9NTC: Synaptic Vesicle Protein 2A

Structure of Synaptic Vesicle Protein 2A Bound to Brivaracetam and UCB1244283. Determined by electron microscopy at 3.05 Å resolution. Released 10 Sept 2025.

Method: Electron microscopy
Resolution: 3.05 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,372
Mol. weight: 77.54 kDa
Ligands: A1B1J, VLX, CLR, A1B1I
Released: 10 Sept 2025

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

Secondary structure: helices and β-sheets

9NTC contains 23 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: 23 helices, 0 β-strands

Element	Residues	Length
α-helix	143-159	17
α-helix	164-188	25
α-helix	207-209	3
α-helix	210-229	20
α-helix	231-248	18
α-helix	258-270	13
α-helix	272-280	9
α-helix	281-283	3
α-helix	286-294	9
α-helix	297-314	18
α-helix	333-339	7
α-helix	342-351	10
α-helix	355-357	3
α-helix	358-363	6
α-helix	368-383	16
α-helix	426-437	12
α-helix	444-482	39
α-helix	594-622	29
α-helix	624-641	18
α-helix	642-644	3
α-helix	648-675	28
α-helix	682-706	25
α-helix	714-730	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Synaptic vesicle glycoprotein 2A	A	protein	686	Homo sapiens	Q7L0J3 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9NTC_1 Synaptic vesicle glycoprotein 2A (chains A)
MGYYRGEGTQDEEEGGASSDATEGHDEDDEIYEGEYQGIPRAESGGKGERMADGAPLAGV
RGGLSDGEGPPGGRGEAQRRKEREELAQQYEAILRECGHGRFQWTLYFVLGLALMADGVE
VFVVGFVLPSAEKDMCLSDSNKGMLGLIVYLGMMVGAFLWGGLADRLGRRQCLLISLSVN
SVFAFFSSFVQGYGTFLFCRLLSGVGIGGSIPIVFSYFSEFLAQEKRGEHLSWLCMFWMI
GGVYAAAMAWAIIPHYGWSFQMGSAYQFHSWRVFVLVCAFPSVFAIGALTTQPESPRFFL
ENGKHDEAWMVLKQVHDTNMRAKGHPERVFSVTHIKTIHQEDELIEIQSDTGTWYQRWGV
RALSLGGQVWGNFLSCFGPEYRRITLMMMGVWFTMSFSYYGLTVWFPDMIRHLQAVDYAS
RTKVFPGERVEHVTFNFTLENQIHRGGQYFNDKFIGLRLKSVSFEDSLFEECYFEDVTSS
NTFFRNCTFINTVFYNTDLFEYKFVNSRLINSTFLHNKEGCPLDVTGTGEGAYMVYFVSF
LGTLAVLPGNIVSALLMDKIGRLRMLAGSSVMSCVSCFFLSFGNSESAMIALLCLFGGVS
IASWNALDVLTVELYPSDKRTTAFGFLNALCKLAAVLGISIFTSFVGITKAAPILFASAA
LALGSSLALKLPETRGQVLQLEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
A1B1J	(3R)-4-(3,5-dimethylphenyl)-N-(2-methoxyphenyl)-3-methylbutanamide	C20 H25 N O2	1
VLX	(2S)-2-[(4R)-2-oxidanylidene-4-propyl-pyrrolidin-1-yl]butanamide	C11 H20 N2 O2	1
CLR	Cholesterol	C27 H46 O	1
A1B1I	(3S)-4-(3,5-dimethylphenyl)-N-(2-methoxyphenyl)-3-methylbutanamide	C20 H25 N O2	1

Primary citation

Mechanisms underlying allosteric modulation of antiseizure medication binding to synaptic vesicle protein 2A (SV2A). Mittal, A., Martin, M.F., Provins, L. et al. Proc Natl Acad Sci U S A (2025) 122:e2510239122-e2510239122. DOI 10.1073/pnas.2510239122 · 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

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