SMTL ID : 8fhd.1

Cryo-EM structure of human voltage-gated sodium channel Nav1.6

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]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-MAN-MAN-MAN-MAN-MAN.1: 12 residues within 4Å: Chain A: N.279, W.284, F.288, G.299, F.300, W.302, E.303, N.326, Q.338, C.339, M.340, K.341 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.302, A:E.303, A:Q.338, A:Q.338 Hydrophobic interactions: A:W.284

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.2: 3 residues within 4Å: Chain B: F.54, Y.124, N.135 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.54

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

NAG.3: 4 residues within 4Å: Chain A: N.1371, N.1372, E.1375, D.1429 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.1371, A:N.1372, A:E.1375, A:D.1429 NAG.4: 2 residues within 4Å: Chain A: N.295, T.297 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.295, A:T.297 NAG.5: 6 residues within 4Å: Chain A: N.1358, T.1360, S.1361, F.1365, L.1379, I.1387 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.1365 NAG.6: 3 residues within 4Å: Chain A: E.304, N.308, T.310 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.304, A:N.308 NAG.24: 3 residues within 4Å: Chain B: N.93, R.96, F.107 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.96 NAG.25: 2 residues within 4Å: Chain B: T.109, N.110 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.109 NAG.26: 3 residues within 4Å: Chain B: E.84, R.85, N.114 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.61

4 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.7: 4 residues within 4Å: Chain A: T.1261, N.1262, A.1263, W.1266 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.1266, A:W.1266 Y01.9: 3 residues within 4Å: Chain A: Y.1439, I.1442, I.1446 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.1439, A:I.1442, A:I.1446 Y01.19: 8 residues within 4Å: Chain A: L.768, A.771, H.774, P.776, N.1398, V.1399 Ligands: LPE.10, Y01.20 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.768, A:A.771, A:N.1398, A:V.1399, A:V.1399 Salt bridges: A:H.774 Y01.20: 5 residues within 4Å: Chain A: N.1398, G.1400, Y.1403 Ligands: PCW.11, Y01.19 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.1403 Hydrogen bonds: A:N.1398

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.8: 5 residues within 4Å: Chain A: L.854, S.857, W.858, P.859, L.1332 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.854, A:W.858, A:L.1332

5 x LPE: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

LPE.10: 3 residues within 4Å: Chain A: T.778, F.781 Ligands: Y01.19 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.778 LPE.12: 8 residues within 4Å: Chain A: L.1320, I.1664, F.1665, F.1668, N.1672, V.1741, F.1744 Ligands: LPE.13 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.1320 Hydrogen bonds: A:S.1748 pi-Cation interactions: A:F.1668 LPE.13: 7 residues within 4Å: Chain A: A.1263, W.1264, L.1298, L.1304, N.1318, V.1321 Ligands: LPE.12 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.1298, A:L.1304 LPE.17: 8 residues within 4Å: Chain A: D.329, K.385, T.386, M.388, G.1655, F.1659, M.1662, M.1695 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.1659 Hydrogen bonds: A:K.385 LPE.18: 9 residues within 4Å: Chain A: L.1209, S.1212, A.1216, F.1217, R.1225, F.1659, L.1660, F.1663, F.1691 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.1209, A:F.1659, A:L.1660, A:F.1663

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

PCW.11: 13 residues within 4Å: Chain A: W.1338, G.1400, Y.1403, L.1404, P.1739, S.1740, I.1743, F.1744, V.1747, S.1748, I.1751 Ligands: Y01.20, P3X.23 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.1338, A:Y.1403, A:I.1743, A:F.1744, A:F.1744, A:F.1744, A:V.1747, A:I.1751, A:I.1751 PCW.14: 12 residues within 4Å: Chain A: Y.348, Y.350, S.357, W.358, F.360, L.361, F.364, E.946, Q.950, A.951, L.954, M.958 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.358, A:F.360, A:F.360, A:L.361, A:L.361, A:F.364, A:A.951, A:L.954, A:M.958 Hydrogen bonds: A:S.357, A:Q.950 PCW.16: 12 residues within 4Å: Chain A: L.1495, K.1498, K.1499, T.1582, I.1583, G.1584, I.1587, F.1588, V.1591, L.1628, M.1645 Ligands: P5S.15 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.1587, A:L.1628

2 x P5S: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine(Non-covalent)

P5S.15: 9 residues within 4Å: Chain A: G.1496, I.1583, W.1585, K.1635, R.1638, L.1641, F.1642, M.1645 Ligands: PCW.16 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.1585, A:W.1585 Hydrogen bonds: A:G.1496 Salt bridges: A:K.1635, A:R.1638, A:R.1638 P5S.21: 8 residues within 4Å: Chain A: W.1185, R.1188, K.1189, F.1192, Y.1254, G.1255, F.1256, K.1258 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.1188 Salt bridges: A:R.1188, A:K.1189, A:K.1189, A:K.1258

1 x 9Z9: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en(Non-covalent)

9Z9.22: 12 residues within 4Å: Chain A: L.407, A.411, F.972, L.973, L.976, I.1460, I.1464, I.1762, I.1765, L.1766, F.1769 Ligands: P3X.23 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.411, A:F.972, A:F.972, A:L.973, A:L.976, A:I.1460, A:I.1464, A:I.1464, A:I.1765, A:L.1766, A:F.1769

1 x P3X: (5E,17R,20S)-23-amino-20-hydroxy-14,20-dioxo-15,19,21-trioxa-20lambda~5~-phosphatricos-5-en-17-yl hexadecanoate(Non-covalent)

P3X.23: 26 residues within 4Å: Chain A: S.871, V.872, T.879, L.882, F.930, L.933, C.934, N.965, L.971, I.1327, L.1331, C.1334, A.1410, F.1412, I.1448, I.1449, F.1450, S.1452, F.1453, F.1454, T.1455, L.1456, F.1459, L.1755 Ligands: PCW.11, 9Z9.22 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:V.872, A:T.879, A:L.882, A:F.930, A:L.971, A:L.1331, A:L.1331, A:F.1412, A:I.1448, A:I.1449, A:F.1450, A:F.1453, A:F.1453, A:F.1454, A:F.1454, A:T.1455, A:F.1459, A:L.1755 Hydrogen bonds: A:N.965

Links

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Citation

Fan, X. et al., Cryo-EM structure of human voltage-gated sodium channel Na v 1.6. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2023-02-08

Peptides

Sodium channel protein type 8 subunit alpha: A
Sodium channel subunit beta-1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Membrane

We predict this structure to be a membrane protein.
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Sodium channel protein type 8 subunit alpha

Sodium channel subunit beta-1

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