SMTL ID : 7w9m.1

Cryo-EM structure of human Nav1.7(E406K) in complex with auxiliary beta subunits, ProTx-II and tetrodotoxin (S6IV pi helix conformer)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

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.1: 5 residues within 4Å: Chain B: F.54, E.56, Y.124, L.126, N.135 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.56 NAG-NAG.2: 5 residues within 4Å: Chain A: N.1395, T.1397, D.1398, F.1402, S.1420 No protein-ligand interaction detected (PLIP)

1 x 9SR: (1R,5R,6R,7R,9S,11S,12S,13S,14S)-3-amino-14-(hydroxymethyl)-8,10-dioxa-2,4-diazatetracyclo[7.3.1.1~7,11~.0~1,6~]tetradec-3-ene-5,9,12,13,14-pentol (non-preferred name)(Non-covalent)

9SR.3: 12 residues within 4Å: Chain A: D.404, Y.405, E.407, E.970, E.973, F.1448, K.1449, G.1450, W.1451, T.1452, G.1742, D.1744 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:D.404, A:D.404, A:Y.405, A:G.1450, A:W.1451, A:T.1452, A:T.1452, A:T.1452, A:G.1742 Salt bridges: A:E.407, A:E.970, A:E.973

6 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.5: 3 residues within 4Å: Chain A: N.1409, E.1412, K.1466 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.1409, A:K.1466 NAG.11: 1 residues within 4Å: Chain A: N.1418 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1418 NAG.13: 2 residues within 4Å: Chain B: N.93, R.96 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.96 NAG.14: 2 residues within 4Å: Chain B: G.33, N.110 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.33, B:N.110 NAG.15: 2 residues within 4Å: Chain B: Q.61, N.114 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.61, B:N.114

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

P5S.6: 10 residues within 4Å: Chain A: W.1222, R.1225, Y.1229, L.1285, W.1288, I.1289, A.1290, G.1292, Y.1293, T.1295 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.1289, A:Y.1293 Hydrogen bonds: A:W.1222, A:T.1295 Salt bridges: A:R.1225, A:R.1225

5 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.7: 3 residues within 4Å: Chain A: T.1298, W.1303, L.1307 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.1303, A:L.1307 Y01.8: 2 residues within 4Å: Chain A: K.1294, F.1297 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.1297 Salt bridges: A:K.1294 Y01.9: 2 residues within 4Å: Chain A: L.888, W.892 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.888, A:W.892, A:W.892 Y01.10: 11 residues within 4Å: Chain A: N.252, A.255, T.258, F.259, V.261, I.919, I.922, F.923, V.926, L.930, M.993 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.255, A:T.258, A:V.261, A:I.919, A:I.922, A:F.923, A:L.930 Y01.12: 2 residues within 4Å: Chain A: Y.1472, Y.1475 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.1472, A:Y.1472

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

LPE.16: 1 residues within 4Å: Chain B: Y.182 No protein-ligand interaction detected (PLIP)

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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