SMTL ID : 9viz.1

Cryo-EM structure of palytoxin-bound Na+,K+-ATPase in the transient state of dephosphorylation (E2~P)

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 B: H.107, D.111, N.114, S.116, L.163, T.166 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.163 NAG-NAG-BMA-MAN-MAN-FUC.5: 6 residues within 4Å: Chain E: H.107, D.111, N.114, S.116, L.163, T.166 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E: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 B: N.159, E.230, Q.264 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-NAG-MAN.6: 3 residues within 4Å: Chain E: 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 B: N.194, T.196, Y.206 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.196 NAG-NAG-BMA-MAN-FUC.7: 3 residues within 4Å: Chain E: N.194, T.196, Y.206 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E: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 B: N.267 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain E: N.267 No protein-ligand interaction detected (PLIP)

8 x CLR: CHOLESTEROL(Non-covalent)

CLR.9: 9 residues within 4Å: Chain A: F.872, E.880, S.991, F.994 Chain B: T.61, K.68 Chain D: L.1005 Ligands: PCW.31, PCW.33 6 PLIP interactions: 1 interactions with chain D, 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: D:L.1005, B:T.61, A:F.872 Hydrogen bonds: B:K.68, B:K.68, A:S.991 CLR.22: 6 residues within 4Å: Chain A: E.852 Chain B: R.28, W.33, Y.40, Y.44 Ligands: PCW.16 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.33, B:Y.40, B:Y.44 Hydrogen bonds: B:R.28, B:R.28 CLR.23: 5 residues within 4Å: Chain B: G.49, I.52, G.53, Q.56 Ligands: CLR.43 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.52, B:Q.56 CLR.24: 11 residues within 4Å: Chain A: Y.975, P.990, W.993, F.994, F.997 Chain C: L.39, G.43, V.46 Ligands: PCW.12, PCW.28, PCW.48 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:P.990, A:W.993, A:F.994, A:F.997, A:F.997, C:V.46 CLR.29: 9 residues within 4Å: Chain A: L.1005 Chain D: F.872, E.880, S.991, F.994 Chain E: T.61, K.68 Ligands: PCW.11, PCW.13 6 PLIP interactions: 2 interactions with chain D, 3 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: D:F.872, E:T.61, A:L.1005 Hydrogen bonds: D:S.991, E:K.68, E:K.68 CLR.42: 6 residues within 4Å: Chain D: E.852 Chain E: R.28, W.33, Y.40, Y.44 Ligands: PCW.36 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:W.33, E:Y.40, E:Y.44 Hydrogen bonds: E:R.28, E:R.28 CLR.43: 5 residues within 4Å: Chain E: G.49, I.52, G.53, Q.56 Ligands: CLR.23 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:I.52, E:Q.56 CLR.44: 11 residues within 4Å: Chain D: Y.975, P.990, W.993, F.994, F.997 Chain F: L.39, G.43, V.46 Ligands: PCW.28, PCW.32, PCW.48 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: D:P.990, D:W.993, D:F.994, D:F.997, D:F.997, F:V.46

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

PCW.10: 4 residues within 4Å: Chain A: H.295, H.298, I.299 Ligands: PCW.16 Ligand excluded by PLIP PCW.11: 18 residues within 4Å: Chain A: I.865, Y.999, I.1002, L.1005, Y.1006, M.1009, I.1013, G.1020, W.1021, V.1022, Q.1024 Chain B: K.35, L.38, F.39, F.43, L.47, I.50 Ligands: CLR.29 Ligand excluded by PLIP PCW.12: 14 residues within 4Å: Chain A: W.936, F.950, Q.951, G.953, M.954, K.955, T.967, F.997, S.1000, L.1001 Ligands: PCW.13, CLR.24, PCW.28, PCW.33 Ligand excluded by PLIP PCW.13: 16 residues within 4Å: Chain A: R.946, S.948, F.950, Q.951, F.1004, L.1005, E.1008, F.1012, R.1015 Chain D: F.994, L.1001 Chain E: T.61 Ligands: PCW.12, CLR.29, PCW.32, PCW.33 Ligand excluded by PLIP PCW.14: 9 residues within 4Å: Chain A: N.132, Y.136, V.140, V.810, C.814, L.817, V.822, A.982, L.983 Ligand excluded by PLIP PCW.15: 5 residues within 4Å: Chain A: F.151, Y.154, V.347, T.350, K.354 Ligand excluded by PLIP PCW.16: 16 residues within 4Å: Chain A: H.295, I.299, V.303, L.307, F.311, L.796, K.845, T.846, K.848, N.851, E.852, Y.859 Chain B: F.16, F.37 Ligands: PCW.10, CLR.22 Ligand excluded by PLIP PCW.25: 3 residues within 4Å: Chain A: L.351, R.358 Chain C: K.62 Ligand excluded by PLIP PCW.26: 12 residues within 4Å: Chain A: F.972, C.976, P.977 Chain C: Y.37, R.40, V.41, L.44, I.45, A.48, C.51, V.52 Ligands: PCW.27 Ligand excluded by PLIP PCW.27: 5 residues within 4Å: Chain C: Y.37, V.49, I.53 Ligands: PCW.26, PCW.28 Ligand excluded by PLIP PCW.28: 8 residues within 4Å: Chain A: P.990, F.994 Chain C: Y.34 Ligands: PCW.12, CLR.24, PCW.27, CLR.44, PCW.48 Ligand excluded by PLIP PCW.30: 4 residues within 4Å: Chain D: H.295, H.298, I.299 Ligands: PCW.36 Ligand excluded by PLIP PCW.31: 18 residues within 4Å: Chain D: I.865, Y.999, I.1002, L.1005, Y.1006, M.1009, I.1013, G.1020, W.1021, V.1022, Q.1024 Chain E: K.35, L.38, F.39, F.43, L.47, I.50 Ligands: CLR.9 Ligand excluded by PLIP PCW.32: 14 residues within 4Å: Chain D: W.936, F.950, Q.951, G.953, M.954, K.955, T.967, F.997, S.1000, L.1001 Ligands: PCW.13, PCW.33, CLR.44, PCW.48 Ligand excluded by PLIP PCW.33: 16 residues within 4Å: Chain A: F.994, L.1001 Chain B: T.61 Chain D: R.946, S.948, F.950, Q.951, F.1004, L.1005, E.1008, F.1012, R.1015 Ligands: CLR.9, PCW.12, PCW.13, PCW.32 Ligand excluded by PLIP PCW.34: 9 residues within 4Å: Chain D: N.132, Y.136, V.140, V.810, C.814, L.817, V.822, A.982, L.983 Ligand excluded by PLIP PCW.35: 5 residues within 4Å: Chain D: F.151, Y.154, V.347, T.350, K.354 Ligand excluded by PLIP PCW.36: 16 residues within 4Å: Chain D: H.295, I.299, V.303, L.307, F.311, L.796, K.845, T.846, K.848, N.851, E.852, Y.859 Chain E: F.16, F.37 Ligands: PCW.30, CLR.42 Ligand excluded by PLIP PCW.45: 3 residues within 4Å: Chain D: L.351, R.358 Chain F: K.62 Ligand excluded by PLIP PCW.46: 12 residues within 4Å: Chain D: F.972, C.976, P.977 Chain F: Y.37, R.40, V.41, L.44, I.45, A.48, C.51, V.52 Ligands: PCW.47 Ligand excluded by PLIP PCW.47: 5 residues within 4Å: Chain F: Y.37, V.49, I.53 Ligands: PCW.46, PCW.48 Ligand excluded by PLIP PCW.48: 8 residues within 4Å: Chain D: P.990, F.994 Chain F: Y.34 Ligands: CLR.24, PCW.28, PCW.32, CLR.44, PCW.47 Ligand excluded by PLIP

2 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.17: 9 residues within 4Å: Chain A: G.225, D.381, K.382, T.383, T.622, G.623, K.703, N.725 Ligands: MG.18 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.381 ALF.37: 9 residues within 4Å: Chain D: G.225, D.381, K.382, T.383, T.622, G.623, K.703, N.725 Ligands: MG.38 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.381

2 x MG: MAGNESIUM ION(Non-covalent)

MG.18: 4 residues within 4Å: Chain A: D.381, T.383, D.722 Ligands: ALF.17 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.381, A:T.383, A:D.722 MG.38: 4 residues within 4Å: Chain D: D.381, T.383, D.722 Ligands: ALF.37 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.381, D:T.383, D:D.722

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

NA.19: 4 residues within 4Å: Chain A: P.338, T.784, N.788, D.816 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.784 NA.20: 5 residues within 4Å: Chain A: V.284, L.730, K.731, A.733, D.752 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.752 NA.39: 4 residues within 4Å: Chain D: P.338, T.784, N.788, D.816 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.816 NA.40: 5 residues within 4Å: Chain D: V.284, L.730, K.731, A.733, D.752 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.752

2 x 01: palytoxin

01.21: 28 residues within 4Å: Chain A: L.115, A.119, I.122, Q.123, T.126, D.128, N.134, L.141, L.316, I.317, G.319, Y.320, S.321, W.322, L.323, E.324, I.327, V.334, A.335, V.337, E.339, E.791, F.795, F.798, L.805, T.809, I.812, D.816 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:A.119, A:I.122, A:T.126, A:L.316, A:W.322, A:L.323, A:I.327, A:A.335, A:F.795, A:F.795, A:F.795, A:L.805, A:I.812 Hydrogen bonds: A:N.134, A:L.316, A:I.317, A:I.317, A:G.319, A:E.324, A:E.324, A:A.335 01.41: 28 residues within 4Å: Chain D: L.115, A.119, I.122, Q.123, T.126, D.128, N.134, L.141, L.316, I.317, G.319, Y.320, S.321, W.322, L.323, E.324, I.327, V.334, A.335, V.337, E.339, E.791, F.795, F.798, L.805, T.809, I.812, D.816 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:A.119, D:I.122, D:T.126, D:L.316, D:W.322, D:L.323, D:I.327, D:A.335, D:F.795, D:F.795, D:F.795, D:L.805, D:I.812 Hydrogen bonds: D:N.134, D:L.316, D:I.317, D:I.317, D:G.319, D:E.324, D:E.324, D:A.335

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
C

B
B

E
D

C
G

F
E

Membrane

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

Na+,K+-ATPase beta subunit

FXYD domain-containing ion transport regulator

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