9ARK: Botulinum neurotoxin

Name: PDB 9ARK: CryoEM structure of BoNT-NTNH-OrfX2 complex from Clostridium botulinum E1, minor class
Published: 2025-01-22
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

CryoEM structure of BoNT-NTNH-OrfX2 complex from Clostridium botulinum E1, minor class. Determined by electron microscopy at 4.1 Å resolution. Released 22 Jan 2025.

Method: Electron microscopy
Resolution: 4.1 Å
Organism: Clostridium botulinum E1 str. 'BoNT E Beluga'
Chains: 3
Atoms: 24,165
Mol. weight: 365.25 kDa
Released: 22 Jan 2025

Explore 9ARK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9ARK contains 114 α-helices and 198 β-strands across 3 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: 47 helices, 87 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
β-strand	18-22	5	1
β-strand	30-36	7	1
β-strand	39-41	3	1
α-helix	52-55	4
β-strand	60-61	2	2
β-strand	67-68	2	3
α-helix	77-96	20
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	161-164	4	1
β-strand	167	1	4
β-strand	171	1	4
α-helix	173-175	3
β-strand	182-185	4	1
β-strand	190-195	6	5
β-strand	201-203	3	5
α-helix	206-221	16
β-strand	232-233	2	6
β-strand	235	1	7
β-strand	241	1	8
β-strand	247-248	2	6
α-helix	249-255	7
α-helix	257-262	6
α-helix	265-287	23
α-helix	294-296	3
α-helix	299-306	8
β-strand	309-310	2	9
β-strand	318-319	2	9
α-helix	321-333	13
α-helix	336-343	8
β-strand	356-360	5	5
β-strand	370	1	10
β-strand	374	1	10
α-helix	378-384	7
β-strand	388	1	5
α-helix	393-395	3
β-strand	396-397	2	5
β-strand	404-405	2	3
β-strand	408-416	9	11
β-strand	422-430	9	11
α-helix	431-433	3
β-strand	435	1	8
β-strand	438	1	7
α-helix	440-442	3
α-helix	446-448	3
β-strand	452	1	12
α-helix	468-473	6
β-strand	496	1	4
β-strand	505-506	2	2
β-strand	510-513	4	11
α-helix	519-524	6
α-helix	528-529	2
β-strand	536-538	3	13
α-helix	541-546	6
β-strand	550-552	3	13
α-helix	557-564	8
α-helix	571-587	17
β-strand	591-592	2	14
β-strand	601-602	2	14
α-helix	604-606	3
α-helix	607-610	4
α-helix	615-619	5
α-helix	621-628	8
α-helix	629-631	3
α-helix	643-647	5
β-strand	649	1	12
α-helix	657-659	3
α-helix	660-688	29
α-helix	689-693	5
α-helix	694-725	32
α-helix	744-780	37
α-helix	782-799	18
α-helix	801-804	4
α-helix	809-818	10
β-strand	822	1	15
α-helix	823-826	4
α-helix	837-848	12
β-strand	851-854	4	16
β-strand	855-857	3	17
β-strand	862-864	3	17
β-strand	871-876	6	18
β-strand	879-880	2	16
β-strand	887-891	5	16
β-strand	896-901	6	18
β-strand	909-910	2	19
β-strand	916-922	7	16
β-strand	926	1	20
α-helix	928-930	3
β-strand	937-943	7	18
β-strand	949-955	7	18
β-strand	958-964	7	18
β-strand	970-976	7	18
β-strand	982	1	21
β-strand	990-997	8	16
β-strand	1002-1007	6	16
β-strand	1010-1016	7	16
β-strand	1023-1024	2	19
β-strand	1025-1034	10	18
β-strand	1041-1050	10	16
α-helix	1056-1065	10
β-strand	1071	1	22
β-strand	1073	1	23
β-strand	1079	1	23
α-helix	1080	1
β-strand	1081	1	24
β-strand	1085-1090	6	25
β-strand	1096	1	26
β-strand	1099-1100	2	25
β-strand	1105	1	27
β-strand	1106-1107	2	25
α-helix	1110	1
β-strand	1111	1	26
α-helix	1112-1113	2
β-strand	1114-1115	2	21
β-strand	1118-1119	2	21
β-strand	1126-1131	6	25
β-strand	1141	1	24
β-strand	1143	1	22
β-strand	1147-1153	7	25
β-strand	1159-1161	3	25
β-strand	1162-1164	3	27
β-strand	1174	1	25
β-strand	1175-1177	3	27
β-strand	1186-1191	6	25
β-strand	1198-1203	6	25
β-strand	1208-1215	8	25
β-strand	1218-1222	5	25
α-helix	1224-1227	4
β-strand	1240-1243	4	25
β-strand	1249	1	20

Chain B: 50 helices, 74 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	28
β-strand	29-36	8	28
β-strand	39-41	3	28
α-helix	55-57	3
α-helix	58-59	2
β-strand	63	1	29
β-strand	64	1	30
α-helix	72-91	20
α-helix	93-104	12
α-helix	106-109	4
β-strand	110-111	2	31
β-strand	117-118	2	31
β-strand	119	1	32
β-strand	122-124	3	33
β-strand	125	1	28
β-strand	131-133	3	33
β-strand	136-139	4	28
β-strand	144	1	30
β-strand	149-152	4	28
α-helix	155-160	6
β-strand	166-169	4	28
β-strand	174-176	3	34
β-strand	177-178	2	35
β-strand	181-182	2	35
α-helix	183-184	2
α-helix	185-200	16
α-helix	204-206	3
β-strand	210-216	7	36
β-strand	223-228	6	36
α-helix	229-234	6
α-helix	239-242	4
α-helix	253-268	16
α-helix	269-273	5
α-helix	281-290	10
α-helix	295-299	5
α-helix	303-310	8
α-helix	322-325	4
β-strand	330-332	3	34
β-strand	339-340	2	37
β-strand	343-344	2	37
α-helix	347-350	4
α-helix	354	1
β-strand	355	1	34
α-helix	356	1
α-helix	357-360	4
β-strand	362	1	29
β-strand	368-373	6	38
β-strand	379-385	7	38
β-strand	391-393	3	36
β-strand	402-403	2	39
α-helix	404	1
α-helix	423-427	5
α-helix	430-433	4
α-helix	434-436	3
β-strand	439	1	32
β-strand	457-461	5	38
α-helix	466-472	7
β-strand	482-483	2	40
α-helix	486-491	6
β-strand	497-498	2	40
α-helix	502-510	9
α-helix	515-516	2
α-helix	520-538	19
β-strand	542-546	5	41
β-strand	549-553	5	41
α-helix	557-561	5
α-helix	571-577	7
α-helix	579-582	4
α-helix	591-592	2
β-strand	593-594	2	39
α-helix	608-636	29
α-helix	637-642	6
α-helix	643-676	34
α-helix	682-721	40
α-helix	722-726	5
α-helix	727-751	25
α-helix	757-765	9
α-helix	771-774	4
α-helix	779-786	8
α-helix	789-797	9
β-strand	801-804	4	42
β-strand	805-809	5	43
β-strand	814-818	5	43
β-strand	825-827	3	15
β-strand	833-836	4	42
β-strand	841-845	5	42
β-strand	853-855	3	15
α-helix	857-860	4
β-strand	867-875	9	42
β-strand	883-890	8	15
β-strand	893-900	8	15
β-strand	903-909	7	15
β-strand	915-920	6	15
β-strand	928-936	9	42
β-strand	941-946	6	42
β-strand	949-954	6	42
β-strand	967-969	3	15
β-strand	977-985	9	42
α-helix	991-1002	12
β-strand	1008	1	44
α-helix	1013	1
β-strand	1014	1	44
α-helix	1015	1
β-strand	1016	1	45
β-strand	1020-1025	6	46
β-strand	1028	1	46
β-strand	1033-1038	6	46
β-strand	1041-1046	6	46
α-helix	1054-1057	4
β-strand	1058-1063	6	46
β-strand	1070	1	45
β-strand	1076-1082	7	46
β-strand	1086-1091	6	46
β-strand	1097	1	47
β-strand	1098-1101	4	46
β-strand	1109-1114	6	46
β-strand	1122-1126	5	46
β-strand	1129-1131	3	46
β-strand	1132-1133	2	47
β-strand	1137	1	48
β-strand	1140	1	48
β-strand	1143-1144	2	47
α-helix	1153-1156	4
β-strand	1158-1161	4	46

Chain C: 17 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	175-180	6	49
α-helix	181-191	11
β-strand	197-204	8	50
β-strand	207-215	9	50
β-strand	219-220	2	51
β-strand	228-234	7	51
β-strand	235-242	8	50
β-strand	245-248	4	50
β-strand	249	1	52
β-strand	254-260	7	51
β-strand	261-266	6	53
β-strand	280-286	7	53
β-strand	298	1	51
β-strand	302-303	2	51
β-strand	306	1	52
α-helix	315-329	15
β-strand	340-343	4	53
α-helix	350-355	6
β-strand	357-364	8	49
β-strand	368-370	3	54
β-strand	378-380	3	54
β-strand	386-393	8	49
β-strand	404	1	49
α-helix	409-413	5
β-strand	417-421	5	49
α-helix	423-435	13
α-helix	443-445	3
β-strand	446-448	3	55
β-strand	455-457	3	55
β-strand	461-466	6	56
α-helix	468-470	3
β-strand	473-477	5	56
β-strand	483-487	5	55
β-strand	490-494	5	55
β-strand	498-499	2	55
β-strand	508-523	16	55
β-strand	526-533	8	55
β-strand	538-544	7	55
α-helix	545-550	6
α-helix	552-567	16
α-helix	577-586	10
β-strand	588-590	3	55
β-strand	593-599	7	55
α-helix	602-609	8
α-helix	614-633	20
α-helix	643-651	9
α-helix	656-673	18
α-helix	683-696	14
α-helix	699-701	3
α-helix	706-713	8
β-strand	716-717	2	53
β-strand	722-726	5	49
β-strand	731-732	2	49
β-strand	734-743	10	49

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Botulinum neurotoxin	A	protein	1252	Clostridium botulinum E1 str. 'BoNT E Beluga'	Q00496 (AlphaFold model)
Peptidase M27	B	protein	1163	Clostridium botulinum E1 str. 'BoNT E Beluga'	P46082 (AlphaFold model)
Toxin	C	protein	748	Clostridium botulinum E1 str. 'BoNT E Beluga'	C1FUH4 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9ARK_1 Botulinum neurotoxin (chains A)
MPKINSFNYNDPVNDRTILYIKPGGCQEFYKSFNIMKNIWIIPERNVIGTTPQDFHPPTS
LKNGDSSYYDPNYLQSDEEKDRFLKIVTKIFNRINNNLSGGILLEELSKANPYLGNDNTP
DNQFHIGDASAVEIKFSNGSQDILLPNVIIMGAEPDLFETNSSNISLRNNYMPSNHGFGS
IAIVTFSPEYSFRFNDNSMNEFIQDPALTLMAALIASLHGLYGAKGITTKYTITQKQNPL
ITNIRGTNIEEFLTFGGTDLNIITSAQSNDIYTNLLADYKKIASKLSKVQVSNPLLNPYK
DVFEAKYGLDKDASGIYSVNINKFNDIFKKLYSFTEFDLATKFQVKCRQTYIGQYKYFKL
SNLLNDSIYNISEGYNINNLKVNFRGQNANLNPRIITPITGRGLVKKIIRFCKNIVSVKG
IRKSICIEINNGELFFVASENSYNDDNINTPKEIDDTVTSNNNYENDLDQVILNFNSESA
PGLSDEKLNLTIQNDAYIPKYDSNGTSDIEQHDVNELNVFFYLDAQKVPEGENNVNLTSS
IDTALLEQPKIYTFFSSEFINNVNKPVQAALFVSWIQQVLVDFTTEANQKSTVDKIADIS
IVVPYIGLALNIGNEAQKGNFKDALELLGAGILLEFEPELLIPTILVFTIKSFLGSSDNK
NKVIKAINNALKERDEKWKEVYSFIVSNWMTKINTQFNKRKEQMYQALQNQVNAIKTIIE
SKYNSYTLEEKNELTNKYDIKQIENELNQKVSIAMNNIDRFLTESSISYLMKLINEVKIN
KLREYDENVKTYLLNYIIQHGSILGESQQELNSMVTDTLNNSIPFKLSSYTDDKILISYF
NKFFKRIKSSSVLNMRYKNDKYVDTSGYDSNININGDVYKYPTNKNQFGIYNDKLSEVNI
SQNDYIIYDNKYKNFSISFWVRIPNYDNKIVNVNNEYTIINCMRDNNSGWKVSLNHNEII
WTLQDNAGINQKLAFNYGNANGISDYINKWIFVTITNDRLGDSKLYINGNLIDQKSILNL
GNIHVSDNILFKIVNCSYTRYIGIRYFNIFDKELDETEIQTLYSNEPNTNILKDFWGNYL
LYDKEYYLLNVLKPNNFIDRRKDSTLSINNIRSTILLANRLYSGIKVKIQRVNNSSTNDN
LVRKNDQVYINFVASKTHLFPLYADTATTNKEKTIKISSSGNRFNQVVVMNSVGNNCTMN
FKNNNGNNIGLLGFKADTVVASTWYYTHMRDHTNSNGCFWNFISEEHGWQEK

Sequence of entity 2 (B), FASTA

>9ARK_2 Peptidase M27 (chains B)
MKINGNLNIDSPVDNKNVAIVRSRKSDVFFKAFQVAPNIWIVPERYYGESLKINEDQKFD
GGIYDSNFLSTNNEKDDFLQATIKLLQRINNNVVGAKLLSLISTAIPFPYENNTEDYRQT
NYLSSKNNEHYYTANLVIFGPGSNIIKNNVIYYKKEYAESGMGTMLEIWFQPFLTHKYDE
FYVDPALELIKCLIKSLYYLYGIKPNDNLNIPYRLRNEFNSLEYSELDMIDFLISGGIDY
KLLNTNPYWFIDKYFIDTSKNFEKYKNDYEIKIKNNNYIANSIKLYLEQKFKINVKDIWE
LNLSYFSKEFQIMMPERYNNALNHYYRKEYYVIDYFKNYNINGFKNGQIKTKLPLSKYNK
EIINKPELIVNLINQNNTVLMKSNIYGDGLKGTVDNFYSNYIIPYNLNYEHSINYSYLDN
VNIEEIEKIPPINDEDIYPYRKNADTFIPVYNITKAKEINTTTPLPVNYLQAQMIDSNDI
NLSSDFLKVISSKGSLVYSFLNNTMDYLEFIKYDKPIDTDKKYYKWLKAIFRNYSLDITE
TQEISNQFGDTKIIPWIGRALNILNTNNSFVEEFKNLGPISLINKKENITIPKIKIDEIP
SSMLNFSFKDLSENLFNIYCKNNFYLKKIYYNFLDQWWTQYYSQYFDLICMASKSVLAQE
KLIKKLIQKQLRYLMENSNISSTNLILINLTTTNTLRDISNQSQIAINNIDKFFNNAAMC
VFENNIYPKFTSFMEQCIKNINKSTKEFILKCTNINETEKSHLIMQNSFSNLDFDFLDIQ
NMKNLFNSYTELLIKEQTSPYELSLYAFQEQDNNVIGDTSGKNTLVEYPKDIGLVYGINN
NAIHLTGANQNIKFTNDYFENGLTNNFSIYFWLRNLKQNTIKSKLIGSKEDNCGWEIYFE
NDGLVFNIIDSNGNEKNIYLSNISNNSWHYIVISINRLKDQLLIFIDNILVANEDIKEIL
NIYSSDIISLLSDNNNVYIEGLSVLNKTINSNEILTDYFSDLNNSYIRNFDEEILQYNRT
YELFNYVFPEIAINKIEQNNNIYLSINNENNLNFKPLKFKLLNTNPNKQYVQKWDEVIFS
VLDGTEKYLDISTTNNRIQLVDNKNNAQIFIINNDIFISNCLTLTYNNVNIYLSIKNQDY
NWVICDLNHDIPKKSYLWILKNI

Sequence of entity 3 (C), FASTA

>9ARK_3 Toxin (chains C)
MTNLKPYIIYDWKETILKNSKDNYSINESIPKIFSKKICGGRFFNSTLSGNWKSWTLTDE
GEGPHPVLKCTIDNGYLEIYSNTSSEKHSLKDIEIKVCMSIKPNSDGTHSLCKNSFYIKT
NSLKLSEDRLILSHCLDKLILAWFKDNHKYIELFINRSRIQTRVEGDLSLLGWDIESSVS
YKTMNEFIKKDNLYEKKFHQYMEVRRNEYTIDGEFGPWQMTTGADGQNIRFLCPIKSATY
KINDDVYIAKPDNFIIIQVDLKYFDSKTTIIDPSGLNNGQQFNLKVKTDSTDEINAVILV
GSRITDVNEDLYPGDDVSLEIVFKTWFNANIQKFTQIFSYILLNETSKIPEYQWLKPTQI
SYGSASVTMPDPSNPNKELSNLDASTFAAMAMVENHKNDRPNHAVDNRFLELSKTPAAFA
ISMPEFLKHFLVTGLQAMQIDNLDAFEVSSENLVITNKKKINFGKIQDQNRQVDALIEPN
NFKLAIQNNQVVVEIVDATWQQVVGVTGHFGYRQAYNLILKNENNVYKPMLEESGDVTIS
YMVTEEAWKTTQDAIISATVGLVVGTIIGTAFSKLSDKLYKFLKSKFIVKNKKASLKISG
KDINEVIEMSDISKPQLLSIKKANAKISTEEVGLISQNGSTSLENLAIFKNKPRPIGERV
QILGLKLVSGLITTFGWSIGFVLPDILKDVINANINNNFEVLPGIQQFTQQCIGSIQWPD
NSELKIDFAKLQGVYLLGGNLVKIPESN

Primary citation

Botulinum neurotoxins exploit host digestive proteases to boost their oral toxicity via activating OrfXs/P47. Gao, L., Nowakowska, M.B., Selby, K. et al. Nat Struct Mol Biol (2025) 32:864-875. DOI 10.1038/s41594-024-01479-0 · 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

Browse structure collections

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