SMTL ID : 9viy.1

Cryo-EM structure of palytoxin-bound Na+,K+-ATPase in the E2P state

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: 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 NAG-NAG-BMA-MAN-MAN-FUC.5: 7 residues within 4Å: Chain E: H.107, D.111, N.114, S.116, R.154, 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: 10 residues within 4Å: Chain A: F.872, E.880, S.991, F.994, P.998 Chain B: T.61, K.68 Chain D: L.1005 Ligands: PCW.28, PCW.30 7 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: B:T.61, D:L.1005, A:F.872, A:P.998 Hydrogen bonds: B:K.68, B:K.68, A:S.991 CLR.20: 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.40, B:Y.44 Hydrogen bonds: B:R.28 CLR.21: 4 residues within 4Å: Chain B: G.49, I.52, G.53, Q.56 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.52, B:Q.56 CLR.22: 11 residues within 4Å: Chain A: P.990, W.993, F.994, F.997 Chain C: L.39, V.42, G.43, V.46 Ligands: PCW.12, PCW.25, PCW.42 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:V.46, A:P.990, A:W.993, A:F.994, A:F.997 CLR.26: 10 residues within 4Å: Chain A: L.1005 Chain D: F.872, E.880, S.991, F.994, P.998 Chain E: T.61, K.68 Ligands: PCW.11, PCW.13 7 PLIP interactions: 3 interactions with chain E, 3 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: E:T.61, D:F.872, D:P.998, A:L.1005 Hydrogen bonds: E:K.68, E:K.68, D:S.991 CLR.37: 6 residues within 4Å: Chain D: E.852 Chain E: R.28, W.33, Y.40, Y.44 Ligands: PCW.33 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:W.33, E:Y.40, E:Y.40, E:Y.44 Hydrogen bonds: E:R.28 CLR.38: 4 residues within 4Å: Chain E: G.49, I.52, G.53, Q.56 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:I.52, E:Q.56 CLR.39: 11 residues within 4Å: Chain D: P.990, W.993, F.994, F.997 Chain F: L.39, V.42, G.43, V.46 Ligands: PCW.25, PCW.29, PCW.42 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: D:P.990, D:W.993, D:F.994, D:F.997, F:V.46

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

PCW.10: 1 residues within 4Å: Chain A: H.298 Ligand excluded by PLIP PCW.11: 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, L.47, I.50 Ligands: CLR.26 Ligand excluded by PLIP PCW.12: 13 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.22, PCW.25 Ligand excluded by PLIP PCW.13: 17 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, K.68 Ligands: PCW.12, CLR.26, PCW.29, PCW.30 Ligand excluded by PLIP PCW.14: 4 residues within 4Å: Chain A: L.813, V.981, A.982 Ligands: PCW.15 Ligand excluded by PLIP PCW.15: 9 residues within 4Å: Chain A: L.969, F.972, P.977, G.978, V.981, A.982 Chain C: I.55 Ligands: PCW.14, PCW.23 Ligand excluded by PLIP PCW.16: 12 residues within 4Å: Chain A: H.295, V.303, F.306, L.307, F.311, L.796, K.845, E.852 Chain B: L.26, W.33, F.37 Ligands: CLR.20 Ligand excluded by PLIP PCW.23: 10 residues within 4Å: Chain A: P.977 Chain C: Y.36, Y.37, R.40, V.41, I.45, A.48, C.51, V.52 Ligands: PCW.15 Ligand excluded by PLIP PCW.24: 5 residues within 4Å: Chain C: Y.37, I.45, V.49, I.53 Ligands: PCW.25 Ligand excluded by PLIP PCW.25: 9 residues within 4Å: Chain A: P.990, F.994 Chain C: Y.34, R.38 Ligands: PCW.12, CLR.22, PCW.24, CLR.39, PCW.42 Ligand excluded by PLIP PCW.27: 1 residues within 4Å: Chain D: H.298 Ligand excluded by PLIP PCW.28: 16 residues within 4Å: Chain D: I.865, Y.999, I.1002, L.1005, Y.1006, M.1009, I.1013, G.1020, W.1021, Q.1024 Chain E: K.35, L.38, F.39, L.47, I.50 Ligands: CLR.9 Ligand excluded by PLIP PCW.29: 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.30, CLR.39, PCW.42 Ligand excluded by PLIP PCW.30: 16 residues within 4Å: Chain A: F.994, L.1001 Chain B: T.61, K.68 Chain D: R.946, S.948, F.950, Q.951, F.1004, L.1005, E.1008, F.1012, R.1015 Ligands: CLR.9, PCW.13, PCW.29 Ligand excluded by PLIP PCW.31: 4 residues within 4Å: Chain D: L.813, V.981, A.982 Ligands: PCW.32 Ligand excluded by PLIP PCW.32: 9 residues within 4Å: Chain D: L.969, F.972, P.977, G.978, V.981, A.982 Chain F: I.55 Ligands: PCW.31, PCW.40 Ligand excluded by PLIP PCW.33: 12 residues within 4Å: Chain D: H.295, V.303, F.306, L.307, F.311, L.796, K.845, E.852 Chain E: L.26, W.33, F.37 Ligands: CLR.37 Ligand excluded by PLIP PCW.40: 10 residues within 4Å: Chain D: P.977 Chain F: Y.36, Y.37, R.40, V.41, I.45, A.48, C.51, V.52 Ligands: PCW.32 Ligand excluded by PLIP PCW.41: 5 residues within 4Å: Chain F: Y.37, I.45, V.49, I.53 Ligands: PCW.42 Ligand excluded by PLIP PCW.42: 9 residues within 4Å: Chain D: P.990, F.994 Chain F: Y.34, R.38 Ligands: CLR.22, PCW.25, PCW.29, CLR.39, PCW.41 Ligand excluded by PLIP

4 x MG: MAGNESIUM ION(Non-covalent)

MG.17: 5 residues within 4Å: Chain A: D.381, T.383, D.722, G.723, D.726 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.383, A:D.722 MG.18: 5 residues within 4Å: Chain A: V.284, L.730, K.731, A.733, D.752 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.752 MG.34: 5 residues within 4Å: Chain D: D.381, T.383, D.722, G.723, D.726 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.383, D:D.722 MG.35: 5 residues within 4Å: Chain D: V.284, L.730, K.731, A.733, D.752 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.752

2 x 01: palytoxin

01.19: 21 residues within 4Å: Chain A: A.119, I.122, Q.123, T.126, L.137, L.316, I.317, Y.320, W.322, L.323, E.324, I.327, G.331, V.334, A.335, V.337, E.339, E.791, T.809, I.812, D.816 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:A.119, A:Q.123, A:T.126, A:L.316, A:L.323, A:I.327, A:A.335 Hydrogen bonds: A:Q.123, A:T.126, A:L.316, A:A.335, A:T.809 01.36: 21 residues within 4Å: Chain D: A.119, I.122, Q.123, T.126, L.137, L.316, I.317, Y.320, W.322, L.323, E.324, I.327, G.331, V.334, A.335, V.337, E.339, E.791, T.809, I.812, D.816 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:A.119, D:Q.123, D:T.126, D:L.316, D:L.323, D:I.327, D:A.335 Hydrogen bonds: D:Q.123, D:T.126, D:L.316, D:A.335, D: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

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

Na+,K+-ATPase beta subunit

FXYD domain-containing ion transport regulator

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