2NP0: Botulinum neurotoxin type B

Crystal structure of the Botulinum neurotoxin type B complexed with synaptotagamin-II ectodomain. Determined by X-ray diffraction at 2.62 Å resolution. Released 26 Dec 2006.

Method: X-ray diffraction
Resolution: 2.62 Å
Organisms: Clostridium botulinum, Mus musculus
Chains: 2
Atoms: 11,182
Mol. weight: 153.59 kDa
Ligands: CA, ZN
Released: 26 Dec 2006

Explore 2NP0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2NP0 contains 62 α-helices and 86 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: 61 helices, 86 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	42-48	7	1
α-helix	55-58	4
β-strand	63-64	2	2
α-helix	70	1
β-strand	71-72	2	3
β-strand	73	1	4
α-helix	81-98	18
α-helix	102-113	12
α-helix	115-117	3
β-strand	127-128	2	5
β-strand	136-140	5	1
α-helix	143	1
α-helix	147-148	2
β-strand	150-154	5	1
β-strand	157-161	5	1
β-strand	165	1	4
β-strand	170-172	3	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	198-202	5	7
β-strand	219-220	2	7
α-helix	221-222	2
α-helix	223-238	16
α-helix	247	1
β-strand	248	1	8
β-strand	250	1	9
β-strand	257	1	10
α-helix	258-259	2
β-strand	263	1	8
α-helix	265-271	7
α-helix	275-278	4
α-helix	281-304	24
β-strand	307-308	2	5
α-helix	316-327	12
β-strand	330-331	2	11
β-strand	337-338	2	11
α-helix	341-349	9
α-helix	350-354	5
α-helix	357-364	8
β-strand	377-382	6	7
β-strand	392	1	12
β-strand	396	1	12
α-helix	400-402	3
α-helix	406-411	6
β-strand	412	1	7
α-helix	417-419	3
β-strand	420-422	3	7
α-helix	423-424	2
β-strand	428-429	2	3
β-strand	432-437	6	13
β-strand	445-449	5	13
α-helix	450-452	3
β-strand	454	1	10
α-helix	455	1
β-strand	457	1	9
α-helix	459-461	3
α-helix	465-467	3
β-strand	470-472	3	14
α-helix	487-490	4
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	526-531	6	13
α-helix	536-541	6
β-strand	553-555	3	15
α-helix	558-563	6
β-strand	567-569	3	15
α-helix	576-580	5
α-helix	589-605	17
α-helix	623-627	5
α-helix	638-645	8
α-helix	646-650	5
α-helix	655-658	4
α-helix	660-664	5
β-strand	665-667	3	14
α-helix	674-706	33
α-helix	708-738	31
α-helix	752-781	30
α-helix	782-786	5
α-helix	787-811	25
α-helix	813-815	3
α-helix	820-830	11
α-helix	834-837	4
α-helix	839-841	3
α-helix	846-856	11
α-helix	859-862	4
β-strand	863-866	4	16
β-strand	867-868	2	17
β-strand	875-876	2	17
β-strand	883-886	4	18
β-strand	891-892	2	16
β-strand	898-900	3	16
β-strand	908-911	4	18
β-strand	925-932	8	16
α-helix	934-937	4
α-helix	941-946	6
β-strand	948-956	9	18
β-strand	959-966	8	18
β-strand	969-975	7	18
β-strand	981-987	7	18
β-strand	1002-1008	7	16
β-strand	1012-1017	6	16
β-strand	1020-1026	7	16
α-helix	1038	1
β-strand	1039-1045	7	18
β-strand	1053-1061	9	16
α-helix	1064-1066	3
α-helix	1067-1078	12
β-strand	1082	1	19
β-strand	1084	1	20
β-strand	1090	1	20
α-helix	1091	1
β-strand	1092	1	21
β-strand	1097	1	22
β-strand	1098-1101	4	23
β-strand	1107-1111	5	22
β-strand	1118-1122	5	22
α-helix	1123-1124	2
β-strand	1125	1	24
β-strand	1136	1	24
β-strand	1144-1148	5	22
β-strand	1159	1	21
β-strand	1161	1	19
β-strand	1165-1172	8	22
β-strand	1175-1180	6	22
β-strand	1181-1182	2	25
β-strand	1189-1191	3	22
β-strand	1193-1196	4	22
β-strand	1203-1204	2	25
β-strand	1207-1210	4	22
β-strand	1220	1	23
β-strand	1221-1225	5	22
β-strand	1233-1244	12	22
α-helix	1245	1
β-strand	1251-1259	9	22
α-helix	1261-1264	4
β-strand	1279-1282	4	23
β-strand	1285	1	26
β-strand	1288	1	26

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	48-58	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Botulinum neurotoxin type B	A	protein	1290	Clostridium botulinum	P10844 (AlphaFold model)
Synaptotagmin-2	B	protein	21	Mus musculus	P46097 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2NP0_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

Sequence of entity 2 (B), FASTA

>2NP0_2 Synaptotagmin-2 (chains B)
GESQEDMFAKLKEKFFNEINK

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	3
ZN	Zinc ion	Zn	1

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

Primary citation

Structural basis of cell surface receptor recognition by botulinum neurotoxin B. Chai, Q., Arndt, J.W., Dong, M. et al. Nature (2006) 444:1096-1100. DOI 10.1038/nature05411 · 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
1S0E 1.9 Å, Crystal structure of botulinum neurotoxin type B at pH 6.0
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

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