8JLH: SV2A dimer

Cryo-EM structure of SV2A dimer in complex with BoNT/A2 Hc and levetiracetam. Determined by electron microscopy at 2.9 Å resolution. Released 1 May 2024.

Method: Electron microscopy
Resolution: 2.9 Å
Organisms: Homo sapiens, Clostridium botulinum
Chains: 4
Atoms: 12,610
Mol. weight: 268.66 kDa
Ligands: UKX, NAG
Released: 1 May 2024

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

Secondary structure: helices and β-sheets

8JLH contains 39 α-helices and 109 β-strands across 4 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: 27 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	138-159	22
α-helix	163-182	20
α-helix	185-197	13
α-helix	204-229	26
α-helix	231-251	21
α-helix	256-270	15
α-helix	272-280	9
α-helix	281-283	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	485-493	9	2
β-strand	496-497	2	3
β-strand	500-512	13	2
β-strand	515-517	3	3
β-strand	520-527	8	2
β-strand	530-532	3	2
β-strand	535-537	3	3
β-strand	540-542	3	2
β-strand	545-547	3	2
β-strand	550-552	3	2
β-strand	555-557	3	3
α-helix	563-565	3
β-strand	566-567	2	2
β-strand	570-572	3	2
β-strand	574-577	4	3
α-helix	579-581	3
α-helix	592-618	27
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: 3 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	877-884	8	4
β-strand	887-890	4	4
β-strand	897-900	4	5
β-strand	905-906	2	4
β-strand	913-916	4	4
β-strand	924-927	4	5
β-strand	941-948	8	4
α-helix	955-957	3
β-strand	962-968	7	6
β-strand	973-979	7	6
β-strand	982-988	7	6
β-strand	994-1000	7	6
β-strand	1015-1021	7	4
β-strand	1027-1031	5	4
β-strand	1034-1039	6	4
β-strand	1052-1055	4	5
β-strand	1058	1	6
β-strand	1067-1075	9	4
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	1111-1115	5	10
β-strand	1122-1125	4	10
β-strand	1134-1137	4	10
β-strand	1142-1145	4	3
β-strand	1149-1152	4	3
β-strand	1159-1164	6	10
β-strand	1173	1	9
β-strand	1175	1	7
β-strand	1178-1186	9	10
β-strand	1189-1195	7	10
β-strand	1204-1209	6	10
β-strand	1218	1	10
β-strand	1220-1226	7	10
β-strand	1232-1240	9	10
β-strand	1246-1255	10	10
β-strand	1258-1264	7	10
α-helix	1266-1272	7
β-strand	1282-1285	4	10

Chain C: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	478-482	5
β-strand	485-488	4	11
β-strand	491-493	3	2
β-strand	496-497	2	12
β-strand	500-507	8	11
β-strand	510-512	3	2
β-strand	515-517	3	12
β-strand	520-527	8	11
β-strand	530-532	3	2
β-strand	535-537	3	12
β-strand	540-542	3	11
β-strand	545-547	3	11
β-strand	550-552	3	2
β-strand	555-557	3	12
α-helix	563-565	3
β-strand	566-567	2	11
β-strand	570-572	3	2
β-strand	574-577	4	12
α-helix	579-581	3

Chain D: 6 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	877-884	8	13
β-strand	887-890	4	13
β-strand	897-900	4	14
β-strand	905-906	2	13
β-strand	914-917	4	13
β-strand	924-927	4	14
α-helix	930-932	3
β-strand	941-948	8	13
α-helix	955-957	3
β-strand	962-968	7	14
β-strand	973-979	7	14
β-strand	982-988	7	14
β-strand	994-1000	7	14
β-strand	1015-1021	7	13
β-strand	1027-1031	5	13
β-strand	1034-1039	6	13
β-strand	1052-1058	7	14
β-strand	1066-1075	10	13
α-helix	1081-1091	11
β-strand	1096	1	15
β-strand	1098	1	16
β-strand	1104	1	16
β-strand	1106	1	17
β-strand	1112-1115	4	18
β-strand	1122-1125	4	19
β-strand	1134-1137	4	19
β-strand	1142-1144	3	12
β-strand	1150-1152	3	12
β-strand	1159-1164	6	19
β-strand	1173	1	17
β-strand	1175	1	15
β-strand	1179-1186	8	19
β-strand	1189-1194	6	19
β-strand	1195	1	20
β-strand	1204-1205	2	19
α-helix	1206	1
β-strand	1207-1209	3	19
α-helix	1211-1214	4
β-strand	1218	1	20
β-strand	1221-1226	6	19
β-strand	1232-1240	9	19
β-strand	1246-1255	10	19
β-strand	1258-1264	7	19
α-helix	1266-1272	7
β-strand	1282-1285	4	18

Molecules and chains

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

Sequence of entity 1 (A, C), FASTA

>8JLH_1 Synaptic vesicle glycoprotein 2A (chains A, C)
MDYKDDDDKEEGFRDRAAFIRGAKDIAKEVKKHAAKKVVKGLDRVQDEYSRRSYSRFEEE
DDDDDFPAPSDGYYRGEGTQDEEEGGASSDATEGHDEDDEIYEGEYQGIPRAESGGKGER
MADGAPLAGVRGGLSDGEGPPGGRGEAQRRKEREELAQQYEAILRECGHGRFQWTLYFVL
GLALMADGVEVFVVGFVLPSAEKDMCLSDSNKGMLGLIVYLGMMVGAFLWGGLADRLGRR
QCLLISLSVNSVFAFFSSFVQGYGTFLFCRLLSGVGIGGSIPIVFSYFSEFLAQEKRGEH
LSWLCMFWMIGGVYAAAMAWAIIPHYGWSFQMGSAYQFHSWRVFVLVCAFPSVFAIGALT
TQPESPRFFLENGKHDEAWMVLKQVHDTNMRAKGHPERVFSVTHIKTIHQEDELIEIQSD
TGTWYQRWGVRALSLGGQVWGNFLSCFGPEYRRITLMMMGVWFTMSFSYYGLTVWFPDMI
RHLQAVDYASRTKVFPGERVEHVTFNFTLENQIHRGGQYFNDKFIGLRLKSVSFEDSLFE
ECYFEDVTSSNTFFRNCTFINTVFYNTDLFEYKFVNSRLINSTFLHNKEGCPLDVTGTGE
GAYMVYFVSFLGTLAVLPGNIVSALLMDKIGRLRMLAGSSVMSCVSCFFLSFGNSESAMI
ALLCLFGGVSIASWNALDVLTVELYPSDKRTTAFGFLNALCKLAAVLGISIFTSFVGITK
AAPILFASAALALGSSLALKLPETRGQVLQ

Sequence of entity 2 (B, D), FASTA

>8JLH_2 Botulinum neurotoxin (chains B, D)
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	4

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
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
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

About this viewer

MolViewer shows 8JLH 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.