SMTL ID : 7w9l.1

Cryo-EM structure of human Nav1.7(E406K)-beta1-beta2 complex

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, S.1420, Q.1421 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 1 residues within 4Å: Chain A: N.1409 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 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.124 Hydrogen bonds: 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.326 NAG.11: 1 residues within 4Å: Chain A: N.1418 No protein-ligand interaction detected (PLIP) NAG.34: 1 residues within 4Å: Chain B: N.93 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.93 NAG.35: 3 residues within 4Å: Chain B: G.33, R.89, N.110 No protein-ligand interaction detected (PLIP) NAG.36: 3 residues within 4Å: Chain B: Q.61, T.112, N.114 No protein-ligand interaction detected (PLIP)

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

P5S.5: 14 residues within 4Å: Chain A: W.1221, W.1222, R.1225, Y.1229, L.1285, W.1288, I.1289, A.1290, Y.1291, G.1292, Y.1293, T.1295 Ligands: LPE.28, LPE.29 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.1221, A:W.1221, A:L.1285, A:W.1288, A:I.1289, A:Y.1293 Salt bridges: A:R.1225, A:R.1225 P5S.20: 13 residues within 4Å: Chain A: L.431, G.1532, S.1533, K.1535, W.1621, F.1624, V.1667, R.1674, L.1677, F.1678, L.1680, M.1681 Ligands: PCW.21 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.431, A:W.1621, A:F.1624, A:V.1667, A:L.1677, A:L.1680, A:M.1681 Salt bridges: A:K.1535, A:R.1674, A:R.1674 P5S.32: 3 residues within 4Å: Chain A: I.1610, H.1614 Ligands: PCW.31 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.1610 Hydrogen bonds: A:H.1614

6 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.6: 5 residues within 4Å: Chain A: T.1298, A.1300, W.1303, L.1307 Ligands: Y01.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.1298, A:A.1300, A:W.1303, A:L.1307, A:L.1307 Y01.7: 3 residues within 4Å: Chain A: F.1297 Ligands: Y01.6, LPE.29 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.1297 Y01.8: 9 residues within 4Å: Chain A: V.798, T.801, V.885, L.888, W.892, P.893, L.1369, I.1373, L.1376 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.798, A:V.798, A:T.801, A:V.885, A:W.892, A:W.892, A:W.892, A:P.893, A:L.1369, A:I.1373, A:L.1376 Y01.10: 11 residues within 4Å: Chain A: N.252, A.255, T.258, F.259, V.261, L.262, I.919, F.923, V.926, L.930, M.993 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.255, A:T.258, A:V.261, A:L.262, A:I.919, A:V.926, A:L.930 Hydrogen bonds: A:N.252 Y01.12: 3 residues within 4Å: Chain A: E.872, Y.1472, Y.1475 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.1475, A:Y.1475, A:Y.1475 Hydrogen bonds: A:E.872, A:Y.1472 Y01.33: 12 residues within 4Å: Chain A: L.802, A.805, M.806, H.808, L.1372, L.1376, N.1434, G.1436, Y.1439 Ligands: LPE.13, LPE.15, PCW.16 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.802, A:L.1376 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)

9Z9.9: 13 residues within 4Å: Chain A: L.441, A.445, K.449, Q.453, L.1003, F.1006, L.1007, L.1010, L.1011, I.1496, I.1500, I.1802, F.1806 15 PLIP interactions: 15 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:I.1500, A:I.1802, A:I.1802, A:F.1806, A:F.1806 Hydrogen bonds: A:K.449, A:Q.453

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

LPE.13: 5 residues within 4Å: Chain A: L.802, M.806, H.808 Ligands: LPE.15, Y01.33 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.802 Salt bridges: A:H.808 LPE.14: 7 residues within 4Å: Chain A: S.1753, P.1776, S.1777, I.1780, F.1781, S.1785 Ligands: PCW.16 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.1780, A:F.1781 Hydrogen bonds: A:S.1753 LPE.15: 3 residues within 4Å: Ligands: LPE.13, PCW.16, 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, V.1778, F.1781, Y.1782 Ligands: LPE.18 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.1341, A:L.1344, A:L.1344, A:L.1693, A:L.1696, A:L.1696 Hydrogen bonds: A:V.1697 pi-Cation interactions: A:F.1704 LPE.18: 11 residues within 4Å: Chain A: N.1299, A.1300, W.1301, L.1304, L.1335, L.1338, L.1341, L.1344, V.1354, N.1355 Ligands: LPE.17 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.1304, A:L.1335, A:L.1338, A:L.1341 LPE.22: 7 residues within 4Å: Chain A: F.430, T.1518, E.1520, Y.1524, L.1684, P.1685, F.1688 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.430, A:L.1684 Hydrogen bonds: A:Y.1524 LPE.23: 5 residues within 4Å: Chain A: Y.1524, A.1527, M.1528, M.1681 Ligands: PCW.30 No protein-ligand interaction detected (PLIP) LPE.24: 9 residues within 4Å: Chain A: D.363, K.419, T.420, M.422, F.1695, M.1698, M.1731, F.1735 Ligands: LPE.25 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.1695, A:F.1735 LPE.25: 6 residues within 4Å: Chain A: Y.1258, R.1261, T.1726, G.1728 Ligands: LPE.24, LPE.26 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.1258 LPE.26: 10 residues within 4Å: Chain A: L.1246, S.1249, A.1253, F.1254, K.1262, F.1347, M.1350, L.1696, F.1727 Ligands: LPE.25 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.1246, A:F.1347 Hydrogen bonds: A:A.1253 LPE.27: 5 residues within 4Å: Chain A: V.296, S.300, M.1572, L.1666 Ligands: PCW.19 No protein-ligand interaction detected (PLIP) LPE.28: 6 residues within 4Å: Chain A: W.1221, W.1222, R.1225, Y.1293 Ligands: P5S.5, LPE.29 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.1225 LPE.29: 4 residues within 4Å: Chain A: K.1294 Ligands: P5S.5, Y01.7, LPE.28 No protein-ligand interaction detected (PLIP) LPE.37: 4 residues within 4Å: Chain A: I.1224 Chain B: M.178, I.179, Y.182 No protein-ligand interaction detected (PLIP)

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

PCW.16: 13 residues within 4Å: Chain A: L.1368, L.1372, W.1375, G.1436, L.1437, Y.1439, L.1440, L.1443, I.1780, V.1784 Ligands: LPE.14, LPE.15, Y01.33 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.1368, A:L.1372, A:W.1375, A:W.1375, A:L.1437, A:Y.1439, A:Y.1439, A:L.1443, A:I.1780, A:V.1784 PCW.19: 12 residues within 4Å: Chain A: G.383, Y.384, S.391, W.392, F.394, F.398, Q.984, L.988, I.989, M.992, M.993 Ligands: LPE.27 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.392, A:F.394, A:F.394, A:F.398, A:F.398, A:F.398, A:L.988, A:I.989, A:M.992 Hydrogen bonds: A:S.391, A:Q.984 PCW.21: 15 residues within 4Å: Chain A: L.1531, Q.1537, T.1618, V.1619, G.1620, I.1623, F.1624, V.1627, I.1631, A.1658, I.1660, G.1661, L.1664 Ligands: P5S.20, PCW.30 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.1623, A:V.1627, A:V.1627, A:I.1631, A:I.1660, A:I.1660, A:L.1664 Hydrogen bonds: A:G.1620 PCW.30: 7 residues within 4Å: Chain A: K.1534, I.1623, V.1627, I.1631 Ligands: PCW.21, LPE.23, PCW.31 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.1623, A:V.1627, A:I.1631 PCW.31: 10 residues within 4Å: Chain A: H.1614, F.1617, I.1623, F.1626, V.1627, I.1630, I.1631, V.1634 Ligands: PCW.30, P5S.32 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.1623, A:V.1627, A:I.1631, A:V.1634 Salt bridges: 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

2022-06-01

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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