9ARJ: Toxin

Name: PDB 9ARJ: CryoEM structure of BoNT-NTNH-OrfX2 complex from Clostridium botulinum E1, major 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, major class. Determined by electron microscopy at 3.4 Å resolution. Released 22 Jan 2025.

Method: Electron microscopy
Resolution: 3.4 Å
Organism: Clostridium botulinum E1 str. 'BoNT E Beluga'
Chains: 3
Atoms: 24,188
Mol. weight: 365.25 kDa
Released: 22 Jan 2025

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

Secondary structure: helices and β-sheets

9ARJ contains 114 α-helices and 180 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, 74 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	12-13	2
β-strand	18-22	5	12
β-strand	30-36	7	12
β-strand	39-42	4	12
α-helix	52-55	4
β-strand	60-61	2	13
β-strand	67-68	2	14
α-helix	77-96	20
α-helix	98-108	11
α-helix	111-113	3
α-helix	124-126	3
β-strand	132-135	4	12
β-strand	141-144	4	12
β-strand	148-151	4	12
β-strand	161-164	4	12
β-strand	167	1	15
β-strand	171	1	15
α-helix	173-175	3
β-strand	182-185	4	12
β-strand	190-195	6	16
β-strand	201-203	3	16
α-helix	206-221	16
α-helix	225-228	4
β-strand	232-233	2	17
β-strand	235	1	18
α-helix	236-237	2
β-strand	241	1	19
α-helix	245-246	2
β-strand	247-248	2	17
α-helix	249-255	7
α-helix	259-261	3
α-helix	265-286	22
α-helix	297-306	10
β-strand	309-311	3	20
β-strand	317-319	3	20
α-helix	321-333	13
α-helix	336-342	7
β-strand	356-360	5	16
α-helix	378-387	10
β-strand	388	1	16
α-helix	393-395	3
β-strand	396-397	2	16
β-strand	404-405	2	14
β-strand	408-416	9	21
β-strand	422-430	9	21
α-helix	431-433	3
β-strand	435	1	19
β-strand	438	1	18
α-helix	468-473	6
β-strand	505-506	2	13
β-strand	510-513	4	21
α-helix	519-526	8
α-helix	528-529	2
β-strand	536-538	3	22
α-helix	541-546	6
β-strand	550-552	3	22
α-helix	557-564	8
α-helix	569-571	3
α-helix	572-587	16
β-strand	591-592	2	23
β-strand	601-602	2	23
α-helix	604-606	3
α-helix	607-610	4
α-helix	615-619	5
α-helix	621-628	8
α-helix	629-632	4
α-helix	638-640	3
α-helix	643-648	6
α-helix	650-652	3
α-helix	662-725	64
α-helix	744-780	37
α-helix	782-800	19
α-helix	809-820	12
β-strand	822	1	24
α-helix	823-825	3
α-helix	836-850	15
β-strand	851-854	4	25
β-strand	855-857	3	26
β-strand	862-864	3	26
β-strand	871-875	5	27
α-helix	878	1
β-strand	879-880	2	25
α-helix	881	1
β-strand	888-891	4	25
β-strand	897-901	5	27
β-strand	915-922	8	25
β-strand	926	1	28
β-strand	937-943	7	27
β-strand	949-955	7	27
β-strand	958-964	7	27
β-strand	970-976	7	27
β-strand	990-997	8	25
β-strand	1002-1007	6	25
β-strand	1010-1016	7	25
β-strand	1025-1031	7	27
β-strand	1041-1050	10	25
α-helix	1056-1065	10
β-strand	1071	1	29
β-strand	1073	1	30
β-strand	1079	1	30
α-helix	1080	1
β-strand	1081	1	31
β-strand	1086-1090	5	32
β-strand	1099-1101	3	32
β-strand	1105-1107	3	32
β-strand	1114	1	33
β-strand	1119	1	33
β-strand	1126-1131	6	32
β-strand	1141	1	31
β-strand	1143	1	29
β-strand	1147-1153	7	32
β-strand	1159-1164	6	32
β-strand	1172-1177	6	32
β-strand	1186-1193	8	32
β-strand	1196-1203	8	32
β-strand	1208-1215	8	32
β-strand	1218-1222	5	32
α-helix	1224-1227	4
β-strand	1240-1243	4	32
β-strand	1249	1	28

Chain B: 49 helices, 71 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	34
β-strand	29-36	8	34
β-strand	39-41	3	34
α-helix	58-59	2
β-strand	63	1	35
β-strand	64	1	36
α-helix	72-91	20
α-helix	93-104	12
α-helix	106-110	5
β-strand	111-113	3	37
β-strand	116-117	2	37
β-strand	119	1	38
β-strand	123-125	3	34
β-strand	131-132	2	34
β-strand	136-139	4	34
β-strand	144	1	36
β-strand	149-152	4	34
α-helix	155-159	5
β-strand	166-169	4	34
β-strand	174-176	3	39
β-strand	177-178	2	40
β-strand	181-182	2	40
α-helix	183-184	2
α-helix	185-201	17
β-strand	210-215	6	41
β-strand	224-228	5	41
α-helix	229-235	7
α-helix	237-243	7
α-helix	254-272	19
α-helix	281-290	10
α-helix	295-300	6
α-helix	303-310	8
α-helix	322-325	4
β-strand	330-332	3	39
β-strand	339-340	2	42
β-strand	343-344	2	42
α-helix	347-350	4
α-helix	354	1
β-strand	355	1	39
α-helix	356	1
α-helix	357-360	4
β-strand	362	1	35
β-strand	368-373	6	43
β-strand	379-385	7	43
β-strand	391-393	3	41
α-helix	398-400	3
β-strand	402-403	2	44
α-helix	423-427	5
α-helix	429-433	5
β-strand	439	1	38
α-helix	445-447	3
β-strand	457-461	5	43
α-helix	464-465	2
α-helix	466-472	7
β-strand	482-483	2	45
α-helix	486-491	6
β-strand	497-498	2	45
α-helix	502-510	9
α-helix	515-517	3
α-helix	520-538	19
β-strand	542-546	5	46
β-strand	549-553	5	46
α-helix	557-561	5
α-helix	570-577	8
α-helix	579-582	4
α-helix	591-592	2
β-strand	593-594	2	44
α-helix	597-600	4
α-helix	601-603	3
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	757-767	11
α-helix	779-783	5
α-helix	789-797	9
β-strand	801-804	4	47
β-strand	805-809	5	48
β-strand	814-818	5	48
β-strand	825-827	3	49
β-strand	833-836	4	47
β-strand	841-845	5	47
β-strand	852-855	4	49
α-helix	857-860	4
β-strand	867-875	9	47
β-strand	883-890	8	24
β-strand	893-900	8	24
β-strand	903-909	7	24
β-strand	915-920	6	24
β-strand	929-936	8	47
β-strand	941-946	6	47
β-strand	949-955	7	47
β-strand	967-970	4	49
β-strand	977-985	9	47
α-helix	991-1002	12
β-strand	1008	1	50
α-helix	1013	1
β-strand	1014	1	50
α-helix	1015	1
β-strand	1021	1	51
β-strand	1022-1025	4	52
β-strand	1028	1	52
β-strand	1033-1038	6	51
β-strand	1041-1046	6	51
α-helix	1054-1057	4
β-strand	1059-1062	4	51
β-strand	1075-1077	3	52
β-strand	1078-1082	5	51
β-strand	1086-1091	6	51
β-strand	1097	1	53
β-strand	1098-1101	4	51
α-helix	1104-1106	3
β-strand	1110-1114	5	52
β-strand	1122-1126	5	52
β-strand	1129-1130	2	52
β-strand	1132-1137	6	53
β-strand	1140-1144	5	53
β-strand	1158-1161	4	52

Chain C: 18 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	175-179	5	1
α-helix	182-191	10
β-strand	198-204	7	2
β-strand	207-214	8	2
α-helix	216-218	3
β-strand	219-220	2	3
β-strand	226	1	1
β-strand	229-234	6	3
β-strand	237-242	6	2
β-strand	245-248	4	2
β-strand	249	1	4
α-helix	250	1
β-strand	254-259	6	3
β-strand	261-267	7	5
β-strand	280-286	7	5
β-strand	298-303	6	3
β-strand	306	1	4
α-helix	315-329	15
β-strand	340-343	4	5
α-helix	350-355	6
β-strand	359-365	7	1
β-strand	368-370	3	6
β-strand	378-380	3	6
β-strand	386-392	7	1
α-helix	408-413	6
β-strand	417-421	5	1
α-helix	423-437	15
β-strand	446-449	4	7
β-strand	454-457	4	7
α-helix	468-470	3
β-strand	483-487	5	8
β-strand	490-503	14	8
β-strand	506-523	18	8
β-strand	526-533	8	8
β-strand	538-543	6	8
α-helix	545-550	6
α-helix	552-563	12
α-helix	564-568	5
α-helix	577-586	10
β-strand	590	1	9
β-strand	593	1	9
β-strand	594-599	6	8
α-helix	602-609	8
α-helix	614-632	19
α-helix	643-649	7
α-helix	656-673	18
α-helix	683-696	14
α-helix	706-712	7
β-strand	722-725	4	10
β-strand	732	1	11
β-strand	734	1	11
β-strand	735-739	5	1
β-strand	740-743	4	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Toxin	C	protein	748	Clostridium botulinum E1 str. 'BoNT E Beluga'	A0A6B4JMW3 (AlphaFold model)
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)

Sequence of entity 1 (C), FASTA

>9ARJ_1 Toxin (chains C)
MTNLKPYIIYDWKETILKNSKDNYSINESIPKIFSKKICGGRFFNSTLSGNWKSWTLTDE
GEGPHPVLKCTIDNGYLEIYSNTSSEKHSLKDIEIKVCMSIKPNSDGTHSLCKNSFYIKT
NSLKLSEDRLILSHCLDKLILAWFKDNHKYIELFINRSRIQTRVEGDLSLLGWDIESSVS
YKTMNEFIKKDNLYEKKFHQYMEVRRNEYTIDGEFGPWQMTTGADGQNIRFLCPIKSATY
KINDDVYIAKPDNFIIIQVDLKYFDSKTTIIDPSGLNNGQQFNLKVKTDSTDEINAVILV
GSRITDVNEDLYPGDDVSLEIVFKTWFNANIQKFTQIFSYILLNETSKIPEYQWLKPTQI
SYGSASVTMPDPSNPNKELSNLDASTFAAMAMVENHKNDRPNHAVDNRFLELSKTPAAFA
ISMPEFLKHFLVTGLQAMQIDNLDAFEVSSENLVITNKKKINFGKIQDQNRQVDALIEPN
NFKLAIQNNQVVVEIVDATWQQVVGVTGHFGYRQAYNLILKNENNVYKPMLEESGDVTIS
YMVTEEAWKTTQDAIISATVGLVVGTIIGTAFSKLSDKLYKFLKSKFIVKNKKASLKISG
KDINEVIEMSDISKPQLLSIKKANAKISTEEVGLISQNGSTSLENLAIFKNKPRPIGERV
QILGLKLVSGLITTFGWSIGFVLPDILKDVINANINNNFEVLPGIQQFTQQCIGSIQWPD
NSELKIDFAKLQGVYLLGGNLVKIPESN

Sequence of entity 2 (A), FASTA

>9ARJ_2 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 3 (B), FASTA

>9ARJ_3 Peptidase M27 (chains B)
MKINGNLNIDSPVDNKNVAIVRSRKSDVFFKAFQVAPNIWIVPERYYGESLKINEDQKFD
GGIYDSNFLSTNNEKDDFLQATIKLLQRINNNVVGAKLLSLISTAIPFPYENNTEDYRQT
NYLSSKNNEHYYTANLVIFGPGSNIIKNNVIYYKKEYAESGMGTMLEIWFQPFLTHKYDE
FYVDPALELIKCLIKSLYYLYGIKPNDNLNIPYRLRNEFNSLEYSELDMIDFLISGGIDY
KLLNTNPYWFIDKYFIDTSKNFEKYKNDYEIKIKNNNYIANSIKLYLEQKFKINVKDIWE
LNLSYFSKEFQIMMPERYNNALNHYYRKEYYVIDYFKNYNINGFKNGQIKTKLPLSKYNK
EIINKPELIVNLINQNNTVLMKSNIYGDGLKGTVDNFYSNYIIPYNLNYEHSINYSYLDN
VNIEEIEKIPPINDEDIYPYRKNADTFIPVYNITKAKEINTTTPLPVNYLQAQMIDSNDI
NLSSDFLKVISSKGSLVYSFLNNTMDYLEFIKYDKPIDTDKKYYKWLKAIFRNYSLDITE
TQEISNQFGDTKIIPWIGRALNILNTNNSFVEEFKNLGPISLINKKENITIPKIKIDEIP
SSMLNFSFKDLSENLFNIYCKNNFYLKKIYYNFLDQWWTQYYSQYFDLICMASKSVLAQE
KLIKKLIQKQLRYLMENSNISSTNLILINLTTTNTLRDISNQSQIAINNIDKFFNNAAMC
VFENNIYPKFTSFMEQCIKNINKSTKEFILKCTNINETEKSHLIMQNSFSNLDFDFLDIQ
NMKNLFNSYTELLIKEQTSPYELSLYAFQEQDNNVIGDTSGKNTLVEYPKDIGLVYGINN
NAIHLTGANQNIKFTNDYFENGLTNNFSIYFWLRNLKQNTIKSKLIGSKEDNCGWEIYFE
NDGLVFNIIDSNGNEKNIYLSNISNNSWHYIVISINRLKDQLLIFIDNILVANEDIKEIL
NIYSSDIISLLSDNNNVYIEGLSVLNKTINSNEILTDYFSDLNNSYIRNFDEEILQYNRT
YELFNYVFPEIAINKIEQNNNIYLSINNENNLNFKPLKFKLLNTNPNKQYVQKWDEVIFS
VLDGTEKYLDISTTNNRIQLVDNKNNAQIFIINNDIFISNCLTLTYNNVNIYLSIKNQDY
NWVICDLNHDIPKKSYLWILKNI

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 A0A6B4JMW3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8FBF 1.85 Å, Crystal structure of OrfX2 from Clostridium botulinum E1

Browse structure collections

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