8JLI: SV2A dimer in complex levetiracetam

Cryo-EM structure of SV2A dimer in complex levetiracetam. Determined by electron microscopy at 3.38 Å resolution. Released 1 May 2024.

Method
Electron microscopy
Resolution
3.38 Å
Organism
Homo sapiens
Chains
2
Atoms
9,248
Mol. weight
167.89 kDa
Ligands
UKX
Released
1 May 2024

Explore 8JLI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8JLI contains 51 α-helices and 24 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.

Chain A: 25 helices, 12 β-strands

ElementResiduesLengthSheet
α-helix138-15922
α-helix163-18220
α-helix185-19713
α-helix206-22924
α-helix231-25121
α-helix256-27015
α-helix272-2809
α-helix281-2833
α-helix289-2946
α-helix295-2973
α-helix298-31417
β-strand322-32321
β-strand329-33021
α-helix332-35120
α-helix355-3573
α-helix358-3636
α-helix368-38518
α-helix422-43817
α-helix445-48137
β-strand485-496122
β-strand500-527282
β-strand530-53232
β-strand535-54282
β-strand545-54732
β-strand550-55232
β-strand555-55952
α-helix563-5653
β-strand566-56722
β-strand570-57232
β-strand575-57732
α-helix579-5813
α-helix593-62230
α-helix624-64118
α-helix648-67528
α-helix682-70423
α-helix713-73018
α-helix734-7352
Chain B: 26 helices, 12 β-strands
ElementResiduesLengthSheet
α-helix138-15922
α-helix163-18220
α-helix185-19713
α-helix209-22921
α-helix231-25121
α-helix256-27015
α-helix272-2809
α-helix281-2833
α-helix289-2946
α-helix295-2973
α-helix298-31417
β-strand322-32323
β-strand329-33023
α-helix332-35120
α-helix355-3573
α-helix358-3636
α-helix368-38518
α-helix422-43817
α-helix445-48238
β-strand485-496124
β-strand500-527284
β-strand530-53234
β-strand535-54284
β-strand545-54734
β-strand550-55234
β-strand555-55954
α-helix563-5653
β-strand566-56724
β-strand570-57234
β-strand575-57734
α-helix579-5813
α-helix593-62230
α-helix624-64118
α-helix642-6443
α-helix648-67528
α-helix682-70423
α-helix713-73018
α-helix734-7352

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Synaptic vesicle glycoprotein 2AA, Bprotein750Homo sapiensQ7L0J3 (AlphaFold model)
Sequence of entity 1 (A, B), FASTA
>8JLI_1 Synaptic vesicle glycoprotein 2A (chains A, B)
MDYKDDDDKEEGFRDRAAFIRGAKDIAKEVKKHAAKKVVKGLDRVQDEYSRRSYSRFEEE
DDDDDFPAPSDGYYRGEGTQDEEEGGASSDATEGHDEDDEIYEGEYQGIPRAESGGKGER
MADGAPLAGVRGGLSDGEGPPGGRGEAQRRKEREELAQQYEAILRECGHGRFQWTLYFVL
GLALMADGVEVFVVGFVLPSAEKDMCLSDSNKGMLGLIVYLGMMVGAFLWGGLADRLGRR
QCLLISLSVNSVFAFFSSFVQGYGTFLFCRLLSGVGIGGSIPIVFSYFSEFLAQEKRGEH
LSWLCMFWMIGGVYAAAMAWAIIPHYGWSFQMGSAYQFHSWRVFVLVCAFPSVFAIGALT
TQPESPRFFLENGKHDEAWMVLKQVHDTNMRAKGHPERVFSVTHIKTIHQEDELIEIQSD
TGTWYQRWGVRALSLGGQVWGNFLSCFGPEYRRITLMMMGVWFTMSFSYYGLTVWFPDMI
RHLQAVDYASRTKVFPGERVEHVTFNFTLENQIHRGGQYFNDKFIGLRLKSVSFEDSLFE
ECYFEDVTSSNTFFRNCTFINTVFYNTDLFEYKFVNSRLINSTFLHNKEGCPLDVTGTGE
GAYMVYFVSFLGTLAVLPGNIVSALLMDKIGRLRMLAGSSVMSCVSCFFLSFGNSESAMI
ALLCLFGGVSIASWNALDVLTVELYPSDKRTTAFGFLNALCKLAAVLGISIFTSFVGITK
AAPILFASAALALGSSLALKLPETRGQVLQ

Ligands and cofactors

IDNameFormulaCopies
UKX(2S)-2-(2-oxidanylidenepyrrolidin-1-yl)butanamideC8 H14 N2 O22

Primary citation

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:

Browse structure collections

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