SMTL ID : 9vj0.1

Cryo-EM structure of Na+,K+-ATPase that forms a cation channel with palytoxin (ATP form)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-mer

Ligands

2 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: 6 residues within 4Å: Chain A: H.107, D.111, N.114, S.116, L.163, T.166 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.163 NAG-NAG-BMA-MAN-MAN-FUC.5: 6 residues within 4Å: Chain D: H.107, D.111, N.114, S.116, L.163, T.166 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.163

2 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 A: N.159, E.230, Q.264 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-NAG-MAN.6: 3 residues within 4Å: Chain D: N.159, E.230, Q.264 No protein-ligand interaction detected (PLIP)

2 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 A: N.194, T.196, Y.206 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.196 NAG-NAG-BMA-MAN-FUC.7: 3 residues within 4Å: Chain D: N.194, T.196, Y.206 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:T.196

2 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 A: N.267 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain D: N.267 No protein-ligand interaction detected (PLIP)

10 x CLR: CHOLESTEROL(Non-covalent)

CLR.9: 6 residues within 4Å: Chain A: C.46, G.49, I.50, G.53, Q.56 Ligands: PCW.33 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.50, A:Q.56 CLR.10: 6 residues within 4Å: Chain A: R.28, W.33, Y.40, Y.44 Chain B: E.852 Ligands: PCW.16 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.33, A:Y.40, A:Y.40 Hydrogen bonds: A:R.28 CLR.11: 12 residues within 4Å: Chain B: W.936, T.967, Y.975, P.990, W.993, F.997 Chain C: L.39, V.42, V.46 Ligands: PCW.13, PCW.14, PCW.27 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:T.967, B:Y.975, B:P.990, B:W.993, B:W.993, B:W.993, B:F.997, C:V.46 CLR.12: 11 residues within 4Å: Chain A: V.57, T.61, K.68 Chain B: F.872, E.880, S.991 Chain E: L.1005 Ligands: PCW.28, CLR.32, PCW.33, PCW.35 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.57, A:T.61, B:F.872 Hydrogen bonds: A:K.68, A:K.68 CLR.18: 5 residues within 4Å: Chain B: I.111, L.115, L.323, I.330 Ligands: 01.25 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.111, B:L.115, B:I.330 CLR.29: 6 residues within 4Å: Chain D: C.46, G.49, I.50, G.53, Q.56 Ligands: PCW.28 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:I.50, D:Q.56 CLR.30: 6 residues within 4Å: Chain D: R.28, W.33, Y.40, Y.44 Chain E: E.852 Ligands: PCW.37 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:W.33, D:Y.40, D:Y.40 Hydrogen bonds: D:R.28 CLR.31: 12 residues within 4Å: Chain E: W.936, T.967, Y.975, P.990, W.993, F.997 Chain F: L.39, V.42, V.46 Ligands: PCW.34, PCW.35, PCW.48 8 PLIP interactions: 7 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:T.967, E:Y.975, E:P.990, E:W.993, E:W.993, E:W.993, E:F.997, F:V.46 CLR.32: 11 residues within 4Å: Chain B: L.1005 Chain D: V.57, T.61, K.68 Chain E: F.872, E.880, S.991 Ligands: CLR.12, PCW.14, PCW.28, PCW.33 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:V.57, D:T.61, E:F.872 Hydrogen bonds: D:K.68, D:K.68 CLR.39: 5 residues within 4Å: Chain E: I.111, L.115, L.323, I.330 Ligands: 01.46 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:I.111, E:L.115, E:I.330

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

PCW.13: 15 residues within 4Å: Chain B: W.936, I.949, Q.952, G.953, M.954, K.955, L.963, T.967, F.997, S.1000 Chain C: L.50 Ligands: CLR.11, PCW.14, PCW.27, PCW.35 Ligand excluded by PLIP PCW.14: 14 residues within 4Å: Chain B: F.950, Q.951, L.1001, F.1004, L.1005, F.1012 Chain E: F.994, L.1001 Ligands: CLR.11, PCW.13, PCW.27, CLR.32, PCW.34, PCW.35 Ligand excluded by PLIP PCW.15: 8 residues within 4Å: Chain B: L.969, F.972, C.976, P.977, G.978, V.981, A.982 Ligands: PCW.26 Ligand excluded by PLIP PCW.16: 13 residues within 4Å: Chain A: Y.44, F.51, I.52, I.55, L.59 Chain B: T.793, M.864, F.871, F.875, P.885, M.886, I.889 Ligands: CLR.10 Ligand excluded by PLIP PCW.17: 5 residues within 4Å: Chain B: I.299, T.846, E.852, R.853, I.855 Ligand excluded by PLIP PCW.26: 9 residues within 4Å: Chain B: P.977 Chain C: Y.36, Y.37, R.40, V.41, L.44, I.45, V.52 Ligands: PCW.15 Ligand excluded by PLIP PCW.27: 8 residues within 4Å: Chain B: F.964, P.990 Chain C: Y.34, V.42, L.50 Ligands: CLR.11, PCW.13, PCW.14 Ligand excluded by PLIP PCW.28: 13 residues within 4Å: Chain A: K.35 Chain B: L.1001, I.1002, L.1005, Y.1006, M.1009, G.1020 Chain D: I.50, V.57 Ligands: CLR.12, CLR.29, CLR.32, PCW.33 Ligand excluded by PLIP PCW.33: 13 residues within 4Å: Chain A: I.50, V.57 Chain D: K.35 Chain E: L.1001, I.1002, L.1005, Y.1006, M.1009, G.1020 Ligands: CLR.9, CLR.12, PCW.28, CLR.32 Ligand excluded by PLIP PCW.34: 15 residues within 4Å: Chain E: W.936, I.949, Q.952, G.953, M.954, K.955, L.963, T.967, F.997, S.1000 Chain F: L.50 Ligands: PCW.14, CLR.31, PCW.35, PCW.48 Ligand excluded by PLIP PCW.35: 14 residues within 4Å: Chain B: F.994, L.1001 Chain E: F.950, Q.951, L.1001, F.1004, L.1005, F.1012 Ligands: CLR.12, PCW.13, PCW.14, CLR.31, PCW.34, PCW.48 Ligand excluded by PLIP PCW.36: 8 residues within 4Å: Chain E: L.969, F.972, C.976, P.977, G.978, V.981, A.982 Ligands: PCW.47 Ligand excluded by PLIP PCW.37: 13 residues within 4Å: Chain D: Y.44, F.51, I.52, I.55, L.59 Chain E: T.793, M.864, F.871, F.875, P.885, M.886, I.889 Ligands: CLR.30 Ligand excluded by PLIP PCW.38: 5 residues within 4Å: Chain E: I.299, T.846, E.852, R.853, I.855 Ligand excluded by PLIP PCW.47: 9 residues within 4Å: Chain E: P.977 Chain F: Y.36, Y.37, R.40, V.41, L.44, I.45, V.52 Ligands: PCW.36 Ligand excluded by PLIP PCW.48: 8 residues within 4Å: Chain E: F.964, P.990 Chain F: Y.34, V.42, L.50 Ligands: CLR.31, PCW.34, PCW.35 Ligand excluded by PLIP

2 x MG: MAGNESIUM ION(Non-covalent)

MG.19: 2 residues within 4Å: Chain B: D.722 Ligands: ATP.20 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.722 MG.40: 2 residues within 4Å: Chain E: D.722 Ligands: ATP.41 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.722

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.20: 17 residues within 4Å: Chain B: K.382, T.383, D.455, S.457, E.458, F.487, S.489, K.492, Q.494, K.513, R.556, L.558, T.622, G.623, D.624, R.697 Ligands: MG.19 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:K.382, B:T.383, B:T.383, B:S.457, B:S.489, B:Q.494, B:Q.494, B:R.556, B:G.623, B:D.624 Salt bridges: B:K.492, B:R.556 pi-Stacking: B:F.487, B:F.487 ATP.41: 17 residues within 4Å: Chain E: K.382, T.383, D.455, S.457, E.458, F.487, S.489, K.492, Q.494, K.513, R.556, L.558, T.622, G.623, D.624, R.697 Ligands: MG.40 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:K.382, E:T.383, E:T.383, E:S.457, E:S.489, E:Q.494, E:Q.494, E:R.556, E:G.623, E:D.624 Salt bridges: E:K.492, E:R.556 pi-Stacking: E:F.487, E:F.487

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

NA.21: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.339 NA.22: 4 residues within 4Å: Chain B: T.784, S.787, N.788, D.820 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.816 NA.23: 4 residues within 4Å: Chain B: Y.783, T.786, Q.935, D.938 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.783, B:S.787, B:Q.935, B:D.938 NA.24: 3 residues within 4Å: Chain B: K.731, A.733, D.752 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.731 NA.42: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.339 NA.43: 4 residues within 4Å: Chain E: T.784, S.787, N.788, D.820 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.784 NA.44: 4 residues within 4Å: Chain E: Y.783, T.786, Q.935, D.938 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:S.787, E:Q.935, E:Q.935, E:D.938 NA.45: 3 residues within 4Å: Chain E: K.731, A.733, D.752 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.752

2 x 01: palytoxin

01.25: 25 residues within 4Å: Chain B: L.115, A.119, I.122, L.316, I.317, G.319, Y.320, W.322, L.323, E.324, I.327, F.328, G.331, V.334, A.335, V.337, E.339, E.791, I.792, F.795, L.805, T.809, I.812, D.816 Ligands: CLR.18 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.115, B:I.122, B:L.316, B:W.322, B:F.328, B:A.335, B:I.792, B:F.795, B:F.795, B:L.805 Hydrogen bonds: B:L.316, B:I.317, B:V.337, B:T.809, B:T.809 01.46: 25 residues within 4Å: Chain E: L.115, A.119, I.122, L.316, I.317, G.319, Y.320, W.322, L.323, E.324, I.327, F.328, G.331, V.334, A.335, V.337, E.339, E.791, I.792, F.795, L.805, T.809, I.812, D.816 Ligands: CLR.39 15 PLIP interactions: 15 interactions with chain E Hydrophobic interactions: E:L.115, E:I.122, E:L.316, E:W.322, E:F.328, E:A.335, E:I.792, E:F.795, E:F.795, E:L.805 Hydrogen bonds: E:L.316, E:I.317, E:V.337, E:T.809, E:T.809

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kanai, R. et al., How palytoxin transforms the Na + ,K + pump into a cation channel. Proc.Natl.Acad.Sci.USA (2025)

Release Date

2025-10-01

Peptides

Na+,K+-ATPase beta subunit: AD
Na, K-ATPase alpha subunit: BE
FXYD domain-containing ion transport regulator: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

D
B

B
C

E
A

C
E

F
G

Membrane

We predict this structure to be a membrane protein.
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Na+,K+-ATPase beta subunit

Na, K-ATPase alpha subunit

FXYD domain-containing ion transport regulator

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