3FFZ: Botulinum neurotoxin type E

Domain organization in Clostridium butulinum neurotoxin type E is unique: Its implication in faster translocation. Determined by X-ray diffraction at 2.65 Å resolution. Released 16 Dec 2008.

Method: X-ray diffraction
Resolution: 2.65 Å
Organism: Clostridium botulinum
Chains: 2
Atoms: 20,217
Mol. weight: 287.91 kDa
Ligands: ZN
Released: 16 Dec 2008

Explore 3FFZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3FFZ contains 79 α-helices and 158 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: 42 helices, 79 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	1
β-strand	30-36	7	1
β-strand	39-45	7	1
α-helix	52-55	4
β-strand	60-61	2	2
β-strand	66-68	3	3
β-strand	69	1	4
α-helix	77-95	19
α-helix	98-109	12
β-strand	132-135	4	1
β-strand	141-144	4	1
β-strand	148-152	5	1
β-strand	156	1	4
β-strand	161-164	4	1
β-strand	167	1	5
α-helix	173-175	3
β-strand	182-186	5	1
β-strand	190-194	5	6
β-strand	202-203	2	6
α-helix	206-221	16
β-strand	232-233	2	7
β-strand	235	1	8
β-strand	241	1	9
β-strand	247-248	2	7
α-helix	249-255	7
α-helix	257-262	6
α-helix	265-282	18
α-helix	299-306	8
β-strand	309-311	3	10
β-strand	317-319	3	10
α-helix	321-332	12
α-helix	336-342	7
β-strand	356-360	5	6
α-helix	361	1
β-strand	370	1	11
β-strand	374	1	11
α-helix	378-387	10
β-strand	388	1	6
α-helix	393-395	3
β-strand	396-397	2	6
β-strand	404-406	3	3
β-strand	408-416	9	12
β-strand	422-430	9	12
α-helix	431-433	3
β-strand	435	1	9
β-strand	438	1	8
β-strand	452-453	2	13
α-helix	468-472	5
β-strand	496	1	5
β-strand	505-506	2	2
β-strand	510-513	4	12
α-helix	519-525	7
α-helix	528-529	2
β-strand	536-538	3	14
α-helix	541-546	6
β-strand	550-552	3	14
α-helix	557-560	4
α-helix	566-567	2
α-helix	569-571	3
α-helix	572-579	8
α-helix	582-587	6
β-strand	591	1	15
β-strand	602	1	15
α-helix	606-610	5
α-helix	615-619	5
α-helix	621-628	8
α-helix	630-632	3
α-helix	643-648	6
β-strand	649-650	2	13
α-helix	660-692	33
α-helix	694-718	25
α-helix	722-724	3
α-helix	728-731	4
α-helix	744-779	36
α-helix	781-799	19
α-helix	805-807	3
α-helix	808-818	11
β-strand	851-854	4	16
β-strand	855-858	4	17
β-strand	861-864	4	17
β-strand	871-876	6	18
β-strand	879-880	2	16
β-strand	888-891	4	16
β-strand	896-901	6	18
β-strand	916-922	7	16
β-strand	937-944	8	18
β-strand	948-955	8	18
β-strand	958-964	7	18
β-strand	970-976	7	18
β-strand	982	1	19
β-strand	991-997	7	16
β-strand	1002-1007	6	16
β-strand	1010-1016	7	16
β-strand	1028-1034	7	18
β-strand	1041-1050	10	16
α-helix	1053-1055	3
α-helix	1056-1063	8
β-strand	1071	1	20
β-strand	1073	1	21
β-strand	1074	1	22
β-strand	1079	1	21
β-strand	1081	1	23
β-strand	1085-1090	6	22
β-strand	1096-1100	5	22
β-strand	1105-1111	7	22
α-helix	1112-1113	2
β-strand	1114-1115	2	19
β-strand	1118-1119	2	19
α-helix	1120	1
β-strand	1126-1131	6	22
β-strand	1141	1	23
β-strand	1143	1	20
β-strand	1147-1155	9	22
β-strand	1158-1165	8	22
β-strand	1173-1177	5	22
β-strand	1186-1192	7	22
β-strand	1197-1203	7	22
β-strand	1208-1215	8	22
β-strand	1218-1222	5	22
α-helix	1224-1227	4
β-strand	1240-1243	4	22

Chain B: 37 helices, 79 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	24
β-strand	30-36	7	24
β-strand	39-45	7	24
α-helix	52-55	4
β-strand	60-61	2	25
β-strand	66-68	3	26
α-helix	81-95	15
α-helix	98-108	11
β-strand	132-135	4	24
β-strand	141-144	4	24
β-strand	148-152	5	24
β-strand	161-164	4	24
α-helix	173-175	3
β-strand	182-186	5	24
β-strand	190-194	5	27
β-strand	202-203	2	27
α-helix	206-221	16
β-strand	232-233	2	28
β-strand	235	1	29
α-helix	236-237	2
β-strand	241	1	30
β-strand	247-248	2	28
α-helix	249-255	7
α-helix	257-261	5
α-helix	265-287	23
α-helix	299-306	8
β-strand	309-311	3	31
β-strand	317-319	3	31
α-helix	321-332	12
α-helix	336-341	6
β-strand	356-359	4	27
β-strand	370	1	32
β-strand	374	1	32
α-helix	378-384	7
β-strand	388	1	27
α-helix	393-395	3
β-strand	404-406	3	26
β-strand	408-413	6	33
β-strand	425-430	6	33
α-helix	431-433	3
β-strand	435	1	30
β-strand	438	1	29
α-helix	440-442	3
β-strand	452	1	34
α-helix	468-472	5
β-strand	487-488	2	24
β-strand	505-506	2	25
β-strand	510-513	4	33
α-helix	519-524	6
β-strand	536-538	3	35
α-helix	541-546	6
β-strand	550-552	3	35
α-helix	557-561	5
α-helix	583-586	4
β-strand	591-592	2	36
β-strand	601-602	2	36
α-helix	606-610	5
α-helix	615-619	5
α-helix	621-628	8
α-helix	642-648	7
β-strand	649	1	34
α-helix	662-688	27
α-helix	689-693	5
α-helix	694-723	30
α-helix	746-779	34
α-helix	781-799	19
α-helix	808-818	11
α-helix	828-829	2
α-helix	839-841	3
β-strand	851-854	4	37
β-strand	855-857	3	38
β-strand	862-864	3	38
β-strand	871-875	5	39
β-strand	879-881	3	37
β-strand	884-891	8	37
β-strand	897-901	5	39
β-strand	915-922	8	37
β-strand	937-940	4	39
β-strand	943-944	2	39
β-strand	948-949	2	39
β-strand	952-955	4	39
β-strand	958-964	7	39
β-strand	970-976	7	39
β-strand	982	1	40
β-strand	990-997	8	37
β-strand	1003-1007	5	37
β-strand	1011	1	37
β-strand	1028-1034	7	39
β-strand	1041-1050	10	37
α-helix	1056-1065	10
β-strand	1071	1	41
β-strand	1073	1	42
β-strand	1079	1	42
β-strand	1081	1	43
β-strand	1086-1090	5	44
β-strand	1096-1100	5	44
β-strand	1105	1	45
β-strand	1106-1111	6	44
α-helix	1112-1113	2
β-strand	1114-1115	2	40
β-strand	1118-1119	2	40
α-helix	1120	1
β-strand	1126-1131	6	44
β-strand	1141	1	43
β-strand	1143	1	41
β-strand	1147-1153	7	44
β-strand	1159-1161	3	44
β-strand	1162-1164	3	45
β-strand	1172-1174	3	44
β-strand	1175-1177	3	45
β-strand	1186-1192	7	44
β-strand	1197-1203	7	44
β-strand	1208-1215	8	44
β-strand	1218-1222	5	44
α-helix	1225-1228	4
β-strand	1240-1243	4	44

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Botulinum neurotoxin type E	A, B	protein	1252	Clostridium botulinum	Q00496 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3FFZ_1 Botulinum neurotoxin type E (chains A, B)
MPKINSFNYNDPVNDRTILYIKPGGCQEFYKSFNIMKNIWIIPERNVIGTTPQDFHPPTS
LKNGDSSYYDPNYLQSDEEKDRFLKIVTKIFNRINNNLSGGILLEELSKANPYLGNDNTP
DNQFHIGDASAVEIKFSNGSQDILLPNVIIMGAEPDLFETNSSNISLRNNYMPSNHGFGS
IAIVTFSPEYSFRFNDNCMNEFIQDPALTLMHELIHSLHGLYGAKGITTKYTITQKQNPL
ITNIRGTNIEEFLTFGGTDLNIITSAQSNDIYTNLLADYKKIASKLSKVQVSNPLLNPYK
DVFEAKYGLDKDASGIYSVNINKFNDIFKKLYSFTEFDLATKFQVKCRQTYIGQYKYFKL
SNLLNDSIYNISEGYNINNLKVNFRGQNANLNPRIITPITGRGLVKKIIRFCKNIVSVKG
IRKSICIEINNGELFFVASENSYNDDNINTPKEIDDTVTSNNNYENDLDQVILNFNSESA
PGLSDEKLNLTIQNDAYIPKYDSNGTSDIEQHDVNELNVFFYLDAQKVPEGENNVNLTSS
IDTALLEQPKIYTFFSSEFINNVNKPVQAALFVSWIQQVLVDFTTEANQKSTVDKIADIS
IVVPYIGLALNIGNEAQKGNFKDALELLGAGILLEFEPELLIPTILVFTIKSFLGSSDNK
NKVIKAINNALKERDEKWKEVYSFIVSNWMTKINTQFNKRKEQMYQALQNQVNAIKTIIE
SKYNSYTLEEKNELTNKYDIKQIENELNQKVSIAMNNIDRFLTESSISYLMKIINEVKIN
KLREYDENVKTYLLNYIIQHGSILGESQQELNSMVTDTLNNSIPFKLSSYTDDKILISYF
NKFFKRIKSSSVLNMRYKNDKYVDTSGYDSNININGDVYKYPTNKNQFGIYNDKLSEVNI
SQNDYIIYDNKYKNFSISFWVRIPNYDNKIVNVNNEYTIINCMRDNNSGWKVSLNHNEII
WTLQDNAGINQKLAFNYGNANGISDYINKWIFVTITNDRLGDSKLYINGNLIDQKSILNL
GNIHVSDNILFKIVNCSYTRYIGIRYFNIFDKELDETEIQTLYSNEPNTNILKDFWGNYL
LYDKEYYLLNVLKPNNFIDRRKDSTLSINNIRSTILLANRLYSGIKVKIQRVNNSSTNDN
LVRKNDQVYINFVASKTHLFPLYADTATTNKEKTIKISSSGNRFNQVVVMNSVGNNCTMN
FKNNNGNNIGLLGFKADTVVASTWYYTHMRDHTNSNGCFWNFISEEHGWQEK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

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

Primary citation

Domain organization in Clostridium botulinum neurotoxin type E is unique: its implication in faster translocation. Kumaran, D., Eswaramoorthy, S., Furey, W. et al. J Mol Biol (2009) 386:233-245. DOI 10.1016/j.jmb.2008.12.027 · PubMed

Other PDB entries of the same protein (UniProt Q00496 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1T3C 1.9 Å, Clostridium botulinum type E catalytic domain E212Q mutant
1T3A 2.16 Å, Crystal structure of Clostridium botulinum neurotoxin type E catalytic domain
1ZKW 2.17 Å, Crystal structure of Arg347Ala mutant of botulinum neurotoxin E catalytic domain
1ZL6 2.4 Å, Crystal structure of Tyr350Ala mutant of Clostridium botulinum neurotoxin E catalytic…
7K84 2.5 Å, Crystal structure of BoNT/E LC-HN domain in complex with VHH JLE-E5
1ZKX 2.52 Å, Crystal structure of Glu158Ala/Thr159Ala/Asn160Ala- a triple mutant of Clostridium…
7UIA 2.59 Å, Crystal structure of BoNT/E receptor binding domain in complex with SV2 and VHH
1ZL5 2.6 Å, Crystal structure of Glu335Gln mutant of Clostridium botulinum neurotoxin E catalytic…
1ZN3 2.6 Å, Crystal structure of Glu335Ala mutant of Clostridium botulinum neurotoxin type E
7UIB 2.77 Å, Crystal structure of BoNT/E receptor binding domain in complex with SV2, VHH, and sialic…
7UIE 3.23 Å, Crystal structure of HcE-JLE-G6
9ARJ 3.4 Å, CryoEM structure of BoNT-NTNH-OrfX2 complex from Clostridium botulinum E1, major class

Browse structure collections

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