8JLE

Cryo-EM structure of SV2A LD4 in complex with BoNT/A2 Hc in the SV2A-levetiracetam-BoNT/A2 Hc complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.82 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for antiepileptic drugs and botulinum neurotoxin recognition of SV2A.

Yamagata, A.Ito, K.Suzuki, T.Dohmae, N.Terada, T.Shirouzu, M.

(2024) Nat Commun 15: 3027-3027

  • DOI: https://doi.org/10.1038/s41467-024-47322-4
  • Primary Citation of Related Structures:  
    8JLC, 8JLE, 8JLF, 8JLG, 8JLH, 8JLI, 8JS8, 8JS9, 8K77

  • PubMed 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. 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 C, and either LEV or BRV. The large fourth luminal domain of SV2A binds to BoNT/A2 H C 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.


  • Organizational Affiliation

    Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan. atsushi.yamagata@riken.jp.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Synaptic vesicle glycoprotein 2A108Homo sapiensMutation(s): 0 
Gene Names: SV2A
UniProt & NIH Common Fund Data Resources
Find proteins for Q7L0J3 (Homo sapiens)
Explore Q7L0J3 
Go to UniProtKB:  Q7L0J3
PHAROS:  Q7L0J3
GTEx:  ENSG00000159164 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7L0J3
Glycosylation
Glycosylation Sites: 3Go to GlyGen: Q7L0J3-1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Botulinum neurotoxin426Clostridium botulinumMutation(s): 0 
UniProt
Find proteins for Q45894 (Clostridium botulinum (strain Kyoto / Type A2))
Explore Q45894 
Go to UniProtKB:  Q45894
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ45894
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseC [auth E]3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.82 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2024-05-01 
  • Deposition Author(s): Yamagata, A.

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP22H02564

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-01
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Database references
  • Version 1.2: 2024-10-16
    Changes: Data collection, Structure summary