7K84: BoNT/E LC-HN domain

Crystal structure of BoNT/E LC-HN domain in complex with VHH JLE-E5. Determined by X-ray diffraction at 2.5 Å resolution. Released 14 Oct 2020.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Clostridium botulinum, Vicugna pacos
Chains: 2
Atoms: 7,383
Mol. weight: 111.15 kDa
Ligands: ZN
Released: 14 Oct 2020

Explore 7K84 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7K84 contains 47 α-helices and 56 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: 46 helices, 44 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
β-strand	20-22	3	1
β-strand	24	1	2
β-strand	26	1	2
β-strand	30-31	2	1
β-strand	33-36	4	3
β-strand	39-45	7	3
α-helix	52-55	4
β-strand	60-61	2	4
β-strand	66-68	3	5
β-strand	69	1	6
α-helix	77-96	20
α-helix	98-108	11
α-helix	111-113	3
β-strand	132-135	4	1
β-strand	141-144	4	1
β-strand	148-152	5	3
β-strand	156	1	6
β-strand	162-164	3	3
β-strand	167	1	7
α-helix	168-170	3
β-strand	171	1	7
α-helix	173-175	3
β-strand	182-185	4	3
β-strand	190-195	6	8
β-strand	201-203	3	8
α-helix	204-205	2
α-helix	206-221	16
α-helix	225-228	4
β-strand	232-233	2	9
α-helix	234	1
β-strand	235	1	10
α-helix	236-237	2
β-strand	241	1	11
β-strand	247-248	2	9
α-helix	249-255	7
α-helix	257-262	6
α-helix	265-287	23
α-helix	294-296	3
α-helix	297-306	10
β-strand	309-311	3	12
β-strand	317-319	3	12
α-helix	321-333	13
α-helix	336-342	7
β-strand	356-360	5	8
β-strand	370	1	13
β-strand	374	1	13
α-helix	378-387	10
β-strand	388	1	8
α-helix	393-395	3
β-strand	396-397	2	8
β-strand	404-406	3	5
β-strand	408-416	9	14
β-strand	422-430	9	14
α-helix	431-433	3
β-strand	435	1	11
β-strand	438	1	10
α-helix	440-442	3
α-helix	446-449	4
β-strand	453-454	2	15
β-strand	505-506	2	4
β-strand	510-513	4	14
α-helix	519-524	6
α-helix	528-529	2
β-strand	536-538	3	16
α-helix	541-546	6
β-strand	550-552	3	16
α-helix	557-564	8
α-helix	569-571	3
α-helix	572-587	16
β-strand	591	1	17
β-strand	602	1	17
α-helix	606-610	5
α-helix	621-628	8
α-helix	630-633	4
α-helix	642-646	5
β-strand	647	1	18
α-helix	648	1
β-strand	649-650	2	15
α-helix	660-688	29
α-helix	689-693	5
α-helix	694-724	31
α-helix	728-734	7
α-helix	740-779	40
α-helix	781-799	19
α-helix	801-804	4
α-helix	805-807	3
α-helix	808-820	13
α-helix	822-825	4
α-helix	827-829	3

Chain B: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	19
β-strand	10-13	4	20
β-strand	18-24	7	19
β-strand	31-36	6	20
β-strand	43-48	6	20
β-strand	55-57	3	20
β-strand	65-70	6	19
β-strand	75-80	6	19
α-helix	85-87	3
β-strand	89-95	7	20
β-strand	99	1	18
β-strand	112-113	2	20
β-strand	117-122	6	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Botulinum neurotoxin type E	A	protein	850	Clostridium botulinum	Q00496 (AlphaFold model)
Jle-E5	B	protein	128	Vicugna pacos

Sequence of entity 1 (A), FASTA

>7K84_1 Botulinum neurotoxin type E (chains A)
GPLGSMPKINSFNYNDPVNDRTILYIKPGGCQEFYKSFNIMKNIWIIPERNVIGTTPQDF
HPPTSLKNGDSSYYDPNYLQSDEEKDRFLKIVTKIFNRINNNLSGGILLEELSKANPYLG
NDNTPDNQFHIGDASAVEIKFSNGSQDILLPNVIIMGAEPDLFETNSSNISLRNNYMPSN
HGFGSIAIVTFSPEYSFRFNDNSMNEFIQDPALTLMHELIHSLHGLYGAKGITTKYTITQ
KQNPLITNIRGTNIEEFLTFGGTDLNIITSAQSNDIYTNLLADYKKIASKLSKVQVSNPL
LNPYKDVFEAKYGLDKDASGIYSVNINKFNDIFKKLYSFTEFDLATKFQVKCRQTYIGQY
KYFKLSNLLNDSIYNISEGYNINNLKVNFRGQNANLNPRIITPITGRGLVKKIIRFCKNI
VSVKGIRKSICIEINNGELFFVASENSYNDDNINTPKEIDDTVTSNNNYENDLDQVILNF
NSESAPGLSDEKLNLTIQNDAYIPKYDSNGTSDIEQHDVNELNVFFYLDAQKVPEGENNV
NLTSSIDTALLEQPKIYTFFSSEFINNVNKPVQAALFVSWIQQVLVDFTTEANQKSTVDK
IADISIVVPYIGLALNIGNEAQKGNFKDALELLGAGILLEFEPELLIPTILVFTIKSFLG
SSDNKNKVIKAINNALKERDEKWKEVYSFIVSNWMTKINTQFNKRKEQMYQALQNQVNAI
KTIIESKYNSYTLEEKNELTNKYDIKQIENELNQKVSIAMNNIDRFLTESSISYLMKLIN
EVKINKLREYDENVKTYLLNYIIQHGSILGESQQELNSMVTDTLNNSIPFKLSSYTDDKI
LISYFNKFFK

Sequence of entity 2 (B), FASTA

>7K84_2 JLE-E5 (chains B)
GPLGSQVQLVETGGGLVQAGGSLRLSCAASGRSYAMGWFRQGPGKEREFVATISWSSTNT
WYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAASHRFSDYPMRSEDGMDYWGK
GTLVTVSS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Water and common crystallization additives (SO4) are not listed.

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…
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
9ARJ 3.4 Å, CryoEM structure of BoNT-NTNH-OrfX2 complex from Clostridium botulinum E1, major class

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