9OKI: Human SV2A

Cryo-EM structure of human SV2A in complex with UCBJ and UCB1244283. Determined by electron microscopy at 2.67 Å resolution. Released 10 Dec 2025.

Method: Electron microscopy
Resolution: 2.67 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,779
Mol. weight: 68.45 kDa
Ligands: A1B1I, A1CCA
Released: 10 Dec 2025

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

Secondary structure: helices and β-sheets

9OKI contains 25 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: 25 helices, 0 β-strands

Element	Residues	Length
α-helix	140-159	20
α-helix	163-184	22
α-helix	185-189	5
α-helix	190-196	7
α-helix	206-229	24
α-helix	231-249	19
α-helix	255-269	15
α-helix	272-281	10
α-helix	289-294	6
α-helix	297-314	18
α-helix	333-340	8
α-helix	342-351	10
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	648-675	28
α-helix	682-705	24
α-helix	713-730	18
α-helix	734-735	2
α-helix	739-741	3

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

>9OKI_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
A1B1I	(3S)-4-(3,5-dimethylphenyl)-N-(2-methoxyphenyl)-3-methylbutanamide	C20 H25 N O2	1
A1CCA	(4R)-1-[(3-methylpyridin-4-yl)methyl]-4-(3,4,5-trifluorophenyl)pyrrolidin-2-one	C17 H15 F3 N2 O	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
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
8JLF 3.01 Å, Cryo-EM structure of SV2A in complex with BoNT/A2 Hc

Browse structure collections

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