SMTL ID : 7w9t.1

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

Coordinates

PDB Format Compare

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: 3 residues within 4Å: Chain A: N.1395, F.1402, S.1420 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: P.1408, N.1409, S.1411, 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 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.124 Hydrogen bonds: B:R.72, 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: 12 residues within 4Å: Chain A: Y.405, E.407, E.970, E.973, F.1448, K.1449, G.1450, W.1451, T.1452, A.1741, G.1742, D.1744 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Y.405, A:Y.405, A:E.970, A:E.970, A:G.1450, A:W.1451, A:T.1452, A:G.1742 Salt bridges: A:E.407, A:E.973

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.33: 5 residues within 4Å: Chain B: V.91, N.93, G.94, R.96, F.107 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.93, B:R.96 NAG.34: 2 residues within 4Å: Chain B: G.33, N.110 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.110 NAG.35: 1 residues within 4Å: Chain B: N.114 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.114

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

P5S.6: 12 residues within 4Å: Chain A: W.1221, W.1222, R.1225, Y.1229, L.1285, W.1288, A.1290, Y.1291, Y.1293, T.1295 Ligands: LPE.28, LPE.29 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.1221, A:L.1285, A:Y.1293 Salt bridges: A:R.1225, A:R.1225 P5S.20: 12 residues within 4Å: Chain A: L.431, S.1533, W.1621, F.1624, V.1667, K.1671, R.1674, T.1675, L.1677, F.1678, M.1681 Ligands: PCW.21 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.431, A:W.1621, A:F.1624, A:V.1667 Hydrogen bonds: A:S.1533 Salt bridges: A:K.1671, A:R.1674

5 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.7: 3 residues within 4Å: Chain A: N.1299, W.1303, L.1307 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.1303, A:W.1303, A:L.1307, A:L.1307 Y01.8: 5 residues within 4Å: Chain A: Y.1293, K.1294, F.1297, T.1298 Ligands: LPE.29 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.1293, A:Y.1293, A:F.1297, A:F.1297 Y01.9: 8 residues within 4Å: Chain A: V.798, V.885, S.891, W.892, P.893, L.1369, I.1373, L.1376 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.798, A:V.885, A:W.892, A:W.892, A:L.1369, A:I.1373, A:L.1376 Y01.12: 1 residues within 4Å: Chain A: Y.1475 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.1475 Y01.32: 13 residues within 4Å: Chain A: L.802, A.805, H.808, L.1372, I.1373, L.1376, N.1434, V.1435, G.1436, Y.1439 Ligands: LPE.13, LPE.15, PCW.16 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.802, A:L.1372, A:I.1373, A:L.1376, A:V.1435 Hydrogen bonds: A:N.1434 Salt bridges: A:H.808

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

9Z9.10: 13 residues within 4Å: Chain A: L.441, A.445, K.449, F.1006, L.1007, L.1010, I.1496, I.1500, N.1504, Y.1798, I.1799, I.1802, F.1806 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.1006, A:F.1006, A:L.1010, A:I.1500, A:I.1500, A:Y.1798, A:I.1799, A:I.1802, A:I.1802, A:F.1806, A:F.1806

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

LPE.13: 4 residues within 4Å: Chain A: M.806, F.815 Ligands: LPE.15, Y01.32 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.808 LPE.14: 7 residues within 4Å: Chain A: P.1776, S.1777, I.1780, F.1781, V.1784, S.1785 Ligands: PCW.16 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.1781, A:F.1781, A:V.1784 Hydrogen bonds: A:S.1753 LPE.15: 3 residues within 4Å: Ligands: LPE.13, PCW.16, Y01.32 No protein-ligand interaction detected (PLIP) LPE.17: 12 residues within 4Å: Chain A: L.1341, L.1344, L.1696, V.1697, I.1700, Y.1701, F.1704, V.1778, 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.1696, A:V.1697, A:I.1700 Hydrogen bonds: A:S.1785 pi-Cation interactions: A:F.1704 LPE.18: 6 residues within 4Å: Chain A: A.1300, W.1301, V.1354, N.1355, I.1358 Ligands: LPE.17 No protein-ligand interaction detected (PLIP) LPE.22: 10 residues within 4Å: Chain A: F.430, E.1520, Q.1521, Y.1524, L.1684, P.1685, L.1687, F.1688, M.1797 Ligands: LPE.23 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.430, A:F.430, A:F.1688 pi-Cation interactions: A:Y.1524 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 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.426, A:F.1695, A:F.1735 Hydrogen bonds: A:K.419 LPE.25: 7 residues within 4Å: Chain A: K.419, D.1256, T.1726, G.1728, N.1729 Ligands: LPE.24, LPE.26 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.1256, A:N.1729 Salt bridges: A:K.419 pi-Cation interactions: A:Y.1258 LPE.26: 11 residues within 4Å: Chain A: S.1249, A.1253, F.1254, K.1262, F.1347, M.1350, L.1692, L.1696, F.1699, F.1727 Ligands: LPE.25 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.1347, A:L.1692, A:L.1696, A:F.1699 Hydrogen bonds: A:A.1253 LPE.27: 5 residues within 4Å: Chain A: V.296, M.1576, L.1666, A.1670 Ligands: PCW.19 No protein-ligand interaction detected (PLIP) LPE.28: 5 residues within 4Å: Chain A: W.1221, W.1222, R.1225, Y.1293 Ligands: P5S.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.1293 Salt bridges: A:R.1225 LPE.29: 4 residues within 4Å: Chain A: Y.1293, K.1294 Ligands: P5S.6, Y01.8 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.1294 LPE.36: 3 residues within 4Å: Chain A: I.1224 Chain B: M.178, Y.182 No protein-ligand interaction detected (PLIP)

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

PCW.16: 10 residues within 4Å: Chain A: L.1368, C.1371, L.1372, W.1375, G.1436, L.1443, V.1784 Ligands: LPE.14, LPE.15, Y01.32 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.1368, A:L.1372, A:W.1375, A:L.1443, A:V.1784 PCW.19: 12 residues within 4Å: Chain A: Y.382, G.383, Y.384, S.391, W.392, F.394, F.398, Q.984, L.988, M.992, V.996 Ligands: LPE.27 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.392, A:F.394, A:F.398, A:F.398, A:L.988, A:M.992 Hydrogen bonds: A:S.391, A:Q.984 PCW.21: 10 residues within 4Å: Chain A: L.1531, K.1534, T.1618, V.1619, G.1620, I.1623, L.1657, M.1681 Ligands: P5S.20, PCW.30 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.1620 Salt bridges: A:K.1534 PCW.30: 5 residues within 4Å: Chain A: L.1531, K.1534 Ligands: PCW.21, LPE.23, PCW.31 No protein-ligand interaction detected (PLIP) PCW.31: 7 residues within 4Å: Chain A: H.1614, F.1617, I.1623, F.1626, V.1627, I.1631 Ligands: PCW.30 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.1617, A:F.1617, A:I.1623, A:F.1626, A:V.1627, A:I.1631 Hydrogen bonds: A:H.1614

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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