SMTL ID : 7w9p.1

Cryo-EM structure of human Nav1.7(E406K) in complex with auxiliary beta subunits, huwentoxin-IV and saxitoxin (S6IV pi helix conformer)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

3 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: N.1395, T.1397, D.1398, S.1420 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.1409, E.1412 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain B: E.56, R.72, Y.124, N.135 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.124 Hydrogen bonds: B:R.72

1 x 9SL: [(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate(Non-covalent)

9SL.4: 10 residues within 4Å: Chain A: Y.405, E.407, E.970, F.1448, K.1449, G.1450, W.1451, T.1452, G.1742, D.1744 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.405, A:Y.405, A:E.407, A:E.970, A:G.1450, A:T.1452, A:G.1742 Salt bridges: A:E.407

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

NAG.5: 1 residues within 4Å: Chain A: N.326 No protein-ligand interaction detected (PLIP) NAG.11: 1 residues within 4Å: Chain A: N.1418 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1418 NAG.34: 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.35: 2 residues within 4Å: Chain B: G.33, N.110 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.33, B:N.110 NAG.36: 3 residues within 4Å: Chain B: R.89, T.112, N.114 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.112

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

P5S.6: 11 residues within 4Å: Chain A: W.1222, R.1225, Y.1229, W.1288, I.1289, A.1290, Y.1291, G.1292, Y.1293 Ligands: LPE.28, LPE.29 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.1289, A:Y.1293, A:Y.1293 Salt bridges: A:R.1225, A:R.1225 P5S.20: 11 residues within 4Å: Chain A: L.431, G.1532, S.1533, W.1621, F.1624, V.1667, R.1674, T.1675, L.1677, F.1678 Ligands: PCW.21 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.431, A:W.1621, A:W.1621, A:F.1624, A:V.1667, A:L.1677, A:L.1677 Hydrogen bonds: A:S.1533, A:T.1675 Salt bridges: A:R.1674 P5S.32: 5 residues within 4Å: Chain A: L.1609, R.1613, H.1614, F.1617 Ligands: PCW.31 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.1609, A:F.1617 Salt bridges: A:H.1614

6 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.7: 4 residues within 4Å: Chain A: T.1298, N.1299, W.1303, L.1307 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.1303, A:W.1303, A:L.1307 Y01.8: 6 residues within 4Å: Chain A: Y.1293, K.1294, F.1297, T.1298 Ligands: LPE.28, LPE.29 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.1293, A:K.1294, A:F.1297, A:T.1298 Y01.9: 8 residues within 4Å: Chain A: V.798, K.890, W.892, P.893, L.1369, I.1373, L.1376 Ligands: Y01.33 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.798, A:K.890, A:P.893, A:L.1369, A:I.1373, A:L.1376 Hydrogen bonds: A:K.890 Salt bridges: A:K.890 Y01.10: 10 residues within 4Å: Chain A: N.252, A.255, T.258, F.259, V.261, L.262, L.265, V.926, L.930, M.993 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.255, A:T.258, A:F.259, A:V.261, A:L.262, A:L.265, A:L.265, A:V.926 Hydrogen bonds: A:N.252 Y01.12: 2 residues within 4Å: Chain A: Y.1472, Y.1475 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.1475 Y01.33: 8 residues within 4Å: Chain A: L.802, H.808, I.1373, N.1434, G.1436 Ligands: Y01.9, LPE.15, PCW.16 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.802, A:I.1373 Hydrogen bonds: A:N.1434 Salt bridges: A:H.808

13 x LPE: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)(Non-functional Binders)

LPE.13: 10 residues within 4Å: Chain A: S.1753, K.1754, P.1776, S.1777, I.1780, F.1781, V.1784, S.1785 Ligands: 1PW.14, PCW.16 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.1781, A:F.1781, A:V.1784 Hydrogen bonds: A:S.1753, A:K.1754 LPE.15: 1 residues within 4Å: Ligands: Y01.33 No protein-ligand interaction detected (PLIP) LPE.17: 12 residues within 4Å: Chain A: L.1341, L.1344, L.1693, L.1696, V.1697, I.1700, Y.1701, F.1704, F.1781, Y.1782, I.1789 Ligands: LPE.18 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.1341, A:L.1344, A:L.1344, A:L.1693, A:L.1696, A:I.1700 pi-Cation interactions: A:F.1704 LPE.18: 5 residues within 4Å: Chain A: A.1300, W.1301, V.1354, N.1355 Ligands: LPE.17 No protein-ligand interaction detected (PLIP) LPE.22: 9 residues within 4Å: Chain A: F.430, E.1520, Q.1521, Y.1524, L.1684, P.1685, L.1687, F.1688 Ligands: LPE.23 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.430, A:F.430 LPE.23: 6 residues within 4Å: Chain A: Y.1524, A.1527, M.1528, L.1531 Ligands: LPE.22, PCW.30 No protein-ligand interaction detected (PLIP) LPE.24: 10 residues within 4Å: Chain A: D.363, K.419, T.420, M.422, V.426, F.1695, M.1698, M.1731, F.1735 Ligands: LPE.25 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.426, A:F.1695, A:F.1735 Hydrogen bonds: A:K.419, A:K.419 LPE.25: 9 residues within 4Å: Chain A: D.1256, Y.1258, R.1261, K.1262, T.1726, F.1727, G.1728 Ligands: LPE.24, LPE.26 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.1727 Hydrogen bonds: A:Y.1258, A:G.1728 LPE.26: 8 residues within 4Å: Chain A: S.1249, A.1253, F.1254, K.1262, M.1350, F.1695, F.1727 Ligands: LPE.25 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.1695 Hydrogen bonds: A:A.1253 LPE.27: 6 residues within 4Å: Chain A: I.293, S.300, F.390, F.394, M.1576, A.1670 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.390, A:F.394 LPE.28: 7 residues within 4Å: Chain A: W.1221, W.1222, R.1225, Y.1293 Ligands: P5S.6, Y01.8, LPE.29 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.1225 LPE.29: 5 residues within 4Å: Chain A: Y.1293, K.1294 Ligands: P5S.6, Y01.8, LPE.28 No protein-ligand interaction detected (PLIP) LPE.37: 3 residues within 4Å: Chain A: I.1224 Chain B: M.178, I.179 No protein-ligand interaction detected (PLIP)

1 x 1PW: (2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate(Non-covalent)

1PW.14: 16 residues within 4Å: Chain A: Q.403, F.434, I.1364, L.1368, T.1447, F.1495, T.1739, S.1740, I.1787, I.1788, S.1790, F.1791, L.1792, V.1795 Ligands: LPE.13, PCW.16 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.1364, A:L.1368, A:T.1447, A:F.1495, A:F.1495, A:I.1788, A:I.1788, A:F.1791, A:L.1792 Hydrogen bonds: A:Q.403, A:T.1739, A:S.1740, A:I.1787

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

PCW.16: 13 residues within 4Å: Chain A: L.1368, C.1371, L.1372, W.1375, G.1436, L.1437, Y.1439, L.1443, I.1780, V.1784 Ligands: LPE.13, 1PW.14, Y01.33 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.1368, A:L.1372, A:L.1372, A:W.1375, A:L.1437, A:Y.1439, A:L.1443, A:I.1780, A:V.1784 PCW.19: 11 residues within 4Å: Chain A: Y.382, G.383, Y.384, S.391, W.392, F.394, F.398, Q.984, A.985, L.988, M.992 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.392, A:F.394, A:F.398, A:F.398 Hydrogen bonds: A:S.391, A:Q.984 PCW.21: 14 residues within 4Å: Chain A: I.305, L.1531, Q.1537, T.1618, V.1619, G.1620, I.1623, F.1624, L.1657, I.1660, G.1661, M.1681 Ligands: P5S.20, PCW.30 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.305, A:F.1624, A:I.1660 PCW.30: 4 residues within 4Å: Chain A: L.1531, I.1631 Ligands: PCW.21, LPE.23 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.1631 PCW.31: 6 residues within 4Å: Chain A: F.1617, V.1627, I.1630, I.1631, V.1634 Ligands: P5S.32 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.1630, A:I.1630, A:I.1631, A:V.1634, A:V.1634

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, G. et al., High-resolution structures of human Na v 1.7 reveal gating modulation through alpha-pi helical transition of S6 IV. Cell Rep (2022)

Release Date

2022-05-25

Peptides

Sodium channel protein type 9 subunit alpha: A
Sodium channel subunit beta-1: B
Sodium channel subunit beta-2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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Sodium channel protein type 9 subunit alpha

Sodium channel subunit beta-1

Sodium channel subunit beta-2

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