SMTL ID : 7y46.1

Cryo-EM structure of the Na+,K+-ATPase in the E2.2K+ state after addition of ATP

Coordinates

PDB Format

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)

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

ATP.9: 10 residues within 4Å: Chain A: D.381, K.382, T.383, D.455, Q.494, R.556, L.558, T.622, G.623, D.624 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:D.381, A:D.381, A:D.381, A:K.382, A:T.383, A:T.383, A:T.383, A:D.455, A:R.556, A:G.623, A:G.623, A:D.624 Salt bridges: A:R.556 pi-Stacking: A:F.487 ATP.18: 10 residues within 4Å: Chain D: D.381, K.382, T.383, D.455, Q.494, R.556, L.558, T.622, G.623, D.624 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:D.381, D:D.381, D:D.381, D:K.382, D:T.383, D:T.383, D:T.383, D:D.455, D:R.556, D:G.623, D:G.623, D:D.624 Salt bridges: D:R.556 pi-Stacking: D:F.487

6 x K: POTASSIUM ION(Non-covalent)

K.10: 4 residues within 4Å: Chain A: L.730, K.731, A.733, D.752 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:L.730, A:K.731, A:A.733, A:D.752 K.11: 4 residues within 4Å: Chain A: T.784, S.787, N.788, D.816 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.784, A:S.787, A:D.816, H2O.1 K.12: 8 residues within 4Å: Chain A: V.334, A.335, V.337, E.339, N.788, E.791, I.812, D.816 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:A.335 K.19: 4 residues within 4Å: Chain D: L.730, K.731, A.733, D.752 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:L.730, D:K.731, D:A.733, D:D.752 K.20: 4 residues within 4Å: Chain D: T.784, S.787, N.788, D.816 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:T.784, D:S.787, D:D.816, H2O.1 K.21: 8 residues within 4Å: Chain D: V.334, A.335, V.337, E.339, N.788, E.791, I.812, D.816 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:A.335

8 x CLR: CHOLESTEROL(Non-covalent)

CLR.13: 8 residues within 4Å: Chain A: Y.975, P.990, F.994, F.997 Chain C: L.39, V.42, G.43, V.46 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 CLR.14: 9 residues within 4Å: Chain A: F.872, E.880, S.991, F.994, C.995 Chain B: V.57, T.61, K.68 Chain D: L.1005 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.57, B:T.61, A:F.872 Hydrogen bonds: B:K.68, B:K.68, A:S.991 CLR.16: 5 residues within 4Å: Chain A: E.852 Chain B: R.28, W.33, I.36, Y.40 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.33, B:W.33, B:I.36, B:Y.40 Hydrogen bonds: B:R.28 CLR.17: 4 residues within 4Å: Chain B: G.49, I.52, Q.56 Ligands: CLR.26 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.52, B:Q.56 CLR.22: 8 residues within 4Å: Chain D: Y.975, P.990, F.994, F.997 Chain F: L.39, V.42, G.43, V.46 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: D:P.990, D:F.994, D:F.994, D:F.997, F:V.46 CLR.23: 9 residues within 4Å: Chain A: L.1005 Chain D: F.872, E.880, S.991, F.994, C.995 Chain E: V.57, T.61, K.68 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain E Hydrophobic interactions: D:F.872, E:V.57, E:T.61 Hydrogen bonds: D:S.991, E:K.68, E:K.68 CLR.25: 5 residues within 4Å: Chain D: E.852 Chain E: R.28, W.33, I.36, Y.40 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:W.33, E:W.33, E:I.36, E:Y.40 Hydrogen bonds: E:R.28 CLR.26: 4 residues within 4Å: Chain E: G.49, I.52, Q.56 Ligands: CLR.17 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:I.52, E:Q.56

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

PCW.15: 1 residues within 4Å: Chain A: R.358 No protein-ligand interaction detected (PLIP) PCW.24: 1 residues within 4Å: Chain D: R.358 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kanai, R. et al., Cryo-electron microscopy of Na + ,K + -ATPase reveals how the extracellular gate locks in the E2·2K + state. Febs Lett. (2022)

Release Date

2022-07-13

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
C

D
A

B
D

E
B

C
E

F
G

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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