SMTL ID : 9dbn.1

Tarantula venom peptide Protoxin-I bound to full-length human voltage-gated sodium channel 1.8 (NaV1.8)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

5 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 4 residues within 4Å: Chain A: N.319, N.357, C.370, K.372 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 5 residues within 4Å: Chain A: N.1357, T.1359, T.1383, S.1385, F.1386 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.1383 NAG-NAG-BMA.3: 4 residues within 4Å: Chain A: N.1372, N.1373, S.1375, D.1376 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 9 residues within 4Å: Chain A: C.1377, N.1381, G.1384, F.1386, F.1387, W.1388, G.1719, P.1720, P.1725 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 5 residues within 4Å: Chain A: N.861, K.863, N.864, E.904, V.905 No protein-ligand interaction detected (PLIP)

4 x CLR: CHOLESTEROL(Non-covalent)

CLR.6: 7 residues within 4Å: Chain A: V.721, T.724, I.725, L.811, S.814, W.815, L.1338 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.721, A:L.811, A:W.815, A:W.815, A:L.1338 CLR.7: 6 residues within 4Å: Chain A: K.773, F.777, F.803, L.806 Ligands: PCW.12, PCW.13 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.777, A:F.777, A:F.803, A:L.806 CLR.8: 6 residues within 4Å: Chain A: S.386, F.387, I.1536, M.1539, V.1540, T.1542 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.387, A:I.1536, A:M.1539, A:V.1540, A:T.1542 CLR.19: 14 residues within 4Å: Chain A: L.438, T.442, E.446, I.931, L.934, L.935, S.939, V.1459, I.1463, N.1467, V.1759, Y.1762, I.1766, F.1770 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.438, A:L.438, A:T.442, A:L.934, A:L.935, A:I.1463, A:V.1759, A:Y.1762, A:I.1766, A:F.1770

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

PCW.9: 13 residues within 4Å: Chain A: L.428, T.1581, N.1582, G.1583, W.1584, F.1587, L.1629, I.1632, R.1639, L.1642, L.1645, M.1646, L.1649 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.428, A:L.428, A:W.1584, A:W.1584, A:W.1584, A:F.1587, A:L.1629, A:I.1632, A:L.1642, A:L.1645, A:M.1646, A:L.1649 Salt bridges: A:R.1639 PCW.12: 12 residues within 4Å: Chain A: K.773, W.774, F.809, I.822, I.825, G.826, V.829, M.1343, I.1445, F.1449 Ligands: CLR.7, PCW.13 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.774, A:F.809, A:F.809, A:F.809, A:I.822, A:I.825, A:V.829, A:V.829, A:I.1445, A:F.1449 PCW.13: 8 residues within 4Å: Chain A: S.796, N.1436, Y.1438, L.1441, Y.1442, I.1445 Ligands: CLR.7, PCW.12 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.1438, A:L.1441, A:L.1441, A:Y.1442, A:I.1445 Hydrogen bonds: A:S.796

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

LPE.10: 13 residues within 4Å: Chain A: L.839, L.891, V.926, C.1333, W.1337, A.1409, F.1411, I.1447, G.1450, G.1451, F.1452, T.1454, L.1455 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.839, A:V.926, A:F.1452, A:F.1452 Hydrogen bonds: A:I.1447 LPE.11: 9 residues within 4Å: Chain A: V.308, L.312, Y.418, F.421, T.1615, L.1616, V.1619, L.1622, I.1625 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.308, A:L.312, A:L.1622, A:I.1625 LPE.14: 9 residues within 4Å: Chain A: T.1260, A.1262, W.1263, L.1266, V.1316, D.1317, L.1319, V.1320, L.1658 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:A.1262, A:W.1263, A:W.1263, A:L.1266, A:V.1316, A:V.1316, A:L.1319, A:L.1319, A:V.1320, A:L.1658 LPE.15: 10 residues within 4Å: Chain A: L.1208, S.1211, G.1212, F.1216, A.1305, F.1660, L.1661, F.1664, F.1692, A.1693 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.1305, A:F.1660, A:L.1661 LPE.16: 7 residues within 4Å: Chain A: A.728, H.731, G.733, L.1338, N.1397, V.1398 Ligands: P5S.17 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.728, A:L.1338, A:V.1398 Hydrogen bonds: A:A.728, A:N.1397, A:V.1398 Salt bridges: A:H.731

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

P5S.17: 10 residues within 4Å: Chain A: A.1399, M.1400, Y.1402, L.1403, L.1406, A.1741, I.1744, I.1745, T.1748 Ligands: LPE.16 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.1399, A:Y.1402, A:L.1403, A:L.1406, A:A.1741, A:I.1744, A:I.1745 P5S.18: 12 residues within 4Å: Chain A: F.379, N.380, Y.381, A.388, W.389, L.392, F.395, K.908, S.909, L.912, I.913, L.916 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:W.389, A:W.389, A:L.392, A:L.392, A:L.392, A:F.395, A:F.395, A:F.395, A:K.908, A:L.912, A:L.912, A:I.913 Hydrogen bonds: A:N.380 Salt bridges: A:K.908, A:K.908

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neumann, B. et al., Structural basis of inhibition of human Na V 1.8 by the tarantula venom peptide Protoxin-I. Nat Commun (2025)

Release Date

2025-02-19

Peptides

Sodium channel protein type 10 subunit alpha: A
Beta/omega-theraphotoxin-Tp1a: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Sodium channel protein type 10 subunit alpha

Beta/omega-theraphotoxin-Tp1a

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