9PRS: Human SV2A

Cryo-EM structure of human SV2A in complex with Levetiracetam and UCB1244283. Determined by electron microscopy at 3.03 Å resolution. Released 10 Dec 2025.

Method: Electron microscopy
Resolution: 3.03 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,768
Mol. weight: 68.3 kDa
Ligands: A1B1J, UKX
Released: 10 Dec 2025

Explore 9PRS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9PRS contains 24 α-helices and 0 β-strands across 1 chain. 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: 24 helices, 0 β-strands

Element	Residues	Length
α-helix	140-159	20
α-helix	163-184	22
α-helix	185-189	5
α-helix	190-195	6
α-helix	201-203	3
α-helix	206-229	24
α-helix	231-249	19
α-helix	256-269	14
α-helix	272-281	10
α-helix	289-293	5
α-helix	297-314	18
α-helix	333-351	19
α-helix	355-357	3
α-helix	358-363	6
α-helix	367-384	18
α-helix	416-437	22
α-helix	444-481	38
α-helix	594-622	29
α-helix	624-641	18
α-helix	642-644	3
α-helix	648-676	29
α-helix	682-705	24
α-helix	713-730	18
α-helix	734-735	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Synaptic vesicle glycoprotein 2A	A	protein	604	Homo sapiens	Q7L0J3 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9PRS_1 Synaptic vesicle glycoprotein 2A (chains A)
AQRRKEREELAQQYEAILRECGHGRFQWTLYFVLGLALMADGVEVFVVGFVLPSAEKDMC
LSDSNKGMLGLIVYLGMMVGAFLWGGLADRLGRRQCLLISLSVNSVFAFFSSFVQGYGTF
LFCRLLSGVGIGGSIPIVFSYFSEFLAQEKRGEHLSWLCMFWMIGGVYAAAMAWAIIPHY
GWSFQMGSAYQFHSWRVFVLVCAFPSVFAIGALTTQPESPRFFLENGKHDEAWMVLKQVH
DTNMRAKGHPERVFSVTHIKTIHQEDELIEIQSDTGTWYQRWGVRALSLGGQVWGNFLSC
FGPEYRRITLMMMGVWFTMSFSYYGLTVWFPDMIRHLQAVDYASRTKVFPGERVEHVTFN
FTLENQIHRGGQYFNDKFIGLRLKSVSFEDSLFEECYFEDVTSSNTFFRNCTFINTVFYN
TDLFEYKFVNSRLINSTFLHNKEGCPLDVTGTGEGAYMVYFVSFLGTLAVLPGNIVSALL
MDKIGRLRMLAGSSVMSCVSCFFLSFGNSESAMIALLCLFGGVSIASWNALDVLTVELYP
SDKRTTAFGFLNALCKLAAVLGISIFTSFVGITKAAPILFASAALALGSSLALKLPETRG
QVLQ

Ligands and cofactors

ID	Name	Formula	Copies
A1B1J	(3R)-4-(3,5-dimethylphenyl)-N-(2-methoxyphenyl)-3-methylbutanamide	C20 H25 N O2	1
UKX	(2S)-2-(2-oxidanylidenepyrrolidin-1-yl)butanamide	C8 H14 N2 O2	1

Primary citation

Structural pharmacology of SV2A reveals an allosteric modulation mechanism in the major facilitator superfamily. Pidathala, S., Chen, X., Dai, Y. et al. Nat Commun (2025) 16:10748-10748. DOI 10.1038/s41467-025-65781-1 · PubMed

Other PDB entries of the same protein (UniProt Q7L0J3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4V11 1.95 Å, Structure of Synaptotagmin-1 with SV2A peptide phosphorylated at Thr84
9OKH 2.39 Å, Cryo-EM structure of human SV2A in complex with UCBJ
9OKG 2.58 Å, Cryo-EM structure of human SV2A in complex with levetiracetam
9OKI 2.67 Å, Cryo-EM structure of human SV2A in complex with UCBJ and UCB1244283
9OKJ 2.68 Å, Cryo-EM structure of human SV2A in complex with padsevonil
9OKF 2.8 Å, Cryo-EM structure of human SV2A in the apo state
8JLE 2.82 Å, Cryo-EM structure of SV2A LD4 in complex with BoNT/A2 Hc in the…
8JLG 2.87 Å, Cryo-EM structure of SV2A in complex with BoNT/A2 Hc
8JLC 2.88 Å, Cryo-EM structure of SV2A in complex with BoNT/A2 Hc and levetiracetam
8JS8 2.88 Å, Cryo-EM structure of SV2A in complex with BoNT/A2 Hc and levetiracetam
8JLH 2.9 Å, Cryo-EM structure of SV2A dimer in complex with BoNT/A2 Hc and levetiracetam
9PC9 2.91 Å, Structure of Synaptic Vesicle Protein 2A Bound to UCB7361

Browse structure collections

About this viewer

MolViewer shows 9PRS directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.