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Open data
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Basic information
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Title | Cryo-EM structure of SV2A dimer in complex levetiracetam | |||||||||
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![]() | Synaptic vesicle / epilepsy / TRANSPORT PROTEIN | |||||||||
Function / homology | ![]() regulation of gamma-aminobutyric acid secretion / Toxicity of botulinum toxin type F (botF) / Toxicity of botulinum toxin type D (botD) / Toxicity of botulinum toxin type E (botE) / Toxicity of botulinum toxin type A (botA) / synaptic vesicle priming / presynaptic active zone / transmembrane transporter activity / GABA-ergic synapse / neuromuscular junction ...regulation of gamma-aminobutyric acid secretion / Toxicity of botulinum toxin type F (botF) / Toxicity of botulinum toxin type D (botD) / Toxicity of botulinum toxin type E (botE) / Toxicity of botulinum toxin type A (botA) / synaptic vesicle priming / presynaptic active zone / transmembrane transporter activity / GABA-ergic synapse / neuromuscular junction / synaptic vesicle membrane / intracellular calcium ion homeostasis / cell-cell junction / synaptic vesicle / neuron projection / neuronal cell body / glutamatergic synapse / dendrite / protein kinase binding / endoplasmic reticulum / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.38 Å | |||||||||
![]() | Yamagata A | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for antiepileptic drugs and botulinum neurotoxin recognition of SV2A. Authors: Atsushi Yamagata / Kaori Ito / Takehiro Suzuki / Naoshi Dohmae / Tohru Terada / Mikako Shirouzu / ![]() Abstract: More than one percent of people have epilepsy worldwide. Levetiracetam (LEV) is a successful new-generation antiepileptic drug (AED), and its derivative, brivaracetam (BRV), shows improved efficacy. ...More than one percent of people have epilepsy worldwide. Levetiracetam (LEV) is a successful new-generation antiepileptic drug (AED), and its derivative, brivaracetam (BRV), shows improved efficacy. Synaptic vesicle glycoprotein 2a (SV2A), a putative membrane transporter in the synaptic vesicles (SVs), has been identified as a target of LEV and BRV. SV2A also serves as a receptor for botulinum neurotoxin (BoNT), which is the most toxic protein and has paradoxically emerged as a potent reagent for therapeutic and cosmetic applications. Nevertheless, no structural analysis on AEDs and BoNT recognition by full-length SV2A has been available. Here we describe the cryo-electron microscopy structures of the full-length SV2A in complex with the BoNT receptor-binding domain, BoNT/A2 H and either LEV or BRV. The large fourth luminal domain of SV2A binds to BoNT/A2 H through protein-protein and protein-glycan interactions. LEV and BRV occupy the putative substrate-binding site in an outward-open conformation. A propyl group in BRV creates additional contacts with SV2A, explaining its higher binding affinity than that of LEV, which was further supported by label-free spectral shift assay. Numerous LEV derivatives have been developed as AEDs and positron emission tomography (PET) tracers for neuroimaging. Our work provides a structural framework for AEDs and BoNT recognition of SV2A and a blueprint for the rational design of additional AEDs and PET tracers. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
Map data | ![]() | 167.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.5 KB 15.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.9 KB | Display | ![]() |
Images | ![]() | 48.7 KB | ||
Masks | ![]() | 178 MB | ![]() | |
Filedesc metadata | ![]() | 6 KB | ||
Others | ![]() ![]() | 165.3 MB 165.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8jliMC ![]() 8jlcC ![]() 8jleC ![]() 8jlfC ![]() 8jlgC ![]() 8jlhC ![]() 8js8C ![]() 8js9C ![]() 8k77C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Half map: #2
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Sample components
-Entire : SV2A dimer in complex with anti-epileptic drug, levetiracetam
Entire | Name: SV2A dimer in complex with anti-epileptic drug, levetiracetam |
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Components |
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-Supramolecule #1: SV2A dimer in complex with anti-epileptic drug, levetiracetam
Supramolecule | Name: SV2A dimer in complex with anti-epileptic drug, levetiracetam type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Synaptic vesicle glycoprotein 2A
Macromolecule | Name: Synaptic vesicle glycoprotein 2A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 83.774008 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MDYKDDDDKE EGFRDRAAFI RGAKDIAKEV KKHAAKKVVK GLDRVQDEYS RRSYSRFEEE DDDDDFPAPS DGYYRGEGTQ DEEEGGASS DATEGHDEDD EIYEGEYQGI PRAESGGKGE RMADGAPLAG VRGGLSDGEG PPGGRGEAQR RKEREELAQQ Y EAILRECG ...String: MDYKDDDDKE EGFRDRAAFI RGAKDIAKEV KKHAAKKVVK GLDRVQDEYS RRSYSRFEEE DDDDDFPAPS DGYYRGEGTQ DEEEGGASS DATEGHDEDD EIYEGEYQGI PRAESGGKGE RMADGAPLAG VRGGLSDGEG PPGGRGEAQR RKEREELAQQ Y EAILRECG HGRFQWTLYF VLGLALMADG VEVFVVGFVL PSAEKDMCLS DSNKGMLGLI VYLGMMVGAF LWGGLADRLG RR QCLLISL SVNSVFAFFS SFVQGYGTFL FCRLLSGVGI GGSIPIVFSY FSEFLAQEKR GEHLSWLCMF WMIGGVYAAA MAW AIIPHY GWSFQMGSAY QFHSWRVFVL VCAFPSVFAI GALTTQPESP RFFLENGKHD EAWMVLKQVH DTNMRAKGHP ERVF SVTHI KTIHQEDELI EIQSDTGTWY QRWGVRALSL GGQVWGNFLS CFGPEYRRIT LMMMGVWFTM SFSYYGLTVW FPDMI RHLQ AVDYASRTKV FPGERVEHVT FNFTLENQIH RGGQYFNDKF IGLRLKSVSF EDSLFEECYF EDVTSSNTFF RNCTFI NTV FYNTDLFEYK FVNSRLINST FLHNKEGCPL DVTGTGEGAY MVYFVSFLGT LAVLPGNIVS ALLMDKIGRL RMLAGSS VM SCVSCFFLSF GNSESAMIAL LCLFGGVSIA SWNALDVLTV ELYPSDKRTT AFGFLNALCK LAAVLGISIF TSFVGITK A APILFASAAL ALGSSLALKL PETRGQVLQ UniProtKB: Synaptic vesicle glycoprotein 2A |
-Macromolecule #2: (2S)-2-(2-oxidanylidenepyrrolidin-1-yl)butanamide
Macromolecule | Name: (2S)-2-(2-oxidanylidenepyrrolidin-1-yl)butanamide / type: ligand / ID: 2 / Number of copies: 2 / Formula: UKX |
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Molecular weight | Theoretical: 170.209 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 Details: 20 mM Hepes (pH7.5), 150 mM NaCl, 0.001% LMNG, 0.0002% cholesterol hemisuccinate |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 297 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 10001 / Average electron dose: 50.2 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |