SMTL ID : 7tj9.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain A: H.320, N.364, C.377, K.379 No protein-ligand interaction detected (PLIP)

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

PEV.2: 26 residues within 4Å: Chain A: L.445, V.686, L.689, F.690, I.693, F.733, F.737, L.740, V.775, L.778, F.779, T.1195, F.1196, I.1229, I.1232, I.1233, F.1237, L.1240, I.1248, F.1488, Y.1546, I.1547, V.1550, M.1551, L.1554 Ligands: PEV.12 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.445, A:V.686, A:L.689, A:F.690, A:I.693, A:F.733, A:V.775, A:L.778, A:F.779, A:I.1229, A:I.1233, A:I.1233, A:I.1248, A:Y.1546, A:I.1547, A:V.1550, A:L.1554 PEV.6: 11 residues within 4Å: Chain A: F.302, I.309, L.313, R.365, V.424, Y.425, P.1396, L.1402, S.1406, I.1409 Ligands: CLR.18 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.302, A:I.309, A:L.313, A:V.424, A:Y.425, A:Y.425, A:L.1402, A:I.1409 Salt bridges: A:R.365 PEV.12: 22 residues within 4Å: Chain A: L.289, L.292, I.296, F.399, F.402, M.405, A.406, F.444, G.742, W.744, L.748, I.761, Y.764, L.765, M.766, I.768, L.769, N.772, L.776 Ligands: PEV.2, PLM.7, PLM.8 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.289, A:L.292, A:I.296, A:F.399, A:F.402, A:F.402, A:F.444, A:W.744, A:L.748, A:I.761, A:Y.764, A:L.765, A:I.768, A:L.769 Hydrogen bonds: A:Q.407, A:N.772

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

POV.3: 15 residues within 4Å: Chain A: T.1113, F.1117, W.1124, G.1184, N.1185, L.1191, G.1235, V.1236, P.1239, L.1240, L.1243, V.1532, W.1539, L.1540 Ligands: POV.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.1117, A:W.1124, A:L.1243, A:V.1532, A:W.1539, A:W.1539, A:L.1540 POV.4: 5 residues within 4Å: Chain A: S.1525, I.1528, V.1532, S.1533 Ligands: POV.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.1528, A:I.1528, A:V.1532 POV.9: 12 residues within 4Å: Chain A: T.259, T.262, L.266, I.272, L.688, F.695, L.703, N.707, W.759, M.766, I.770 Ligands: PLM.10 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.266, A:I.272, A:L.688, A:F.695, A:I.770

8 x PLM: PALMITIC ACID(Non-covalent)

PLM.5: 6 residues within 4Å: Chain A: L.1000, T.1003, E.1097, R.1098, F.1443, L.1444 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.1000, A:T.1003, A:F.1443, A:L.1444 Salt bridges: A:R.1098 PLM.7: 4 residues within 4Å: Chain A: G.395, W.396 Ligands: PLM.8, PEV.12 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.396 PLM.8: 3 residues within 4Å: Chain A: Q.757 Ligands: PLM.7, PEV.12 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.757 PLM.10: 4 residues within 4Å: Chain A: P.234, W.235, G.283 Ligands: POV.9 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.234, A:W.235, A:W.235 PLM.11: 2 residues within 4Å: Chain A: W.624, F.659 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.624, A:F.659 PLM.14: 3 residues within 4Å: Chain A: M.1130, M.1224, N.1230 No protein-ligand interaction detected (PLIP) PLM.15: 2 residues within 4Å: Chain A: W.1055, R.1104 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.1104 PLM.16: 8 residues within 4Å: Chain A: V.1314, C.1317, F.1318, M.1411, G.1417, P.1418, K.1419 Ligands: Q7G.19 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.1314, A:F.1318 Hydrogen bonds: A:K.1419

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

NAG.13: 3 residues within 4Å: Chain A: M.1157, N.1158, S.1160 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.1160, A:S.1160 NAG.20: 5 residues within 4Å: Chain B: F.63, T.119, N.121, K.136, T.138 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.136, B:T.138 NAG.21: 5 residues within 4Å: Chain B: K.42, Q.93, W.94, N.95, T.106 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:K.42 Hydrogen bonds: B:Q.93 NAG.22: 2 residues within 4Å: Chain B: L.112, N.113 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.112, B:N.113 NAG.23: 2 residues within 4Å: Chain B: G.38, N.109 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:N.109

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.17: 9 residues within 4Å: Chain A: Q.407, V.430, S.437, F.438, M.1446, A.1486, I.1487, I.1542, Y.1546 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.430, A:F.438, A:A.1486, A:I.1487, A:I.1542 Hydrogen bonds: A:Y.1546 CLR.18: 6 residues within 4Å: Chain A: M.1280, I.1409, L.1412, R.1413, M.1429 Ligands: PEV.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.1409, A:L.1412, A:L.1412, A:R.1413

1 x Q7G: 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside(Non-covalent)

Q7G.19: 20 residues within 4Å: Chain A: Q.291, G.294, V.295, I.297, F.301, S.304, I.447, M.450, C.1317, A.1320, I.1321, M.1324, I.1408, M.1411, P.1418, K.1419, V.1420, F.1421, A.1557 Ligands: PLM.16 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.297, A:F.301, A:A.1320, A:I.1321, A:I.1408, A:P.1418, A:P.1418, A:V.1420, A:F.1421 Hydrogen bonds: A:G.294, A:V.295 Salt bridges: A:K.1419

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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