7K7Y: BoNT/E LC-HN domain

Crystal structure of BoNT/E LC-HN domain in complex with VHH JLE-E9. Determined by X-ray diffraction at 3.6 Å resolution. Released 14 Oct 2020.

Method: X-ray diffraction
Resolution: 3.6 Å
Organisms: Clostridium botulinum, Vicugna pacos
Chains: 8
Atoms: 28,699
Mol. weight: 443.27 kDa
Released: 14 Oct 2020

Explore 7K7Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7K7Y contains 157 α-helices and 204 β-strands across 8 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: 39 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	1
β-strand	30-36	7	1
β-strand	39-42	4	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
α-helix	111-113	3
β-strand	132-135	4	1
β-strand	141-144	4	1
β-strand	148-151	4	1
β-strand	156	1	4
β-strand	161-164	4	1
α-helix	165-166	2
β-strand	167	1	5
β-strand	171	1	5
α-helix	173-175	3
β-strand	182-185	4	1
β-strand	190-195	6	6
β-strand	201-203	3	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	265-286	22
α-helix	297-306	10
β-strand	309-311	3	10
β-strand	317-319	3	10
α-helix	321-333	13
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
α-helix	440-442	3
α-helix	446-449	4
β-strand	453-454	2	13
β-strand	505-506	2	2
β-strand	510-513	4	12
α-helix	519-524	6
α-helix	528-529	2
β-strand	536-538	3	14
α-helix	541-546	6
β-strand	550-552	3	14
α-helix	557-563	7
α-helix	566-567	2
α-helix	572-587	16
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	643-647	5
β-strand	649-650	2	13
α-helix	660-688	29
α-helix	689-693	5
α-helix	694-721	28
α-helix	728-733	6
α-helix	740-799	60
α-helix	801-804	4
α-helix	807-819	13
α-helix	822-825	4
α-helix	827-830	4

Chain B: 38 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	48
β-strand	30-36	7	48
β-strand	39-42	4	48
α-helix	52-55	4
β-strand	60-61	2	49
β-strand	66-68	3	50
β-strand	69	1	51
α-helix	77-95	19
α-helix	98-109	12
α-helix	111-113	3
β-strand	132-135	4	48
β-strand	141-144	4	48
β-strand	148-151	4	48
β-strand	156	1	51
β-strand	161-164	4	48
α-helix	165-166	2
β-strand	167	1	52
β-strand	171	1	52
α-helix	173-175	3
β-strand	182-185	4	48
β-strand	190-195	6	53
β-strand	201-203	3	53
α-helix	206-221	16
β-strand	232-233	2	54
β-strand	235	1	55
β-strand	241	1	56
β-strand	247-248	2	54
α-helix	249-255	7
α-helix	257-262	6
α-helix	265-286	22
α-helix	293-306	14
β-strand	309-311	3	57
β-strand	317-319	3	57
α-helix	321-333	13
α-helix	336-342	7
β-strand	356-360	5	53
α-helix	361	1
β-strand	370	1	58
β-strand	374	1	58
α-helix	378-387	10
β-strand	388	1	53
α-helix	393-395	3
β-strand	396-397	2	53
β-strand	404-406	3	50
β-strand	408-416	9	59
β-strand	422-430	9	59
α-helix	431-433	3
β-strand	435	1	56
β-strand	438	1	55
α-helix	440-442	3
α-helix	446-449	4
β-strand	453-454	2	60
β-strand	505-506	2	49
β-strand	510-513	4	59
α-helix	519-525	7
α-helix	528-529	2
β-strand	536-538	3	61
α-helix	541-546	6
β-strand	550-552	3	61
α-helix	557-563	7
α-helix	566-567	2
α-helix	572-587	16
β-strand	591	1	62
β-strand	602	1	62
α-helix	606-610	5
α-helix	615-619	5
α-helix	621-628	8
α-helix	630-632	3
α-helix	643-647	5
β-strand	649-650	2	60
α-helix	660-688	29
α-helix	689-693	5
α-helix	694-721	28
α-helix	728-733	6
α-helix	740-799	60
α-helix	808-818	11
α-helix	822-825	4
α-helix	827-830	4

Chains C and D: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	63
β-strand	11	1	64
β-strand	18-23	6	63
β-strand	32-39	8	65
β-strand	45-51	7	65
β-strand	58-60	3	65
β-strand	68-73	6	63
β-strand	78-83	6	63
α-helix	88-90	3
β-strand	93-100	8	65
β-strand	113-114	2	65
β-strand	118-119	2	65
β-strand	121	1	64

Chain E: 38 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	19
β-strand	30-36	7	19
β-strand	39-41	3	19
α-helix	52-55	4
β-strand	60-61	2	20
β-strand	66-68	3	21
β-strand	69	1	22
α-helix	77-95	19
α-helix	98-109	12
α-helix	111-113	3
β-strand	132-135	4	19
β-strand	141-144	4	19
β-strand	148-151	4	19
β-strand	156	1	22
β-strand	161-164	4	19
α-helix	165-166	2
β-strand	167	1	23
β-strand	171	1	23
α-helix	173-175	3
β-strand	182-185	4	19
β-strand	190-195	6	24
β-strand	201-203	3	24
α-helix	206-221	16
β-strand	232-233	2	25
β-strand	235	1	26
β-strand	241	1	27
β-strand	247-248	2	25
α-helix	249-255	7
α-helix	257-262	6
α-helix	265-286	22
α-helix	297-306	10
β-strand	309-311	3	28
β-strand	317-319	3	28
α-helix	321-333	13
α-helix	336-342	7
β-strand	356-360	5	24
α-helix	361	1
β-strand	370	1	29
β-strand	374	1	29
α-helix	378-387	10
β-strand	388	1	24
α-helix	393-395	3
β-strand	396-397	2	24
β-strand	404-406	3	21
β-strand	408-416	9	30
β-strand	422-430	9	30
α-helix	431-433	3
β-strand	435	1	27
β-strand	438	1	26
α-helix	440-442	3
α-helix	446-449	4
β-strand	453-454	2	31
β-strand	505-506	2	20
β-strand	510-513	4	30
α-helix	519-525	7
α-helix	528-529	2
β-strand	536-538	3	32
α-helix	541-546	6
β-strand	550-552	3	32
α-helix	557-563	7
α-helix	566-567	2
α-helix	572-587	16
β-strand	591	1	33
β-strand	602	1	33
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	31
α-helix	661-688	28
α-helix	689-693	5
α-helix	694-721	28
α-helix	728-733	6
α-helix	740-799	60
α-helix	808-819	12
α-helix	822-825	4
α-helix	827-830	4

Chain F: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	66
β-strand	18-23	6	66
β-strand	32-39	8	67
β-strand	46-51	6	67
β-strand	58-60	3	67
β-strand	69-73	5	66
β-strand	78-83	6	66
α-helix	88-90	3
β-strand	93-100	8	67
β-strand	113-114	2	67
β-strand	118-119	2	67

Chain G: 38 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	34
β-strand	30-36	7	34
β-strand	39-41	3	34
β-strand	66-68	3	35
β-strand	69	1	36
α-helix	77-95	19
α-helix	98-109	12
α-helix	111-113	3
β-strand	132-135	4	34
β-strand	141-144	4	34
β-strand	148-151	4	34
β-strand	156	1	36
β-strand	161-164	4	34
α-helix	165-166	2
β-strand	167	1	37
β-strand	171	1	37
α-helix	173-175	3
β-strand	182-185	4	34
β-strand	190-195	6	38
β-strand	201-203	3	38
α-helix	206-221	16
β-strand	232-233	2	39
β-strand	235	1	40
β-strand	241	1	41
β-strand	247-248	2	39
α-helix	249-255	7
α-helix	257-262	6
α-helix	265-286	22
α-helix	293-306	14
β-strand	309-311	3	42
β-strand	317-319	3	42
α-helix	321-333	13
α-helix	336-342	7
β-strand	356-360	5	38
α-helix	361	1
β-strand	370	1	43
β-strand	374	1	43
α-helix	378-387	10
β-strand	388	1	38
α-helix	393-395	3
β-strand	396-397	2	38
β-strand	404-406	3	35
β-strand	408-416	9	44
β-strand	422-430	9	44
α-helix	431-433	3
β-strand	435	1	41
β-strand	438	1	40
α-helix	440-442	3
α-helix	446-449	4
β-strand	453-454	2	45
β-strand	510-513	4	44
α-helix	519-525	7
α-helix	528-529	2
β-strand	536-538	3	46
α-helix	541-546	6
β-strand	550-552	3	46
α-helix	557-563	7
α-helix	566-567	2
α-helix	572-587	16
β-strand	591	1	47
β-strand	602	1	47
α-helix	606-610	5
α-helix	615-619	5
α-helix	621-628	8
α-helix	630-633	4
α-helix	643-647	5
β-strand	649-650	2	45
α-helix	661-688	28
α-helix	689-693	5
α-helix	694-721	28
α-helix	728-733	6
α-helix	740-799	60
α-helix	805-807	3
α-helix	808-818	11
α-helix	822-825	4
α-helix	827-830	4

Chain H: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	68
β-strand	11	1	69
β-strand	18-23	6	68
β-strand	32-39	8	70
β-strand	45-51	7	70
β-strand	58-60	3	70
β-strand	69-73	5	68
β-strand	78-83	6	68
α-helix	88-90	3
β-strand	92-100	9	70
β-strand	113-114	2	70
β-strand	118-120	3	70
β-strand	121	1	69

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Botulinum neurotoxin type E	A, B, E, G	protein	850	Clostridium botulinum	Q00496 (AlphaFold model)
Jle-E9	C, D, F, H	protein	129	Vicugna pacos

Sequence of entity 1 (A, B, E, G), FASTA

>7K7Y_1 Botulinum neurotoxin type E (chains A, B, E, G)
GPLGSMPKINSFNYNDPVNDRTILYIKPGGCQEFYKSFNIMKNIWIIPERNVIGTTPQDF
HPPTSLKNGDSSYYDPNYLQSDEEKDRFLKIVTKIFNRINNNLSGGILLEELSKANPYLG
NDNTPDNQFHIGDASAVEIKFSNGSQDILLPNVIIMGAEPDLFETNSSNISLRNNYMPSN
HGFGSIAIVTFSPEYSFRFNDNSMNEFIQDPALTLMHELIHSLHGLYGAKGITTKYTITQ
KQNPLITNIRGTNIEEFLTFGGTDLNIITSAQSNDIYTNLLADYKKIASKLSKVQVSNPL
LNPYKDVFEAKYGLDKDASGIYSVNINKFNDIFKKLYSFTEFDLATKFQVKCRQTYIGQY
KYFKLSNLLNDSIYNISEGYNINNLKVNFRGQNANLNPRIITPITGRGLVKKIIRFCKNI
VSVKGIRKSICIEINNGELFFVASENSYNDDNINTPKEIDDTVTSNNNYENDLDQVILNF
NSESAPGLSDEKLNLTIQNDAYIPKYDSNGTSDIEQHDVNELNVFFYLDAQKVPEGENNV
NLTSSIDTALLEQPKIYTFFSSEFINNVNKPVQAALFVSWIQQVLVDFTTEANQKSTVDK
IADISIVVPYIGLALNIGNEAQKGNFKDALELLGAGILLEFEPELLIPTILVFTIKSFLG
SSDNKNKVIKAINNALKERDEKWKEVYSFIVSNWMTKINTQFNKRKEQMYQALQNQVNAI
KTIIESKYNSYTLEEKNELTNKYDIKQIENELNQKVSIAMNNIDRFLTESSISYLMKLIN
EVKINKLREYDENVKTYLLNYIIQHGSILGESQQELNSMVTDTLNNSIPFKLSSYTDDKI
LISYFNKFFK

Sequence of entity 2 (C, D, F, H), FASTA

>7K7Y_2 JLE-E9 (chains C, D, F, H)
GPLGSQLQLVETGGGLVQAGGSLRLSCAASGRTFSSYSMGWFRQAPGKEREYVAAVNSNG
DSTFYADSIKGRFTVSRDAAKNTVYLQMNSLKPEDTALYYCAAVYGRYTYQSPKSYEYWG
QGTQVTVSS

Primary citation

Two VHH Antibodies Neutralize Botulinum Neurotoxin E1 by Blocking Its Membrane Translocation in Host Cells. Lam, K.H., Perry, K., Shoemaker, C.B. et al. Toxins (Basel) (2020) 12. DOI 10.3390/toxins12100616 · 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
3FFZ 2.65 Å, Domain organization in Clostridium butulinum neurotoxin type E is unique: Its…
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

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