SMTL ID : 8t6l.1

Cryo-EM structure of rat cardiac sodium channel NaV1.5 with batrachotoxin analog BTX-B

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.1: 5 residues within 4Å: Chain A: H.279, N.329, R.341, C.342, L.343 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 5 residues within 4Å: Chain A: N.1049, T.1051, E.1052, T.1074, E.1076 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1063, N.1064, S.1066, E.1067 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.4: 10 residues within 4Å: Chain A: E.1069, N.1072, G.1075, L.1077, Y.1078, P.1409, P.1410, C.1412, D.1413, N.1415 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.1078, A:P.1410

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

NAG.5: 3 residues within 4Å: Chain A: N.284, E.338, G.339 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.284 NAG.6: 3 residues within 4Å: Chain A: N.319, W.1368, D.1374 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.1374 Hydrogen bonds: A:N.319 NAG.7: 3 residues within 4Å: Chain A: L.680, N.1058, Q.1123 No protein-ligand interaction detected (PLIP)

10 x LBN: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine(Non-covalent)

LBN.8: 14 residues within 4Å: Chain A: V.259, A.360, W.361, F.363, L.364, F.367, Q.717, S.718, L.721, L.725, L.726, V.729 Ligands: LBN.9, Y01.19 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.259, A:W.361, A:F.363, A:L.364, A:F.367, A:L.721, A:L.725, A:L.726, A:V.729 LBN.9: 4 residues within 4Å: Chain A: M.255, V.256 Ligands: LBN.8, LBN.10 No protein-ligand interaction detected (PLIP) LBN.10: 6 residues within 4Å: Chain A: V.259, V.1216, F.1220, L.1320 Ligands: LBN.9, Y01.20 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.1220, A:L.1320 LBN.11: 6 residues within 4Å: Chain A: Q.582, G.583, F.613, L.616, F.619, F.1032 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.613, A:F.613, A:F.619, A:F.1032 Hydrogen bonds: A:G.583 LBN.12: 4 residues within 4Å: Chain A: G.640, N.644, L.647 Ligands: 9Z9.30 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.647 Hydrogen bonds: A:N.644 LBN.13: 4 residues within 4Å: Chain A: S.135, M.136, M.139, I.234 No protein-ligand interaction detected (PLIP) LBN.14: 10 residues within 4Å: Chain A: S.985, T.988, V.1008, L.1347, Y.1355, F.1358, N.1362, V.1431, L.1434, F.1435 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.1008, A:L.1347, A:L.1347, A:F.1358, A:L.1434 Hydrogen bonds: A:N.1362 LBN.15: 12 residues within 4Å: Chain A: M.1019, L.1022, C.1025, G.1090, P.1429, A.1430, I.1433, L.1434, T.1437, I.1441 Ligands: Y01.23, YIJ.32 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.1022, A:L.1022, A:L.1434, A:T.1437, A:I.1441, A:I.1441 LBN.16: 3 residues within 4Å: Chain A: A.954, W.955, V.1012 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.1012 LBN.17: 11 residues within 4Å: Chain A: S.903, G.904, A.907, F.908, D.910, R.916, L.1350, F.1353, T.1380, A.1382 Ligands: Y01.27 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.907, A:L.1350, A:A.1382 Salt bridges: A:R.916

11 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.18: 9 residues within 4Å: Chain A: V.216, A.218, T.221, F.222, F.656, L.719, L.726, I.730 Ligands: Y01.19 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:A.218, A:F.222, A:F.222, A:F.222, A:F.656, A:F.656, A:L.719, A:L.726, A:I.730 Hydrogen bonds: A:V.216 Y01.19: 3 residues within 4Å: Chain A: S.718 Ligands: LBN.8, Y01.18 No protein-ligand interaction detected (PLIP) Y01.20: 4 residues within 4Å: Chain A: M.1230, S.1237, K.1240 Ligands: LBN.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.1237 Salt bridges: A:K.1240 Y01.21: 5 residues within 4Å: Chain A: P.193, W.194, L.197, L.225, V.241 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.193, A:W.194, A:L.197, A:L.225, A:V.241 Y01.22: 4 residues within 4Å: Chain A: Y.1129, I.1132 Ligands: 9Z9.29, 9Z9.30 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.1129 Y01.23: 5 residues within 4Å: Chain A: L.1026, N.1088, G.1090 Ligands: LBN.15, Y01.24 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1088 Y01.24: 8 residues within 4Å: Chain A: A.538, L.539, H.541, L.1026, N.1088, V.1089, G.1090 Ligands: Y01.23 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.539, A:L.1026, A:N.1088, A:V.1089 Salt bridges: A:H.541 Y01.25: 6 residues within 4Å: Chain A: V.531, L.621, W.625, P.626, L.1023, I.1027 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.531, A:V.531, A:L.621, A:L.1023 Y01.26: 8 residues within 4Å: Chain A: V.264, I.268, Y.390, F.393, L.396, T.1304, V.1308, L.1311 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.264, A:I.268, A:Y.390, A:Y.390, A:F.393, A:T.1304, A:V.1308, A:L.1311 Hydrogen bonds: A:T.1304 Y01.27: 10 residues within 4Å: Chain A: D.332, K.388, I.389, M.391, M.395, F.1342, L.1346, M.1385 Ligands: LBN.17, YIJ.31 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.389, A:F.1342, A:L.1346, A:M.1385 Salt bridges: A:K.388 Y01.28: 8 residues within 4Å: Chain A: L.1224, V.1227, T.1228, V.1231, E.1239, I.1243, L.1244, I.1247 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.1224, A:V.1227, A:V.1231, A:V.1231, A:I.1243, A:L.1244, A:I.1247

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

9Z9.29: 11 residues within 4Å: Chain A: V.609, F.613, M.1035, L.1039, N.1127, Y.1129, M.1130, I.1132, Y.1133, V.1136 Ligands: Y01.22 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.609, A:L.1039, A:Y.1129, A:I.1132, A:Y.1133, A:V.1136 9Z9.30: 10 residues within 4Å: Chain A: F.689, F.690, F.693, Y.1129, I.1132, V.1135, V.1136, I.1139 Ligands: LBN.12, Y01.22 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.689, A:F.690, A:F.693, A:Y.1129, A:I.1132, A:V.1135, A:I.1139

2 x YIJ: (1R)-1-[(5aR,7aR,9R,11aS,11bS,12R,13aR)-9,12-dihydroxy-2,11a-dimethyl-1,2,3,4,7a,8,9,10,11,11a,12,13-dodecahydro-7H-9,11b-epoxy-13a,5a-prop[1]enophenanthro[2,1-f][1,4]oxazepin-14-yl]ethyl benzoate(Non-covalent)

YIJ.31: 15 residues within 4Å: Chain A: Q.372, M.395, I.398, F.399, F.403, L.1338, L.1341, F.1342, G.1345, L.1348, F.1389, T.1393, V.1447, M.1450 Ligands: Y01.27 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.398, A:F.399, A:F.403, A:F.403, A:F.403, A:T.1393, A:V.1447, A:V.1447 YIJ.32: 13 residues within 4Å: Chain A: C.701, W.1029, L.1097, A.1100, T.1101, F.1102, G.1141, T.1145, L.1146, S.1394, I.1440, F.1444 Ligands: LBN.15 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.1029, A:L.1097, A:T.1145, A:L.1146, A:L.1146, A:F.1444 Water bridges: A:S.1394 pi-Stacking: A:F.1102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tonggu, L. et al., Dual receptor-sites reveal the structural basis for hyperactivation of sodium channels by poison-dart toxin batrachotoxin. Nat Commun (2024)

Release Date

2024-03-06

Peptides

Sodium channel protein type 5 subunit alpha,Green fluorescent protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Sodium channel protein type 5 subunit alpha,Green fluorescent protein