5MOY: BoNT/A2 receptor-binding domain

Crystal structure of the BoNT/A2 receptor-binding domain in complex with the luminal domain of its neuronal receptor SV2C. Determined by X-ray diffraction at 2.3 Å resolution. Released 15 Mar 2017.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: Clostridium botulinum, Homo sapiens
Chains: 2
Atoms: 4,346
Mol. weight: 66.06 kDa
Ligands: 2PE
Released: 15 Mar 2017

Explore 5MOY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5MOY contains 9 α-helices and 56 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: 7 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	877-880	4	1
β-strand	881-883	3	2
β-strand	888-890	3	2
β-strand	897-900	4	3
β-strand	904-906	3	1
β-strand	914-917	4	1
β-strand	924-927	4	3
α-helix	930-932	3
β-strand	935-936	2	4
β-strand	941-948	8	1
α-helix	950-952	3
α-helix	955-957	3
β-strand	962-969	8	3
β-strand	972-979	8	3
β-strand	982-988	7	3
β-strand	994-1000	7	3
β-strand	1015-1021	7	1
β-strand	1026-1031	6	1
β-strand	1034-1040	7	1
β-strand	1047-1048	2	4
β-strand	1052-1058	7	3
β-strand	1066-1075	10	1
α-helix	1081-1090	10
β-strand	1096	1	5
β-strand	1098	1	6
β-strand	1104	1	6
α-helix	1105	1
β-strand	1106	1	7
β-strand	1111	1	8
β-strand	1112-1115	4	9
β-strand	1122-1125	4	8
β-strand	1134-1137	4	8
β-strand	1142-1145	4	10
β-strand	1149-1152	4	10
β-strand	1160-1164	5	8
β-strand	1173	1	7
β-strand	1175	1	5
β-strand	1179-1186	8	8
β-strand	1189-1194	6	8
β-strand	1195	1	11
β-strand	1204-1205	2	8
β-strand	1207-1209	3	8
α-helix	1212-1214	3
β-strand	1218	1	11
β-strand	1220-1223	4	8
β-strand	1237-1240	4	8
β-strand	1246-1255	10	8
β-strand	1258-1264	7	8
α-helix	1265-1272	8
β-strand	1282-1285	4	9

Chain B: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	474-475	2
β-strand	476-483	8	10
β-strand	488-493	6	12
β-strand	495-503	9	10
β-strand	506-513	8	12
β-strand	516-518	3	10
β-strand	521-525	5	10
β-strand	526-528	3	12
β-strand	531-533	3	12
β-strand	536-538	3	10
β-strand	541-545	5	10
α-helix	549-551	3
β-strand	552-553	2	12
β-strand	556-558	3	10
β-strand	560-563	4	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Botulinum neurotoxin type A	A	protein	428	Clostridium botulinum	Q45894 (AlphaFold model)
Synaptic vesicle glycoprotein 2C	B	protein	136	Homo sapiens	Q496J9 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5MOY_1 Botulinum neurotoxin type A (chains A)
GSKNIVNTSILSIVYKKDDLIDLSRYGAKINIGDRVYYDSIDKNQIKLINLESSTIEVIL
KNAIVYNSMYENFSTSFWIKIPKYFSKINLNNEYTIINCIENNSGWKVSLNYGEIIWTLQ
DNKQNIQRVVFKYSQMVNISDYINRWIFVTITNNRLTKSKIYINGRLIDQKPISNLGNIH
ASNKIMFKLDGCRDPRRYIMIKYFNLFDKELNEKEIKDLYDSQSNSGILKDFWGNYLQYD
KPYYMLNLFDPNKYVDVNNIGIRGYMYLKGPRGSVVTTNIYLNSTLYEGTKFIIKKYASG
NEDNIVRNNDRVYINVVVKNKEYRLATNASQAGVEKILSALEIPDVGNLSQVVVMKSKDD
QGIRNKCKMNLQDNNGNDIGFIGFHLYDNIAKLVASNWYNRQVGKASRTFGCSWEFIPVD
DGWGESSL

Sequence of entity 2 (B), FASTA

>5MOY_2 Synaptic vesicle glycoprotein 2C (chains B)
MKKHHHHHHGSLVPRGSDVIKPLQSDEYALLTRNVERDKYANFTINFTMENQIHTGMEYD
NGRFIGVKFKSVTFKDSVFKSCTFEDVTSVNTYFKNCTFIDTVFDNTDFEPYKFIDSEFK
NCSFFHNKTGCQITFD

Ligands and cofactors

ID	Name	Formula	Copies
2PE	Nonaethylene glycol	C18 H38 O10	1

Water and common crystallization additives (EDO) are not listed.

Primary citation

Crystal structure of the BoNT/A2 receptor-binding domain in complex with the luminal domain of its neuronal receptor SV2C. Benoit, R.M., Scharer, M.A., Wieser, M.M. et al. Sci Rep (2017) 7:43588-43588. DOI 10.1038/srep43588 · PubMed

Other PDB entries of the same protein (UniProt Q45894 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6F0O 1.6 Å, Botulinum neurotoxin A3 Hc domain
1E1H 1.8 Å, Crystal Structure of recombinant Botulinum Neurotoxin Type A Light Chain,…
2G7N 1.9 Å, Structure of the Light Chain of Botulinum Neurotoxin Serotype A Bound to small Molecule…
6ES1 2.0 Å, Crystal structure of the binding domain from botulinum neurotoxin A2 bound to…
2G7P 2.3 Å, Structure of the Light Chain of Botulinum Neurotoxin Serotype A Bound to Small Molecule…
2G7Q 2.41 Å, Structure of the Light Chain of Botulinum Neurotoxin Serotype A Bound to Small Molecule…
2G7K 2.8 Å, Structure of the Light Chain of Botulinum Neurotoxin, Serotype A Bound to small Molecule…
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

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