5JLV: Botulinum neurotoxin type A

Receptor binding domain of Botulinum neurotoxin A in complex with human glycosylated SV2C. Determined by X-ray diffraction at 2.0 Å resolution. Released 15 Jun 2016.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Clostridium botulinum, Homo sapiens
Chains: 4
Atoms: 9,428
Mol. weight: 128.92 kDa
Ligands: NAG, PO4
Released: 15 Jun 2016

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

Secondary structure: helices and β-sheets

5JLV contains 25 α-helices and 113 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: 11 helices, 43 β-strands

Element	Residues	Length	Sheet
α-helix	872-875	4
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
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	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	1052-1058	7	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	1111-1115	5	9
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	10
β-strand	1204-1205	2	9
β-strand	1207-1209	3	9
α-helix	1211-1213	3
β-strand	1218	1	10
β-strand	1220-1225	6	9
β-strand	1235-1240	6	9
β-strand	1246-1255	10	9
β-strand	1258-1264	7	9
α-helix	1265-1268	4
α-helix	1271	1
α-helix	1275-1280	6
β-strand	1282-1285	4	9

Chain B: 11 helices, 43 β-strands

Element	Residues	Length	Sheet
α-helix	872-875	4
β-strand	879-880	2	11
β-strand	881-884	4	12
β-strand	887-890	4	12
β-strand	897-900	4	13
β-strand	904-906	3	11
β-strand	914-917	4	11
β-strand	924-927	4	13
α-helix	930-932	3
β-strand	935-936	2	14
β-strand	941-948	8	11
α-helix	950-952	3
α-helix	955-957	3
β-strand	962-969	8	13
β-strand	972-979	8	13
β-strand	982-988	7	13
β-strand	994-1000	7	13
β-strand	1004	1	15
β-strand	1015-1021	7	11
β-strand	1026-1031	6	11
β-strand	1034-1040	7	11
β-strand	1047-1048	2	14
β-strand	1052-1058	7	13
β-strand	1066-1075	10	11
α-helix	1081-1092	12
β-strand	1096	1	16
β-strand	1098	1	17
β-strand	1104	1	17
α-helix	1105	1
β-strand	1106	1	18
β-strand	1111-1115	5	19
β-strand	1122-1125	4	19
β-strand	1134-1137	4	19
β-strand	1142-1145	4	15
β-strand	1149-1152	4	15
α-helix	1158	1
β-strand	1159-1164	6	19
β-strand	1173	1	18
β-strand	1175	1	16
β-strand	1179-1186	8	19
β-strand	1189-1194	6	19
β-strand	1195	1	20
β-strand	1204-1205	2	19
β-strand	1207-1209	3	19
α-helix	1211-1213	3
β-strand	1218	1	20
β-strand	1220-1225	6	19
β-strand	1235-1240	6	19
β-strand	1246-1255	10	19
β-strand	1258-1264	7	19
α-helix	1265-1268	4
α-helix	1275-1280	6
β-strand	1282-1285	4	19
α-helix	1293-1295	3

Chain C: 1 helix, 14 β-strands

Element	Residues	Length	Sheet
β-strand	472-474	3	5
β-strand	477-483	7	5
β-strand	487-493	7	21
β-strand	496-503	8	5
β-strand	506-513	8	21
β-strand	516-518	3	5
β-strand	521-523	3	5
β-strand	526-528	3	21
β-strand	531-533	3	21
β-strand	536-538	3	5
β-strand	541-543	3	5
α-helix	549-551	3
β-strand	552-553	2	21
β-strand	556-558	3	5
β-strand	560-563	4	5

Chain D: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	477-483	7	15
β-strand	487-493	7	22
β-strand	496-503	8	15
α-helix	505	1
β-strand	506-513	8	22
β-strand	516-518	3	15
β-strand	521-525	5	15
β-strand	526-528	3	22
β-strand	531-533	3	22
β-strand	536-538	3	15
β-strand	541-545	5	15
α-helix	549-551	3
β-strand	552-553	2	22
β-strand	556-558	3	15
β-strand	560-563	4	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Botulinum neurotoxin type A	A, B	protein	428	Clostridium botulinum	P0DPI1 (AlphaFold model)
Synaptic vesicle glycoprotein 2C	C, D	protein	117	Homo sapiens	Q496J9 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5JLV_1 Botulinum neurotoxin type A (chains A, B)
GPMNIINTSILNLRYESNHLIDLSRYASKINIGSKVNFDPIDKNQIQLFNLESSKIEVIL
KNAIVYNSMYENFSTSFWIRIPKYFNSISLNNEYTIINCMENNSGWKVSLNYGEIIWTLQ
DTQEIKQRVVFKYSQMINISDYINRWIFVTITNNRLNNSKIYINGRLIDQKPISNLGNIH
ASNNIMFKLDGCRDTHRYIWIKYFNLFDKELNEKEIKDLYDNQSNSGILKDFWGDYLQYD
KPYYMLNLYDPNKYVDVNNVGIRGYMYLKGPRGSVMTTNIYLNSSLYRGAKFIIKKYASG
NKDNIVRNNDRVYINVVVKNKEYRLATNASQAGVEKILSALEIPDVGNLSQVVVMKSKND
QGITNKCKMNLQDNNGNDIGFIGFHQFNNIAKLVASNWYNRQIERSSRTLGCSWEFIPVD
DGWGERPL

Sequence of entity 2 (C, D), FASTA

>5JLV_2 Synaptic vesicle glycoprotein 2C (chains C, D)
SHHHHHHHHHSGGGSGGGIEGRVERDKYANFTINFTMENQIHTGMEYDNGRFIGVKFKSV
TFKDSVFKSCTFEDVTSVNTYFKNCTFIDTVFDNTDFEPYKFIDSEFKNCSFFHNKT

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
PO4	Phosphate ion	O4 P	3

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

Primary citation

N-linked glycosylation of SV2 is required for binding and uptake of botulinum neurotoxin A. Yao, G., Zhang, S., Mahrhold, S. et al. Nat Struct Mol Biol (2016) 23:656-662. DOI 10.1038/nsmb.3245 · 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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