SMTL ID : 9fyq.1

Cryo-EM structure of native SV2A in complex with TeNT-Hc, gangliosides and Pro-Macrobody 5

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

2 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.1: 5 residues within 4Å: Chain A: E.533, N.553, V.555, N.573 Chain C: D.65 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.2: 5 residues within 4Å: Chain A: G.508, Q.510, D.528, L.530, N.548 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.530

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

NAG.3: 1 residues within 4Å: Chain A: N.498 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.498

1 x 6UZ: omega-undecylenyl-beta-D-maltopyranoside(Non-covalent)

6UZ.4: 17 residues within 4Å: Chain A: E.490, V.492, V.495, F.497, F.499, L.501, H.506, Y.511, F.516, L.519, L.521, F.526, F.531, F.536, F.546 Chain B: T.312, Y.319 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.492, A:F.497, A:F.516, A:F.516, A:L.519, A:F.526, A:F.526, A:F.531, A:F.536 Hydrogen bonds: B:Y.319, B:Y.319

1 x 01: (2~{R},4~{R},5~{S},6~{S})-2-[(2~{R},3~{R})-3-[(2~{R},3~{S},4~{S},6~{S})-6-[(2~{S},3~{S},4~{R},5~{S},6~{S})-3-[(2~{R},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-2-(hydroxymethyl)-6-[(2~{R},3~{R},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-[2-(octadecanoylamino)-3-oxidanyl-octadec-4-enoxy]-4,5-bis(oxidanyl)oxan-3-yl]oxy-5-oxidanyl-oxan-4-yl]oxy-3-azanyl-6-carboxy-4-oxidanyl-oxan-2-yl]-2,3-bis(oxidanyl)propoxy]-5-azanyl-4-oxidanyl-6-[(1~{R},2~{S})-1,2,3-tris(oxidanyl)propyl]oxane-2-carboxylic acid

01.5: 9 residues within 4Å: Chain B: D.301, D.368, G.369, N.370, R.380, Y.383, A.385, I.388, I.429 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.370, B:R.380, B:R.380, B:Y.383

1 x 02: (2~{S},4~{S},5~{R},6~{S})-5-acetamido-2-[(2~{R},3~{R},4~{R},5~{S},6~{R})-2-[(2~{R},3~{R},4~{S},5~{R},6~{S})-2-[(2~{R},3~{S},4~{R},5~{R},6~{R})-4-[(2~{S},4~{S},5~{S},6~{S})-5-acetamido-2-carboxy-4-oxidanyl-6-[(1~{S},2~{R})-1,2,3-tris(oxidanyl)propyl]oxan-2-yl]oxy-6-[(2~{R},3~{S},4~{R},5~{R},6~{R})-6-[2-(docosanoylamino)-3-oxidanyl-octadec-4-enoxy]-2-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]oxy-2-(hydroxymethyl)-5-oxidanyl-oxan-3-yl]oxy-6-(hydroxymethyl)-5-oxidanyl-3-(2-oxidanylidenepropyl)oxan-4-yl]oxy-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-4-yl]oxy-4-oxidanyl-6-[(1~{R},2~{R})-1,2,3-tris(oxidanyl)propyl]oxane-2-carboxylic acid

02.6: 10 residues within 4Å: Chain B: F.372, N.373, L.375, D.376, T.424, H.425, I.439, S.441, W.443, Y.444 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.373, B:D.376, B:D.376, B:T.424, B:S.441, B:S.441 Salt bridges: B:H.425

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schenck, S. et al., Structures of native SV2A reveal the binding mode for tetanus neurotoxin and anti-epileptic racetams. Nat Commun (2025)

Release Date

2025-05-21

Peptides

Synaptic vesicle glycoprotein 2A: A
Tetanus toxin heavy chain: B
Pro-Macrobody 5,Maltose/maltodextrin-binding periplasmic protein: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

Membrane

We predict this structure to be a membrane protein.
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Synaptic vesicle glycoprotein 2A

Tetanus toxin heavy chain

Pro-Macrobody 5,Maltose/maltodextrin-binding periplasmic protein

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