SMTL ID : 7tj8.1

Cryo-EM structure of the human Nax channel in complex with beta3 solved in nanodiscs

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

3 x PEV: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE(Non-covalent)

PEV.1: 15 residues within 4Å: Chain A: L.445, A.449, E.453, L.689, L.778, S.787, F.1196, F.1237, L.1240, I.1244, I.1248, F.1488, Y.1546, I.1547, V.1550 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.449, A:L.689, A:L.778, A:I.1244, A:I.1248, A:Y.1546, A:I.1547, A:V.1550 PEV.5: 3 residues within 4Å: Chain A: L.313, Y.425, F.428 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.313, A:Y.425, A:F.428 Salt bridges: A:R.365 PEV.13: 15 residues within 4Å: Chain A: L.289, F.399, F.402, A.441, F.444, L.448, L.740, L.748, Y.764, L.765, I.770, N.772, L.776 Ligands: PLM.6, PLM.7 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.289, A:F.399, A:F.444, A:L.748, A:Y.764, A:L.765, A:I.770 Hydrogen bonds: A:L.740, A:N.772

3 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.2: 12 residues within 4Å: Chain A: L.1111, T.1113, F.1117, L.1121, W.1124, G.1184, L.1191, G.1235, V.1236, W.1539, L.1540 Ligands: POV.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.1111, A:F.1117, A:F.1117, A:L.1121, A:W.1124, A:W.1539, A:W.1539, A:L.1540, A:L.1540 POV.3: 3 residues within 4Å: Chain A: I.1528, F.1529 Ligands: POV.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.1528, A:F.1529 POV.8: 6 residues within 4Å: Chain A: T.259, F.695, L.703, N.707, W.759 Ligands: PLM.9 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.695, A:F.695 Hydrogen bonds: A:W.759

6 x PLM: PALMITIC ACID(Non-covalent)(Non-functional Binders)

PLM.4: 4 residues within 4Å: Chain A: C.993, T.1003, F.1096, F.1443 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.1003, A:F.1443 PLM.6: 5 residues within 4Å: Chain A: W.396, Q.757, I.761 Ligands: PLM.7, PEV.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.761 Hydrogen bonds: A:W.396 PLM.7: 2 residues within 4Å: Ligands: PLM.6, PEV.13 No protein-ligand interaction detected (PLIP) PLM.9: 4 residues within 4Å: Chain A: P.234, G.283, I.286 Ligands: POV.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.234, A:I.286 PLM.10: 5 residues within 4Å: Chain A: F.659, F.1127, M.1130, M.1224, N.1230 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.659, A:F.1127, A:N.1230 PLM.11: 3 residues within 4Å: Chain A: G.623, W.624, M.672 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.624, A:W.624 Hydrogen bonds: A:G.623

5 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.12: 5 residues within 4Å: Chain A: H.320, N.364, C.377, V.378, K.379 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.377, A:C.377 NAG.14: 1 residues within 4Å: Chain A: N.1158 No protein-ligand interaction detected (PLIP) NAG.16: 4 residues within 4Å: Chain B: F.63, T.119, N.121, T.138 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.121 NAG.17: 3 residues within 4Å: Chain B: K.42, N.95, T.106 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.42, B:T.106 Hydrogen bonds: B:N.95 NAG.18: 1 residues within 4Å: Chain B: N.109 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.109

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.15: 7 residues within 4Å: Chain A: Q.407, S.433, F.434, I.1439, F.1483, I.1487, Y.1546 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.434, A:I.1439, A:I.1439, A:I.1439, A:F.1483, A:I.1487 Hydrogen bonds: A:Q.407, A:Q.407, A:Y.1546

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Noland, C.L. et al., Structure-guided unlocking of Na X reveals a non-selective tetrodotoxin-sensitive cation channel. Nat Commun (2022)

Release Date

2022-03-30

Peptides

Sodium channel protein type 7 subunit alpha: A
Sodium channel subunit beta-3: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Sodium channel protein type 7 subunit alpha

Sodium channel subunit beta-3

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