen bonds: A:E.852 CLR.21: 5 residues within 4Å: Chain B: G.49, I.50, I.52, G.53, Q.56 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.50, B:I.52, B:Q.56 CLR.22: 10 residues within 4Å: Chain A: Y.975, P.990, F.994, F.997 Chain C: L.39, V.42, G.43, V.46 Ligands: PCW.13, PCW.17 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:P.990, A:F.994, A:F.994, A:F.997, C:V.46

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

PCW.10: 5 residues within 4Å: Chain A: L.351, K.354, R.358, Y.829 Ligands: PCW.18 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.354, A:K.354, A:R.358 PCW.11: 3 residues within 4Å: Chain A: H.295, H.298, I.299 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.295, A:H.298 PCW.12: 16 residues within 4Å: Chain A: I.865, Y.999, I.1002, L.1005, Y.1006, M.1009, I.1013, G.1020, W.1021, Q.1024 Chain B: K.35, L.38, F.39, F.43, L.47, I.50 20 PLIP interactions: 9 interactions with chain B, 11 interactions with chain A Hydrophobic interactions: B:L.38, B:F.39, B:F.39, B:F.43, B:F.43, B:L.47, B:I.50, B:I.50, A:I.865, A:I.865, A:Y.999, A:I.1002, A:I.1002, A:I.1002, A:L.1005, A:Y.1006, A:Y.1006, A:I.1013 Salt bridges: B:K.35 Hydrogen bonds: A:W.1021 PCW.13: 14 residues within 4Å: Chain A: W.936, I.949, F.950, Q.951, G.953, M.954, K.955, T.967, F.997, S.1000, L.1001 Ligands: PCW.14, PCW.17, CLR.22 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.936, A:I.949, A:F.950, A:F.997, A:L.1001 Hydrogen bonds: A:M.954 Salt bridges: A:K.955, A:K.955 PCW.14: 10 residues within 4Å: Chain A: R.946, S.948, F.950, Q.951, F.1004, L.1005, E.1008, F.1012, R.1015 Ligands: PCW.13 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.950, A:F.1004, A:E.1008 Hydrogen bonds: A:Q.951 Salt bridges: A:R.1015 PCW.15: 6 residues within 4Å: Chain A: Y.136, L.813, V.981, A.982, R.984 Ligands: PCW.16 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.813, A:A.982 Salt bridges: A:R.984 PCW.16: 5 residues within 4Å: Chain A: F.972, G.978, A.982 Ligands: PCW.15, PCW.23 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.972, A:A.982 PCW.17: 8 residues within 4Å: Chain A: P.990, F.994 Chain C: Y.34, D.35, R.38 Ligands: PCW.13, CLR.22, PCW.24 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:F.994 Hydrogen bonds: C:Y.34 PCW.18: 5 residues within 4Å: Chain A: F.151, Y.154, K.158, K.354 Ligands: PCW.10 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.154 Hydrogen bonds: A:Y.154 Salt bridges: A:K.158, A:K.354 PCW.19: 13 residues within 4Å: Chain A: H.295, V.303, L.307, F.311, L.796, K.845, N.851, E.852 Chain B: F.16, L.26, W.33, F.37 Ligands: CLR.20 12 PLIP interactions: 5 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:F.16, B:L.26, B:W.33, B:F.37, B:F.37, A:L.307, A:L.307, A:F.311, A:L.796, A:L.796 Hydrogen bonds: A:H.295, A:E.852 PCW.23: 11 residues within 4Å: Chain A: F.972, C.976, P.977 Chain C: Y.36, Y.37, R.40, V.41, I.45, A.48, V.52 Ligands: PCW.16 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:I.45, C:A.48, C:V.52, A:F.972, A:F.972 Salt bridges: C:R.40 PCW.24: 6 residues within 4Å: Chain C: Y.37, I.45, V.46, V.49, I.53 Ligands: PCW.17 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.45, C:V.46, C:I.53 pi-Cation interactions: C:Y.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kanai, R. et al., Cryoelectron microscopy of Na + ,K + -ATPase in the two E2P states with and without cardiotonic steroids. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-04-27

Peptides

Sodium/potassium-transporting ATPase subunit alpha: A
Na+,K+-ATPase beta subunit: B
FXYD domain-containing ion transport regulator: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
E

Membrane

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

Na+,K+-ATPase beta subunit

FXYD domain-containing ion transport regulator

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