4JRA: Botulinum neurotoxin a receptor-binding domain

Crystal structure of the botulinum neurotoxin a receptor-binding domain in complex with the luminal domain of SV2C. Determined by X-ray diffraction at 2.3 Å resolution. Released 20 Nov 2013.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: Clostridium botulinum, Homo sapiens
Chains: 4
Atoms: 8,408
Mol. weight: 135.68 kDa
Released: 20 Nov 2013

Explore 4JRA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4JRA contains 18 α-helices and 125 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: 8 helices, 48 β-strands

Element	Residues	Length	Sheet
β-strand	879-880	2	1
β-strand	881-884	4	2
β-strand	887-890	4	2
β-strand	897-900	4	3
β-strand	905-907	3	1
β-strand	910-917	8	1
β-strand	924-927	4	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	962-968	7	3
β-strand	973-979	7	3
β-strand	982-988	7	3
β-strand	994-1000	7	3
β-strand	1004	1	5
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	1049-1058	10	3
β-strand	1066-1075	10	1
α-helix	1081-1090	10
β-strand	1096	1	6
β-strand	1098	1	7
β-strand	1104	1	7
α-helix	1105	1
β-strand	1106	1	8
β-strand	1111	1	9
β-strand	1112-1115	4	10
β-strand	1122-1125	4	9
β-strand	1134-1137	4	9
β-strand	1142-1145	4	5
β-strand	1149-1152	4	5
α-helix	1158	1
β-strand	1159-1164	6	9
β-strand	1173	1	8
β-strand	1175	1	6
β-strand	1179-1186	8	9
β-strand	1189-1194	6	9
β-strand	1195	1	11
β-strand	1204-1205	2	9
β-strand	1207-1209	3	9
α-helix	1211-1213	3
β-strand	1218	1	11
β-strand	1221-1223	3	9
β-strand	1226	1	12
β-strand	1232	1	12
β-strand	1235	1	13
β-strand	1237-1240	4	9
β-strand	1246-1255	10	9
β-strand	1258-1264	7	9
α-helix	1267-1270	4
β-strand	1281	1	13
β-strand	1282-1285	4	10
α-helix	1293-1295	3

Chain B: 8 helices, 47 β-strands

Element	Residues	Length	Sheet
β-strand	879-884	6	14
β-strand	887-890	4	14
β-strand	897-900	4	15
β-strand	905-906	2	16
β-strand	914-917	4	16
β-strand	924-927	4	15
α-helix	928-929	2
β-strand	935-936	2	17
β-strand	941-948	8	16
α-helix	950-952	3
α-helix	955-957	3
β-strand	962-968	7	15
β-strand	973-979	7	15
β-strand	982-987	6	15
β-strand	996-1000	5	15
β-strand	1015-1021	7	16
β-strand	1026-1031	6	16
β-strand	1034-1040	7	16
β-strand	1047-1048	2	17
β-strand	1052-1058	7	15
β-strand	1066-1070	5	16
β-strand	1072-1074	3	14
β-strand	1075	1	16
α-helix	1081-1091	11
β-strand	1096	1	18
β-strand	1098	1	19
β-strand	1104	1	19
α-helix	1105	1
β-strand	1106	1	20
β-strand	1111	1	21
β-strand	1112-1115	4	22
β-strand	1122-1125	4	23
β-strand	1129	1	21
β-strand	1134-1137	4	23
β-strand	1142-1145	4	24
β-strand	1149-1152	4	24
α-helix	1158-1159	2
β-strand	1160-1164	5	21
β-strand	1173	1	20
β-strand	1175	1	18
β-strand	1179-1186	8	21
β-strand	1189-1195	7	21
β-strand	1204-1205	2	23
β-strand	1206-1209	4	21
α-helix	1211-1213	3
β-strand	1218	1	21
β-strand	1220-1223	4	21
β-strand	1235	1	25
β-strand	1237-1240	4	21
β-strand	1246-1249	4	21
β-strand	1250-1255	6	23
β-strand	1258-1263	6	23
α-helix	1265-1270	6
β-strand	1281	1	25
β-strand	1282-1285	4	22

Chain C: 1 helix, 15 β-strands

Element	Residues	Length	Sheet
β-strand	482	1	26
β-strand	487-488	2	27
β-strand	491	1	28
β-strand	496-498	3	24
β-strand	501-503	3	26
β-strand	506-508	3	27
β-strand	511	1	28
β-strand	512-513	2	29
β-strand	516-518	3	24
β-strand	521-523	3	26
β-strand	526-528	3	27
β-strand	532-533	2	29
β-strand	536-538	3	24
β-strand	541-543	3	26
α-helix	549-551	3
β-strand	557-562	6	24

Chain D: 1 helix, 15 β-strands

Element	Residues	Length	Sheet
β-strand	476-483	8	5
β-strand	486-488	3	30
β-strand	491-493	3	31
β-strand	495-503	9	5
β-strand	506-508	3	30
β-strand	511-513	3	31
β-strand	516-518	3	5
β-strand	521-523	3	5
β-strand	526-528	3	30
β-strand	531-533	3	31
β-strand	536-538	3	5
β-strand	541-543	3	5
α-helix	549-551	3
β-strand	552-553	2	31
β-strand	556-558	3	5
β-strand	560-563	4	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Botulinum neurotoxin type A	A, B	protein	443	Clostridium botulinum	P0DPI1 (AlphaFold model)
Synaptic vesicle glycoprotein 2C	C, D	protein	136	Homo sapiens	Q496J9 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4JRA_1 Botulinum neurotoxin type A (chains A, B)
MKKHHHHHHGSLVPRGSKNIINTSILNLRYESNHLIDLSRYASKINIGSKVNFDPIDKNQ
IQLFNLESSKIEVILKNAIVYNSMYENFSTSFWIRIPKYFNSISLNNEYTIINCMENNSG
WKVSLNYGEIIWTLQDTQEIKQRVVFKYSQMINISDYINRWIFVTITNNRLNNSKIYING
RLIDQKPISNLGNIHASNNIMFKLDGCRDTHRYIWIKYFNLFDKELNEKEIKDLYDNQSN
SGILKDFWGDYLQYDKPYYMLNLYDPNKYVDVNNVGIRGYMYLKGPRGSVMTTNIYLNSS
LYRGTKFIIKKYASGNKDNIVRNNDRVYINVVVKNKEYRLATNASQAGVEKILSALEIPD
VGNLSQVVVMKSKNDQGITNKCKMNLQDNNGNDIGFIGFHQFNNIAKLVASNWYNRQIER
SSRTLGCSWEFIPVDDGWGERPL

Sequence of entity 2 (C, D), FASTA

>4JRA_2 Synaptic vesicle glycoprotein 2C (chains C, D)
MKKHHHHHHGSLVPRGSDVIKPLQSDEYALLTRNVERDKYANFTINFTMENQIHTGMEYD
NGRFIGVKFKSVTFKDSVFKSCTFEDVTSVNTYFKNCTFIDTVFDNTDFEPYKFIDSEFK
NCSFFHNKTGCQITFD

Primary citation

Structural basis for recognition of synaptic vesicle protein 2C by botulinum neurotoxin A. Benoit, R.M., Frey, D., Hilbert, M. et al. Nature (2014) 505:108-111. DOI 10.1038/nature12732 · PubMed

Other PDB entries of the same protein (UniProt P0DPI1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3BON 1.2 Å, Structure of the C. botulinum neurotoxin serotype A with Zn2+ cofactor bound
4EL4 1.2 Å, Crystal structure of the catalytic domain of botulinum neurotoxin BoNT/A C134S/C165S…
3BOK 1.25 Å, Structure of the C. botulinum neurotoxin serotype A apo-enzyme
3BOO 1.4 Å, Structure of the C. botulinum neurotoxin serotype A with an inhibitory peptide bound
5MK6 1.45 Å, Crystal structure of the receptor-binding domain of botulinum neurotoxin A1 (crystal…
3C8B 1.47 Å, Crystal structure of the catalytic domain of botulinum neurotoxin serotype A with…
3DDA 1.5 Å, Crystal structure of the catalytic domain of Botulinum neurotoxin serotype a with a…
3QW7 1.5 Å, Crystal structure of the protease domain of Botulinum Neurotoxin Serotype A with a…
3C8A 1.52 Å, Crystal structure of the catalytic domain of botulinum neurotoxin serotype A with…
3C89 1.58 Å, Crystal structure of the catalytic domain of botulinum neurotoxin serotype A with…
2VU9 1.6 Å, Crystal structure of botulinum neurotoxin serotype a binding domain in complex with GT1B
3C88 1.6 Å, Crystal structure of the catalytic domain of botulinum neurotoxin serotype A with…

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