Cryo-EM structure of SV2A in complex with BoNT/A2 Hc. Determined by electron microscopy at 2.87 Å resolution. Released 1 May 2024.
Explore 8JLG in 3D Show helices and sheets RCSB PDB PDBe
8JLG contains 9 α-helices and 51 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 481-483 | 3 | |
| β-strand | 485-493 | 9 | 1 |
| β-strand | 496 | 1 | 1 |
| β-strand | 500-512 | 13 | 1 |
| β-strand | 515-527 | 13 | 1 |
| β-strand | 530-532 | 3 | 1 |
| β-strand | 535-542 | 8 | 1 |
| β-strand | 545-547 | 3 | 1 |
| β-strand | 550-552 | 3 | 1 |
| β-strand | 555-559 | 5 | 1 |
| β-strand | 566-567 | 2 | 1 |
| β-strand | 570-572 | 3 | 1 |
| β-strand | 574-577 | 4 | 1 |
| α-helix | 579-581 | 3 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 877-884 | 8 | 2 |
| β-strand | 887-890 | 4 | 2 |
| β-strand | 897-900 | 4 | 3 |
| β-strand | 905-906 | 2 | 2 |
| β-strand | 913-917 | 5 | 2 |
| β-strand | 924-927 | 4 | 3 |
| α-helix | 930-932 | 3 | |
| β-strand | 941-948 | 8 | 2 |
| α-helix | 950-952 | 3 | |
| α-helix | 955-957 | 3 | |
| β-strand | 962-968 | 7 | 3 |
| β-strand | 973-979 | 7 | 3 |
| β-strand | 982-988 | 7 | 3 |
| β-strand | 994-1000 | 7 | 3 |
| β-strand | 1014-1021 | 8 | 2 |
| β-strand | 1026-1031 | 6 | 2 |
| β-strand | 1034-1040 | 7 | 2 |
| β-strand | 1052-1058 | 7 | 3 |
| β-strand | 1066-1075 | 10 | 2 |
| α-helix | 1081-1090 | 10 | |
| β-strand | 1096 | 1 | 4 |
| β-strand | 1098 | 1 | 5 |
| β-strand | 1104 | 1 | 5 |
| β-strand | 1106 | 1 | 6 |
| β-strand | 1112-1115 | 4 | 7 |
| β-strand | 1122-1125 | 4 | 7 |
| β-strand | 1134-1137 | 4 | 7 |
| β-strand | 1142-1145 | 4 | 1 |
| β-strand | 1149-1152 | 4 | 1 |
| β-strand | 1159-1164 | 6 | 7 |
| β-strand | 1173 | 1 | 6 |
| β-strand | 1175 | 1 | 4 |
| β-strand | 1178-1186 | 9 | 7 |
| β-strand | 1189-1194 | 6 | 7 |
| β-strand | 1195 | 1 | 8 |
| β-strand | 1204-1205 | 2 | 7 |
| α-helix | 1206 | 1 | |
| β-strand | 1207-1209 | 3 | 7 |
| α-helix | 1211-1213 | 3 | |
| β-strand | 1218 | 1 | 8 |
| β-strand | 1220-1226 | 7 | 7 |
| β-strand | 1232-1240 | 9 | 7 |
| β-strand | 1246-1255 | 10 | 7 |
| β-strand | 1258-1264 | 7 | 7 |
| α-helix | 1266-1272 | 7 | |
| β-strand | 1282-1285 | 4 | 7 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Synaptic vesicle glycoprotein 2A | A | protein | 111 | Homo sapiens | Q7L0J3 (AlphaFold model) |
| Botulinum neurotoxin | B | protein | 426 | Clostridium botulinum | Q45894 (AlphaFold model) |
>8JLG_1 Synaptic vesicle glycoprotein 2A (chains A) YASRTKVFPGERVEHVTFNFTLENQIHRGGQYFNDKFIGLRLKSVSFEDSLFEECYFEDV TSSNTFFRNCTFINTVFYNTDLFEYKFVNSRLINSTFLHNKEGCPLDVTGT
>8JLG_2 Botulinum neurotoxin (chains B) KNIVNTSILSIVYKKDDLIDLSRYGAKINIGDRVYYDSIDKNQIKLINLESSTIEVILKN AIVYNSMYENFSTSFWIKIPKYFSKINLNNEYTIINCIENNSGWKVSLNYGEIIWTLQDN KQNIQRVVFKYSQMVNISDYINRWIFVTITNNRLTKSKIYINGRLIDQKPISNLGNIHAS NKIMFKLDGCRDPRRYIMIKYFNLFDKELNEKEIKDLYDSQSNSGILKDFWGNYLQYDKP YYMLNLFDPNKYVDVNNIGIRGYMYLKGPRGSVVTTNIYLNSTLYEGTKFIIKKYASGNE DNIVRNNDRVYINVVVKNKEYRLATNASQAGVEKILSALEIPDVGNLSQVVVMKSKDDQG IRNKCKMNLQDNNGNDIGFIGFHLYDNIAKLVASNWYNRQVGKASRTFGCSWEFIPVDDG WGESSL
| ID | Name | Formula | Copies |
|---|---|---|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 2 |
Structural basis for antiepileptic drugs and botulinum neurotoxin recognition of SV2A. Yamagata, A., Ito, K., Suzuki, T. et al. Nat Commun (2024) 15:3027-3027. DOI 10.1038/s41467-024-47322-4 · PubMed
Other PDB entries of the same protein (UniProt Q7L0J3 (AlphaFold model), which also has an AlphaFold model), best resolution first:
MolViewer shows 8JLG directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.