8JLC: SV2A

Cryo-EM structure of SV2A in complex with BoNT/A2 Hc and levetiracetam. Determined by electron microscopy at 2.88 Å resolution. Released 1 May 2024.

Method: Electron microscopy
Resolution: 2.88 Å
Organisms: Homo sapiens, Clostridium botulinum
Chains: 2
Atoms: 8,189
Mol. weight: 134.41 kDa
Ligands: UKX, NAG
Released: 1 May 2024

Explore 8JLC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8JLC contains 34 α-helices and 58 β-strands across 2 chains. 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: 29 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	138-159	22
α-helix	163-182	20
α-helix	185-196	12
α-helix	204-208	5
α-helix	210-229	20
α-helix	231-251	21
α-helix	256-270	15
α-helix	272-280	9
α-helix	281-283	3
α-helix	286-288	3
α-helix	290-294	5
α-helix	295-297	3
α-helix	298-314	17
β-strand	322	1	1
β-strand	330	1	1
α-helix	332-351	20
α-helix	355-357	3
α-helix	358-363	6
α-helix	368-385	18
α-helix	400-402	3
α-helix	419-438	20
α-helix	445-482	38
β-strand	485-492	8	2
β-strand	496-497	2	2
β-strand	500-512	13	2
β-strand	515-527	13	2
β-strand	530-532	3	2
β-strand	535-542	8	2
β-strand	545-547	3	2
β-strand	550-552	3	2
β-strand	555-559	5	2
α-helix	563-565	3
β-strand	566-567	2	2
β-strand	570-572	3	2
β-strand	574-577	4	2
α-helix	579-581	3
α-helix	594-622	29
α-helix	624-640	17
α-helix	641-643	3
α-helix	648-675	28
α-helix	682-706	25
α-helix	714-730	17
α-helix	734-735	2

Chain B: 5 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	877-884	8	3
β-strand	887-890	4	3
β-strand	897-900	4	4
β-strand	905-906	2	3
β-strand	914-916	3	3
β-strand	924-927	4	4
α-helix	930-932	3
β-strand	941-948	8	3
α-helix	955-957	3
β-strand	962-966	5	5
β-strand	969	1	6
β-strand	972	1	6
β-strand	973-979	7	5
β-strand	982-988	7	5
β-strand	994-1000	7	5
β-strand	1015-1021	7	3
β-strand	1027-1031	5	3
β-strand	1034-1039	6	3
β-strand	1052-1055	4	4
β-strand	1058	1	5
β-strand	1067-1075	9	3
α-helix	1081-1091	11
β-strand	1096	1	7
β-strand	1098	1	8
β-strand	1104	1	8
β-strand	1106	1	9
β-strand	1112-1115	4	10
β-strand	1122-1124	3	11
β-strand	1135-1137	3	11
β-strand	1142-1144	3	2
β-strand	1150-1152	3	2
β-strand	1159-1164	6	11
β-strand	1173	1	9
β-strand	1175	1	7
β-strand	1179-1186	8	11
β-strand	1189-1194	6	11
β-strand	1195	1	12
β-strand	1204-1205	2	11
α-helix	1206	1
β-strand	1207-1209	3	11
β-strand	1218	1	12
β-strand	1220-1226	7	11
β-strand	1232-1234	3	11
β-strand	1235	1	10
β-strand	1236-1240	5	11
β-strand	1246-1255	10	11
β-strand	1258-1264	7	11
α-helix	1266-1272	7
β-strand	1282-1285	4	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Synaptic vesicle glycoprotein 2A	A	protein	750	Homo sapiens	Q7L0J3 (AlphaFold model)
Botulinum neurotoxin	B	protein	426	Clostridium botulinum	Q45894 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8JLC_1 Synaptic vesicle glycoprotein 2A (chains A)
MDYKDDDDKEEGFRDRAAFIRGAKDIAKEVKKHAAKKVVKGLDRVQDEYSRRSYSRFEEE
DDDDDFPAPSDGYYRGEGTQDEEEGGASSDATEGHDEDDEIYEGEYQGIPRAESGGKGER
MADGAPLAGVRGGLSDGEGPPGGRGEAQRRKEREELAQQYEAILRECGHGRFQWTLYFVL
GLALMADGVEVFVVGFVLPSAEKDMCLSDSNKGMLGLIVYLGMMVGAFLWGGLADRLGRR
QCLLISLSVNSVFAFFSSFVQGYGTFLFCRLLSGVGIGGSIPIVFSYFSEFLAQEKRGEH
LSWLCMFWMIGGVYAAAMAWAIIPHYGWSFQMGSAYQFHSWRVFVLVCAFPSVFAIGALT
TQPESPRFFLENGKHDEAWMVLKQVHDTNMRAKGHPERVFSVTHIKTIHQEDELIEIQSD
TGTWYQRWGVRALSLGGQVWGNFLSCFGPEYRRITLMMMGVWFTMSFSYYGLTVWFPDMI
RHLQAVDYASRTKVFPGERVEHVTFNFTLENQIHRGGQYFNDKFIGLRLKSVSFEDSLFE
ECYFEDVTSSNTFFRNCTFINTVFYNTDLFEYKFVNSRLINSTFLHNKEGCPLDVTGTGE
GAYMVYFVSFLGTLAVLPGNIVSALLMDKIGRLRMLAGSSVMSCVSCFFLSFGNSESAMI
ALLCLFGGVSIASWNALDVLTVELYPSDKRTTAFGFLNALCKLAAVLGISIFTSFVGITK
AAPILFASAALALGSSLALKLPETRGQVLQ

Sequence of entity 2 (B), FASTA

>8JLC_2 Botulinum neurotoxin (chains B)
KNIVNTSILSIVYKKDDLIDLSRYGAKINIGDRVYYDSIDKNQIKLINLESSTIEVILKN
AIVYNSMYENFSTSFWIKIPKYFSKINLNNEYTIINCIENNSGWKVSLNYGEIIWTLQDN
KQNIQRVVFKYSQMVNISDYINRWIFVTITNNRLTKSKIYINGRLIDQKPISNLGNIHAS
NKIMFKLDGCRDPRRYIMIKYFNLFDKELNEKEIKDLYDSQSNSGILKDFWGNYLQYDKP
YYMLNLFDPNKYVDVNNIGIRGYMYLKGPRGSVVTTNIYLNSTLYEGTKFIIKKYASGNE
DNIVRNNDRVYINVVVKNKEYRLATNASQAGVEKILSALEIPDVGNLSQVVVMKSKDDQG
IRNKCKMNLQDNNGNDIGFIGFHLYDNIAKLVASNWYNRQVGKASRTFGCSWEFIPVDDG
WGESSL

Ligands and cofactors

ID	Name	Formula	Copies
UKX	(2S)-2-(2-oxidanylidenepyrrolidin-1-yl)butanamide	C8 H14 N2 O2	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

Structural basis for antiepileptic drugs and botulinum neurotoxin recognition of SV2A. Yamagata, A., Ito, K., Suzuki, T. et al. Nat Commun (2024) 15:3027-3027. DOI 10.1038/s41467-024-47322-4 · 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
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

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