246: SV2A structural pharmacology and allosteric occlusion

Pidathala S et al., Nature Communications - High-resolution cryo-EM structures of human SV2A reveal that orthosteric ligands induce an occluded MFS conformation and a secondary allosteric pocket modulates ligand binding. Key terms: SV2A, allosteric modulation, cryo-EM, levetiracetam, padsevonil.

Study Highlights:
The authors report sub-3 Å cryo-EM structures of human SV2A in the apo state and in complexes with levetiracetam, UCB-J, padsevonil, and the allosteric modulator UCB1244283. Levetiracetam and UCB-J bind the central cavity and drive inward movement of TM1 with Phe188 sealing the lumen, producing complete occlusion with levetiracetam and partial occlusion with UCB-J. UCB1244283 occupies a distinct allosteric site ~13 Å above the orthosteric pocket, reshapes the orthosteric site, lowers UCB-J Kd, increases Bmax, and slows ligand dissociation. Padsevonil binds both orthosteric and allosteric sites, precluding UCB1244283-mediated potentiation and illustrating overlapping but flexible allosteric interactions.

Conclusion:
SV2A uses orthosteric-induced occlusion combined with a secondary allosteric pocket to regulate ligand engagement, offering a structural blueprint for designing SV2A-specific modulators

Music:
Enjoy the music based on this article at the end of the episode.

Article title:
Structural pharmacology of SV2A reveals an allosteric modulation mechanism in the major facilitator superfamily

First author:
Pidathala S

Journal:
Nature Communications

DOI:
10.1038/s41467-025-65781-1

Reference:
Pidathala S., Chen X., Dai Y., Gorgulla C., Niu Y., Liu F., Lee C.-H. Structural pharmacology of SV2A reveals an allosteric modulation mechanism in the major facilitator superfamily. Nature Communications. 2025;16:10748. https://doi.org/10.1038/s41467-025-65781-1

License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

Support:
Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00

Official website https://basebybase.com

On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

Episode link: https://basebybase.com/episodes/sv2a-allosteric-occlusion

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-01-01.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited transcript sections describing SV2A mechanism, ligand-induced occlusion, orthosteric vs allosteric ligands, dual-binding Padsevonil, conditional engagement, and implications for MFS transporters; compared to the original article text.
- transcript topics: SV2A as a major facilitator superfamily transporter in brain; Cryo-EM methods and saposin nanoparticle reconstitution for SV2A; Levetiracetam and UCB-J binding to central cavity and induction of occlusion; TM1 inward movement and Phe188 sealing the central cavity; Allosteric site ~13 Å above orthosteric site; UCB1244283 mechanism; Padsevonil dual orthosteric/allosteric binding

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 7
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- SV2A is a major facilitator superfamily (MFS) transporter abundantly present in synaptic vesicles
- Sub-3 Å cryo-EM structures reported for SV2A in apo form and ligand-bound states
- Levetiracetam and UCB-J bind t...