SMTL ID : 8gz2.1

Cryo-EM structure of human NaV1.6/beta1/beta2-4,9-anhydro-tetrodotoxin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-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: 3 residues within 4Å: Chain B: N.295, G.296, T.297 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 5 residues within 4Å: Chain A: N.131 Chain B: Y.292, E.304, N.308, T.310 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.292 NAG-NAG-BMA.3: 8 residues within 4Å: Chain B: N.279, W.284, W.302, N.326, Q.338, C.339, M.340, K.341 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:M.340, B:K.341 NAG-NAG-BMA.4: 6 residues within 4Å: Chain B: N.1358, T.1360, S.1361, F.1365, N.1383, E.1386 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 3 residues within 4Å: Chain B: N.1371, N.1372, E.1375 No protein-ligand interaction detected (PLIP)

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

NAG.6: 2 residues within 4Å: Chain A: N.135, S.137 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.135 NAG.7: 1 residues within 4Å: Chain B: N.289 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.289

1 x WMK: (1R,2S,3S,4R,5R,9S,11S,12S,14R)-7-amino-2,4,12-trihydroxy-2-(hydroxymethyl)-10,13,15-trioxa-6,8-diazapentacyclo[7.4.1.1~3,12~.0~5,11~.0~5,14~]pentadec-7-en-8-ium (non-preferred name)(Non-covalent)

WMK.8: 11 residues within 4Å: Chain B: D.370, Y.371, E.373, E.936, E.939, F.1412, K.1413, G.1414, W.1415, M.1416, D.1708 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.371 Hydrogen bonds: B:D.370, B:D.370, B:Y.371, B:E.939, B:G.1414, B:W.1415, B:M.1416 Salt bridges: B:E.373, B:E.936, B:E.939

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Y. et al., Structure of human Na V 1.6 channel reveals Na + selectivity and pore blockade by 4,9-anhydro-tetrodotoxin. Nat Commun (2023)

Release Date

2023-03-08

Peptides

Sodium channel subunit beta-1: A
Sodium channel protein type 8 subunit alpha: B
Sodium channel subunit beta-2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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Sodium channel subunit beta-1

Sodium channel protein type 8 subunit alpha

Sodium channel subunit beta-2

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