9PC9: Synaptic Vesicle Protein 2A

Structure of Synaptic Vesicle Protein 2A Bound to UCB7361. Determined by electron microscopy at 2.91 Å resolution. Released 10 Sept 2025.

Method: Electron microscopy
Resolution: 2.91 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,336
Mol. weight: 83.21 kDa
Ligands: A1CHN
Released: 10 Sept 2025

Explore 9PC9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9PC9 contains 22 α-helices and 2 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: 22 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	146-159	14
α-helix	163-184	22
α-helix	185-189	5
α-helix	206-209	4
α-helix	210-229	20
α-helix	231-251	21
α-helix	255-270	16
α-helix	272-281	10
α-helix	289-296	8
α-helix	298-314	17
α-helix	332-351	20
α-helix	358-364	7
α-helix	367-381	15
α-helix	422-437	16
β-strand	440	1	1
β-strand	443	1	1
α-helix	444-481	38
α-helix	595-622	28
α-helix	625-641	17
α-helix	642-644	3
α-helix	648-676	29
α-helix	682-707	26
α-helix	713-732	20
α-helix	734-735	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Synaptic vesicle glycoprotein 2A	A	protein	742	Homo sapiens	Q7L0J3 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9PC9_1 Synaptic vesicle glycoprotein 2A (chains A)
MEEGFRDRAAFIRGAKDIAKEVKKHAAKKVVKGLDRVQDEYSRRSYSRFEEEDDDDDFPA
PSDGYYRGEGTQDEEEGGASSDATEGHDEDDEIYEGEYQGIPRAESGGKGERMADGAPLA
GVRGGLSDGEGPPGGRGEAQRRKEREELAQQYEAILRECGHGRFQWTLYFVLGLALMADG
VEVFVVGFVLPSAEKDMCLSDSNKGMLGLIVYLGMMVGAFLWGGLADRLGRRQCLLISLS
VNSVFAFFSSFVQGYGTFLFCRLLSGVGIGGSIPIVFSYFSEFLAQEKRGEHLSWLCMFW
MIGGVYAAAMAWAIIPHYGWSFQMGSAYQFHSWRVFVLVCAFPSVFAIGALTTQPESPRF
FLENGKHDEAWMVLKQVHDTNMRAKGHPERVFSVTHIKTIHQEDELIEIQSDTGTWYQRW
GVRALSLGGQVWGNFLSCFGPEYRRITLMMMGVWFTMSFSYYGLTVWFPDMIRHLQAVDY
ASRTKVFPGERVEHVTFNFTLENQIHRGGQYFNDKFIGLRLKSVSFEDSLFEECYFEDVT
SSNTFFRNCTFINTVFYNTDLFEYKFVNSRLINSTFLHNKEGCPLDVTGTGEGAYMVYFV
SFLGTLAVLPGNIVSALLMDKIGRLRMLAGSSVMSCVSCFFLSFGNSESAMIALLCLFGG
VSIASWNALDVLTVELYPSDKRTTAFGFLNALCKLAAVLGISIFTSFVGITKAAPILFAS
AALALGSSLALKLPETRGQVLQ

Ligands and cofactors

ID	Name	Formula	Copies
A1CHN	(4S)-1-{[(4S)-2-(methoxymethyl)-6-(trifluoromethyl)imidazo[2,1-b][1,3,4]thiadia…	C15 H16 F6 N4 O2 S	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
8JLF 3.01 Å, Cryo-EM structure of SV2A in complex with BoNT/A2 Hc

Browse structure collections

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