SMTL ID : 7w9k.1

Cryo-EM structure of human Nav1.7-beta1-beta2 complex at 2.2 angstrom resolution

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: 5 residues within 4Å: Chain A: N.1395, T.1397, D.1398, F.1402, S.1420 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: P.1408, N.1409, S.1411, E.1412, K.1466 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain B: F.54, E.56, R.72, Y.124, L.126, N.135 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.54, B:Y.124 Hydrogen bonds: B:R.72, B:R.72

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

NAG.4: 1 residues within 4Å: Chain A: N.326 No protein-ligand interaction detected (PLIP) NAG.11: 1 residues within 4Å: Chain A: N.1418 No protein-ligand interaction detected (PLIP) NAG.37: 5 residues within 4Å: Chain B: V.91, W.92, N.93, R.96, F.107 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.96 NAG.38: 2 residues within 4Å: Chain B: G.33, N.110 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.33 NAG.39: 3 residues within 4Å: Chain B: R.89, T.112, N.114 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.112 Hydrogen bonds: B:N.114

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

P5S.5: 8 residues within 4Å: Chain A: W.1222, R.1225, W.1288, A.1290, G.1292, Y.1293 Ligands: LPE.30, LPE.31 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.1288, A:Y.1293 Hydrogen bonds: A:W.1222 Salt bridges: A:R.1225, A:R.1225 P5S.22: 13 residues within 4Å: Chain A: L.431, G.1532, W.1621, F.1624, V.1667, K.1671, R.1674, T.1675, L.1677, F.1678, L.1680, M.1681 Ligands: PCW.23 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.431, A:W.1621, A:F.1624, A:F.1624, A:F.1624, A:V.1667, A:L.1677, A:L.1677, A:L.1680 Hydrogen bonds: A:G.1532, A:T.1675 Salt bridges: A:K.1671, A:R.1674 P5S.34: 7 residues within 4Å: Chain A: V.1606, L.1609, I.1610, R.1613, H.1614, F.1617 Ligands: PCW.33 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.1606, A:I.1610, A:F.1617 Hydrogen bonds: A:H.1614 Salt bridges: A:H.1614

6 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.6: 2 residues within 4Å: Chain A: T.1298, W.1303 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.1303, A:W.1303 Y01.7: 5 residues within 4Å: Chain A: Y.1293, K.1294, F.1297, T.1298 Ligands: LPE.31 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.1293, A:K.1294, A:K.1294, A:F.1297, A:F.1297, A:F.1297 Y01.8: 11 residues within 4Å: Chain A: V.798, T.801, V.885, L.888, S.891, W.892, P.893, E.1024, L.1369, I.1373, L.1376 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.798, A:V.798, A:T.801, A:V.885, A:L.888, A:W.892, A:W.892, A:W.892, A:W.892, A:P.893, A:L.1369, A:I.1373, A:L.1376 Hydrogen bonds: A:E.1024 Y01.10: 12 residues within 4Å: Chain A: N.252, A.255, T.258, L.262, I.919, I.922, F.923, V.926, L.930, M.986, M.993, I.997 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.255, A:L.262, A:I.919, A:I.922, A:V.926, A:L.930, A:I.997 Hydrogen bonds: A:N.252 Y01.12: 1 residues within 4Å: Chain A: Y.1475 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.1475, A:Y.1475, A:Y.1475, A:Y.1475 Y01.35: 12 residues within 4Å: Chain A: L.802, A.805, H.808, P.810, L.1372, L.1376, N.1434, G.1436, Y.1439 Ligands: LPE.14, LPE.17, PCW.18 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.802, A:P.810, A:L.1376 Salt bridges: A:H.808

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

9Z9.9: 13 residues within 4Å: Chain A: L.441, A.445, E.449, Q.453, L.1003, F.1006, L.1007, L.1011, I.1496, I.1500, Y.1798, I.1802, F.1806 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.441, A:L.441, A:A.445, A:F.1006, A:L.1007, A:L.1011, A:I.1496, A:I.1496, A:Y.1798, A:I.1802, A:I.1802, A:F.1806, A:F.1806 Hydrogen bonds: A:Q.453

1 x NA: SODIUM ION(Non-functional Binders)

NA.13: 5 residues within 4Å: Chain A: D.404, E.970, W.971, I.972, E.973 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.404, A:I.972, A:E.973 Water bridges: A:T.974

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

LPE.14: 5 residues within 4Å: Chain A: M.806, H.808, F.815 Ligands: LPE.17, Y01.35 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.808 LPE.15: 8 residues within 4Å: Chain A: S.1753, P.1776, S.1777, I.1780, F.1781, S.1785 Ligands: 1PW.16, PCW.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.1753, A:P.1776 LPE.17: 3 residues within 4Å: Ligands: LPE.14, PCW.18, Y01.35 No protein-ligand interaction detected (PLIP) LPE.19: 11 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 Ligands: LPE.20 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.1341, A:L.1344, A:L.1344, A:L.1696 Hydrogen bonds: A:V.1697 pi-Cation interactions: A:F.1704 LPE.20: 9 residues within 4Å: Chain A: A.1300, W.1301, L.1335, L.1338, L.1341, V.1354, N.1355, I.1358 Ligands: LPE.19 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.1335 LPE.24: 8 residues within 4Å: Chain A: F.430, E.1520, Q.1521, Y.1524, L.1684, P.1685, F.1688 Ligands: LPE.25 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.430, A:F.430, A:L.1684 Salt bridges: A:E.1520 LPE.25: 6 residues within 4Å: Chain A: Y.1524, A.1527, M.1528, L.1531 Ligands: LPE.24, PCW.32 No protein-ligand interaction detected (PLIP) LPE.26: 9 residues within 4Å: Chain A: D.363, K.419, T.420, M.422, V.426, F.1695, M.1698, M.1731 Ligands: LPE.27 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.426, A:F.1695 Hydrogen bonds: A:T.420 LPE.27: 8 residues within 4Å: Chain A: D.1256, Y.1258, R.1261, T.1726, F.1727, G.1728 Ligands: LPE.26, LPE.28 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.1727, A:F.1727 Hydrogen bonds: A:D.1256, A:Y.1258, A:N.1729 Salt bridges: A:K.419 LPE.28: 11 residues within 4Å: Chain A: L.1246, S.1249, G.1250, A.1253, F.1254, F.1347, M.1350, L.1696, F.1699, F.1727 Ligands: LPE.27 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.1347, A:L.1696, A:L.1696, A:F.1699 Hydrogen bonds: A:A.1253 LPE.29: 11 residues within 4Å: Chain A: I.293, V.296, S.300, F.390, F.394, M.1572, M.1576, L.1666, G.1669, A.1670 Ligands: PCW.21 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.394, A:F.394 LPE.30: 6 residues within 4Å: Chain A: W.1221, W.1222, R.1225, Y.1293 Ligands: P5S.5, LPE.31 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.1293 Salt bridges: A:R.1225 LPE.31: 5 residues within 4Å: Chain A: Y.1293, K.1294 Ligands: P5S.5, Y01.7, LPE.30 No protein-ligand interaction detected (PLIP) LPE.36: 10 residues within 4Å: Chain A: K.1230, I.1231, H.1234, W.1236, F.1237, F.1240 Chain B: W.173, L.174, E.177, C.181 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.1234 pi-Cation interactions: A:H.1234 LPE.40: 5 residues within 4Å: Chain A: I.1224 Chain B: M.178, I.179, Y.182, K.183 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.16: 15 residues within 4Å: Chain A: I.1364, M.1365, L.1368, T.1447, T.1738, T.1739, S.1740, I.1787, I.1788, S.1790, F.1791, L.1792, V.1794 Ligands: LPE.15, PCW.18 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.1364, A:L.1368, A:I.1788, A:I.1788, A:F.1791, A:F.1791, A:L.1792 Hydrogen bonds: A:S.1740, A:I.1787

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

PCW.18: 16 residues within 4Å: Chain A: L.1368, C.1371, L.1372, W.1375, N.1434, G.1436, L.1437, Y.1439, L.1443, I.1780, V.1784, I.1788 Ligands: LPE.15, 1PW.16, LPE.17, Y01.35 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.1368, A:W.1375, A:L.1437, A:Y.1439, A:L.1443, A:I.1780, A:V.1784, A:I.1788 PCW.21: 11 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 Ligands: LPE.29 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.392, A:F.394, A:F.398, A:F.398, A:F.398, A:M.992 Hydrogen bonds: A:S.391, A:Q.984 PCW.23: 13 residues within 4Å: Chain A: L.1531, K.1534, T.1618, V.1619, G.1620, F.1624, V.1627, I.1631, L.1657, I.1660, G.1661 Ligands: P5S.22, PCW.32 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.1624, A:V.1627, A:I.1631, A:I.1660 Hydrogen bonds: A:G.1620 Salt bridges: A:K.1534 PCW.32: 5 residues within 4Å: Chain A: L.1531, K.1534 Ligands: PCW.23, LPE.25, PCW.33 No protein-ligand interaction detected (PLIP) PCW.33: 10 residues within 4Å: Chain A: H.1614, F.1617, I.1623, F.1626, V.1627, I.1630, I.1631, V.1634 Ligands: PCW.32, P5S.34 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.1617, A:F.1626, A:F.1626, A:V.1627, A:V.1627, A:I.1630, A:I.1631, 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

2022-06-01

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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