1S0E: Botulinum neurotoxin type B at pH 6.0

Crystal structure of botulinum neurotoxin type B at pH 6.0. Determined by X-ray diffraction at 1.9 Å resolution. Released 16 Mar 2004.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Clostridium botulinum
Chains: 1
Atoms: 11,445
Mol. weight: 150.98 kDa
Ligands: ZN, CA
Released: 16 Mar 2004

Explore 1S0E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1S0E contains 59 α-helices and 89 β-strands across 1 chain. 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: 59 helices, 89 β-strands

Element	Residues	Length	Sheet
α-helix	12-13	2
β-strand	18-22	5	1
α-helix	24-26	3
β-strand	33-39	7	1
β-strand	42-45	4	1
α-helix	55-58	4
β-strand	63-64	2	2
β-strand	71-72	2	3
β-strand	73	1	4
α-helix	81-99	19
α-helix	102-113	12
α-helix	115-117	3
β-strand	127-128	2	5
β-strand	136-140	5	1
β-strand	150-154	5	1
β-strand	157-160	4	1
β-strand	165	1	4
β-strand	170-173	4	1
β-strand	175-176	2	6
β-strand	179-180	2	6
α-helix	181-183	3
β-strand	190-193	4	1
β-strand	198-199	2	7
β-strand	201-202	2	8
β-strand	219-220	2	8
α-helix	223-238	16
β-strand	248	1	9
β-strand	250	1	10
β-strand	257	1	11
α-helix	258-259	2
β-strand	263	1	9
α-helix	265-271	7
α-helix	275-278	4
α-helix	281-304	24
β-strand	307-308	2	5
α-helix	316-326	11
β-strand	330-331	2	12
β-strand	337-338	2	12
α-helix	341-349	9
α-helix	350-354	5
α-helix	357-364	8
β-strand	380-382	3	7
β-strand	392	1	13
β-strand	396	1	13
α-helix	400-402	3
α-helix	406-411	6
β-strand	412	1	8
α-helix	417-419	3
β-strand	420-422	3	7
α-helix	423-424	2
α-helix	425-427	3
β-strand	428-429	2	3
β-strand	432-436	5	14
β-strand	445-449	5	14
α-helix	450-452	3
β-strand	454	1	11
α-helix	455	1
β-strand	457	1	10
α-helix	459-461	3
α-helix	465-467	3
β-strand	470-472	3	15
α-helix	487-492	6
α-helix	501-504	4
β-strand	506-507	2	1
α-helix	508-510	3
β-strand	516	1	6
β-strand	523-524	2	2
β-strand	526-530	5	14
α-helix	536-541	6
β-strand	553-555	3	16
α-helix	558-563	6
β-strand	567-569	3	16
α-helix	574-580	7
α-helix	586-604	19
α-helix	605-608	4
β-strand	611	1	17
α-helix	612-614	3
β-strand	616	1	17
α-helix	623-627	5
α-helix	638-645	8
α-helix	646-650	5
α-helix	662-664	3
β-strand	665-667	3	15
α-helix	674-702	29
α-helix	703-707	5
α-helix	708-738	31
α-helix	742-746	5
α-helix	752-780	29
α-helix	781-786	6
α-helix	787-811	25
α-helix	813-816	4
α-helix	822-830	9
α-helix	834-837	4
α-helix	839-841	3
α-helix	846-857	12
α-helix	859-862	4
β-strand	863-866	4	18
β-strand	867-869	3	19
β-strand	874-876	3	19
β-strand	883-886	4	20
β-strand	891-892	2	18
β-strand	897-900	4	18
β-strand	908-911	4	20
β-strand	925-932	8	18
α-helix	934-937	4
α-helix	938-940	3
α-helix	941-946	6
β-strand	948-956	9	20
β-strand	959-966	8	20
β-strand	969-975	7	20
β-strand	981-987	7	20
β-strand	1002-1008	7	18
β-strand	1012-1017	6	18
β-strand	1020-1026	7	18
β-strand	1038-1045	8	20
β-strand	1053-1061	9	18
α-helix	1064-1066	3
α-helix	1067-1078	12
β-strand	1082	1	21
β-strand	1084	1	22
β-strand	1090	1	22
α-helix	1091	1
β-strand	1092-1093	2	23
β-strand	1096-1097	2	24
β-strand	1098-1101	4	25
β-strand	1107-1111	5	24
β-strand	1118-1122	5	24
α-helix	1123-1124	2
β-strand	1125	1	26
β-strand	1136	1	26
β-strand	1144-1148	5	24
β-strand	1158-1159	2	23
β-strand	1161	1	21
β-strand	1165-1172	8	24
β-strand	1175-1180	6	24
β-strand	1181-1182	2	27
β-strand	1189-1191	3	24
β-strand	1193-1196	4	24
β-strand	1203-1204	2	27
β-strand	1207-1210	4	24
β-strand	1220	1	25
β-strand	1221-1225	5	24
β-strand	1233-1245	13	24
β-strand	1250-1259	10	24
α-helix	1261-1265	5
β-strand	1279-1282	4	25
β-strand	1285	1	28
β-strand	1288	1	28

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Botulinum neurotoxin type B	A	protein	1290	Clostridium botulinum	P10844 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1S0E_1 Botulinum neurotoxin type B (chains A)
PVTINNFNYNDPIDNNNIIMMEPPFARGTGRYYKAFKITDRIWIIPERYTFGYKPEDFNK
SSGIFNRDVCEYYDPDYLNTNDKKNIFLQTMIKLFNRIKSKPLGEKLLEMIINGIPYLGD
RRVPLEEFNTNIASVTVNKLISNPGEVERKKGIFANLIIFGPGPVLNENETIDIGIQNHF
ASREGFGGIMQMKFCPEYVSVFNNVQENKGASIFNRRGYFSDPALILMHELIHVLHGLYG
IKVDDLPIVPNEKKFFMQSTDAIQAEELYTFGGQDPSIITPSTDKSIYDKVLQNFRGIVD
RLNKVLVCISDPNININIYKNKFKDKYKFVEDSEGKYSIDVESFDKLYKSLMFGFTETNI
AENYKIKTRASYFSDSLPPVKIKNLLDNEIYTIEEGFNISDKDMEKEYRGQNKAINKQAY
EEISKEHLAVYKIQMCKSVKAPGICIDVDNEDLFFIADKNSFSDDLSKNERIEYNTQSNY
IENDFPINELILDTDLISKIELPSENTESLTDFNVDVPVYEKQPAIKKIFTDENTIFQYL
YSQTFPLDIRDISLTSSFDDALLFSNKVYSFFSMDYIKTANKVVEAGLFAGWVKQIVNDF
VIEANKSNTMDKIADISLIVPYIGLALNVGNETAKGNFENAFEIAGASILLEFIPELLIP
VVGAFLLESYIDNKNKIIKTIDNALTKRNEKWSDMYGLIVAQWLSTVNTQFYTIKEGMYK
ALNYQAQALEEIIKYRYNIYSEKEKSNINIDFNDINSKLNEGINQAIDNINNFINGCSVS
YLMKKMIPLAVEKLLDFDNTLKKNLLNYIDENKLYLIGSAEYEKSKVNKYLKTIMPFDLS
IYTNDTILIEMFNKYNSEILNNIILNLRYKDNNLIDLSGYGAKVEVYDGVELNDKNQFKL
TSSANSKIRVTQNQNIIFNSVFLDFSVSFWIRIPKYKNDGIQNYIHNEYTIINCMKNNSG
WKISIRGNRIIWTLIDINGKTKSVFFEYNIREDISEYINRWFFVTITNNLNNAKIYINGK
LESNTDIKDIREVIANGEIIFKLDGDIDRTQFIWMKYFSIFNTELSQSNIEERYKIQSYS
EYLKDFWGNPLMYNKEYYMFNAGNKNSYIKLKKDSPVGEILTRSKYNQNSKYINYRDLYI
GEKFIIRRKSNSQSINDDIVRKEDYIYLDFFNLNQEWRVYTYKYFKKEEEKLFLAPISDS
DEFYNTIQIKEYDEQPTYSCQLLFKKDEESTDEIGLIGIHRFYESGIVFEEYKDYFCISK
WYLKEVKRKPYNLKLGCNWQFIPKDEGWTE

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
CA	Calcium ion	Ca	2

Primary citation

Role of metals in the biological activity of Clostridium botulinum neurotoxins. Eswaramoorthy, S., Kumaran, D., Keller, J. et al. Biochemistry (2004) 43:2209-2216. DOI 10.1021/bi035844k · PubMed

Other PDB entries of the same protein (UniProt P10844 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7NA9 1.76 Å, Crystal structure of BoNT/B-LC-JSG-C1
1EPW 1.9 Å, Crystal structure of clostridium neurotoxin type B
5VMR 1.95 Å, Receptor binding domain of BoNT/B in complex with mini-protein binder Bot.2110.4
1G9B 2.0 Å, Crystal structure of clostridium botulinum neurotoxin B complexed with an inhibitor…
1S0B 2.0 Å, Crystal structure of botulinum neurotoxin type B at pH 4.0
1Z0H 2.0 Å, N-terminal helix reorients in recombinant C-fragment of Clostridium botulinum type B
6G5G 2.0 Å, Crystal structure of an engineered Botulinum Neurotoxin type B mutant E1191M/S1199Y in…
6G5K 2.0 Å, Crystal structure of the binding domain of Botulinum Neurotoxin type B in complex with…
1G9A 2.1 Å, Crystal structure of clostridium botulinum neurotoxin B complexed with an inhibitor…
2NM1 2.15 Å, Structure of BoNT/B in complex with its protein receptor
1F82 2.2 Å, Botulinum neurotoxin type B catalytic domain
1G9D 2.2 Å, Crystal structure of clostridium botulinum neurotoxin B complexed with an inhibitor…

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