Cryo-EM structure of SV2A in complex with BoNT/A2 Hc and levetiracetam. Determined by electron microscopy at 2.88 Å resolution. Released 1 May 2024.
Explore 8JS8 in 3D Show helices and sheets RCSB PDB PDBe
8JS8 contains 35 α-helices and 57 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 | 138-159 | 22 | |
| α-helix | 163-182 | 20 | |
| α-helix | 185-197 | 13 | |
| α-helix | 204-229 | 26 | |
| α-helix | 231-249 | 19 | |
| α-helix | 256-270 | 15 | |
| α-helix | 272-281 | 10 | |
| α-helix | 286-288 | 3 | |
| α-helix | 290-294 | 5 | |
| α-helix | 295-297 | 3 | |
| α-helix | 298-314 | 17 | |
| β-strand | 322 | 1 | 1 |
| β-strand | 330 | 1 | 1 |
| α-helix | 332-351 | 20 | |
| α-helix | 355-357 | 3 | |
| α-helix | 358-363 | 6 | |
| α-helix | 368-385 | 18 | |
| α-helix | 400-402 | 3 | |
| α-helix | 419-438 | 20 | |
| α-helix | 445-482 | 38 | |
| β-strand | 485-492 | 8 | 2 |
| β-strand | 497 | 1 | 2 |
| β-strand | 500-512 | 13 | 2 |
| β-strand | 515-527 | 13 | 2 |
| β-strand | 530-532 | 3 | 2 |
| β-strand | 535-542 | 8 | 2 |
| β-strand | 545-547 | 3 | 2 |
| β-strand | 550-552 | 3 | 2 |
| β-strand | 555-559 | 5 | 2 |
| α-helix | 563-565 | 3 | |
| β-strand | 566-567 | 2 | 2 |
| β-strand | 570-572 | 3 | 2 |
| β-strand | 574-577 | 4 | 2 |
| α-helix | 579-581 | 3 | |
| α-helix | 594-618 | 25 | |
| α-helix | 624-640 | 17 | |
| α-helix | 641-643 | 3 | |
| α-helix | 648-675 | 28 | |
| α-helix | 682-705 | 24 | |
| α-helix | 713-730 | 18 | |
| α-helix | 734-735 | 2 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 877-884 | 8 | 3 |
| β-strand | 887-890 | 4 | 3 |
| β-strand | 897-900 | 4 | 4 |
| β-strand | 905-906 | 2 | 3 |
| β-strand | 914-916 | 3 | 3 |
| β-strand | 924-927 | 4 | 4 |
| α-helix | 930-932 | 3 | |
| β-strand | 941-948 | 8 | 3 |
| α-helix | 950-952 | 3 | |
| α-helix | 955-957 | 3 | |
| β-strand | 962-968 | 7 | 5 |
| β-strand | 973-979 | 7 | 5 |
| β-strand | 982-988 | 7 | 5 |
| β-strand | 994-1000 | 7 | 5 |
| β-strand | 1015-1021 | 7 | 3 |
| β-strand | 1027-1031 | 5 | 3 |
| β-strand | 1034-1039 | 6 | 3 |
| α-helix | 1046-1048 | 3 | |
| β-strand | 1052-1055 | 4 | 4 |
| β-strand | 1058 | 1 | 5 |
| β-strand | 1067-1075 | 9 | 3 |
| α-helix | 1081-1091 | 11 | |
| β-strand | 1096 | 1 | 6 |
| β-strand | 1098 | 1 | 7 |
| β-strand | 1104 | 1 | 7 |
| α-helix | 1105 | 1 | |
| β-strand | 1106 | 1 | 8 |
| β-strand | 1111 | 1 | 9 |
| β-strand | 1112-1115 | 4 | 10 |
| β-strand | 1122-1125 | 4 | 9 |
| β-strand | 1134-1137 | 4 | 9 |
| β-strand | 1142-1144 | 3 | 2 |
| β-strand | 1150-1152 | 3 | 2 |
| α-helix | 1153 | 1 | |
| β-strand | 1159-1164 | 6 | 9 |
| β-strand | 1173 | 1 | 8 |
| β-strand | 1175 | 1 | 6 |
| β-strand | 1179-1186 | 8 | 9 |
| β-strand | 1189-1194 | 6 | 9 |
| β-strand | 1195 | 1 | 11 |
| β-strand | 1204-1205 | 2 | 9 |
| β-strand | 1207-1209 | 3 | 9 |
| β-strand | 1218 | 1 | 11 |
| β-strand | 1221-1226 | 6 | 9 |
| β-strand | 1232-1234 | 3 | 9 |
| β-strand | 1235 | 1 | 10 |
| β-strand | 1236-1240 | 5 | 9 |
| β-strand | 1246-1255 | 10 | 9 |
| β-strand | 1258-1264 | 7 | 9 |
| α-helix | 1266-1272 | 7 | |
| β-strand | 1282-1285 | 4 | 10 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Synaptic vesicle glycoprotein 2A | A | protein | 750 | Homo sapiens | Q7L0J3 (AlphaFold model) |
| Botulinum neurotoxin | B | protein | 426 | Clostridium botulinum | Q45894 (AlphaFold model) |
>8JS8_1 Synaptic vesicle glycoprotein 2A (chains A) MDYKDDDDKEEGFRDRAAFIRGAKDIAKEVKKHAAKKVVKGLDRVQDEYSRRSYSRFEEE DDDDDFPAPSDGYYRGEGTQDEEEGGASSDATEGHDEDDEIYEGEYQGIPRAESGGKGER MADGAPLAGVRGGLSDGEGPPGGRGEAQRRKEREELAQQYEAILRECGHGRFQWTLYFVL GLALMADGVEVFVVGFVLPSAEKDMCLSDSNKGMLGLIVYLGMMVGAFLWGGLADRLGRR QCLLISLSVNSVFAFFSSFVQGYGTFLFCRLLSGVGIGGSIPIVFSYFSEFLAQEKRGEH LSWLCMFWMIGGVYAAAMAWAIIPHYGWSFQMGSAYQFHSWRVFVLVCAFPSVFAIGALT TQPESPRFFLENGKHDEAWMVLKQVHDTNMRAKGHPERVFSVTHIKTIHQEDELIEIQSD TGTWYQRWGVRALSLGGQVWGNFLSCFGPEYRRITLMMMGVWFTMSFSYYGLTVWFPDMI RHLQAVDYASRTKVFPGERVEHVTFNFTLENQIHRGGQYFNDKFIGLRLKSVSFEDSLFE ECYFEDVTSSNTFFRNCTFINTVFYNTDLFEYKFVNSRLINSTFLHNKEGCPLDVTGTGE GAYMVYFVSFLGTLAVLPGNIVSALLMDKIGRLRMLAGSSVMSCVSCFFLSFGNSESAMI ALLCLFGGVSIASWNALDVLTVELYPSDKRTTAFGFLNALCKLAAVLGISIFTSFVGITK AAPILFASAALALGSSLALKLPETRGQVLQ
>8JS8_2 Botulinum neurotoxin (chains B) KNIVNTSILSIVYKKDDLIDLSRYGAKINIGDRVYYDSIDKNQIKLINLESSTIEVILKN AIVYNSMYENFSTSFWIKIPKYFSKINLNNEYTIINCIENNSGWKVSLNYGEIIWTLQDN KQNIQRVVFKYSQMVNISDYINRWIFVTITNNRLTKSKIYINGRLIDQKPISNLGNIHAS NKIMFKLDGCRDPRRYIMIKYFNLFDKELNEKEIKDLYDSQSNSGILKDFWGNYLQYDKP YYMLNLFDPNKYVDVNNIGIRGYMYLKGPRGSVVTTNIYLNSTLYEGTKFIIKKYASGNE DNIVRNNDRVYINVVVKNKEYRLATNASQAGVEKILSALEIPDVGNLSQVVVMKSKDDQG IRNKCKMNLQDNNGNDIGFIGFHLYDNIAKLVASNWYNRQVGKASRTFGCSWEFIPVDDG WGESSL
| ID | Name | Formula | Copies |
|---|---|---|---|
| UKX | (2S)-2-(2-oxidanylidenepyrrolidin-1-yl)butanamide | C8 H14 N2 O2 | 1 |
| 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:
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