9ARL: Botulinum neurotoxin type A

Name: PDB 9ARL: CryoEM structure of BoNT-NTNH-OrfX2 complex from Clostridium botulinum strain A1-ST7B, 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 strain A1-ST7B, major class. Determined by electron microscopy at 4.0 Å resolution. Released 22 Jan 2025.

Method: Electron microscopy
Resolution: 4.0 Å
Organisms: Clostridium botulinum A str. Hall, Clostridium botulinum A
Chains: 3
Atoms: 24,054
Mol. weight: 369.59 kDa
Released: 22 Jan 2025

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

Secondary structure: helices and β-sheets

9ARL contains 117 α-helices and 189 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: 51 helices, 80 β-strands

Element	Residues	Length	Sheet
α-helix	13-14	2
β-strand	19-23	5	1
β-strand	26	1	2
β-strand	33-39	7	1
β-strand	42-45	4	1
α-helix	54-56	3
α-helix	61-62	2
α-helix	81-100	20
α-helix	102-113	12
α-helix	115-117	3
β-strand	126-128	3	3
α-helix	131-133	3
β-strand	134-138	5	1
α-helix	139	1
β-strand	144-148	5	1
β-strand	151-154	4	1
β-strand	165-166	2	1
β-strand	168	1	4
β-strand	184-187	4	1
β-strand	192-196	5	5
α-helix	200-202	3
β-strand	213-214	2	5
α-helix	217-232	16
α-helix	236-238	3
β-strand	242	1	6
β-strand	245	1	7
β-strand	252	1	8
β-strand	259	1	6
α-helix	260-266	7
α-helix	276-298	23
β-strand	302-304	3	3
β-strand	306	1	9
α-helix	310-321	12
β-strand	324-325	2	10
β-strand	331-332	2	10
α-helix	335-342	8
α-helix	343-348	6
α-helix	351-358	8
β-strand	372-375	4	5
β-strand	385	1	11
β-strand	389	1	11
α-helix	399-404	6
β-strand	405	1	5
α-helix	410-412	3
β-strand	414-416	3	5
β-strand	426-431	6	12
β-strand	453-458	6	12
α-helix	459-461	3
β-strand	463	1	8
β-strand	466	1	7
α-helix	468-470	3
β-strand	479-481	3	13
α-helix	485-490	6
α-helix	492-494	3
α-helix	496-505	10
β-strand	517	1	9
β-strand	525	1	2
β-strand	528	1	4
α-helix	531-538	8
β-strand	542	1	12
β-strand	545	1	12
α-helix	550-555	6
β-strand	567-569	3	14
α-helix	572-577	6
β-strand	581-583	3	14
α-helix	588-595	8
α-helix	603-617	15
α-helix	637-641	5
α-helix	649-658	10
α-helix	661-663	3
α-helix	673-678	6
β-strand	679-681	3	13
α-helix	682-683	2
α-helix	688-717	30
α-helix	718-722	5
α-helix	723-753	31
α-helix	756-761	6
α-helix	766-795	30
α-helix	796-800	5
α-helix	801-825	25
α-helix	834-846	13
α-helix	853-855	3
α-helix	862-875	14
β-strand	877-880	4	15
β-strand	881-884	4	16
β-strand	887-890	4	16
β-strand	897-900	4	17
β-strand	905-906	2	15
β-strand	913-916	4	15
β-strand	924-927	4	17
β-strand	935-936	2	18
β-strand	941-948	8	15
α-helix	950-952	3
α-helix	955-957	3
β-strand	962-968	7	17
β-strand	973-979	7	17
β-strand	982-988	7	17
β-strand	994-1000	7	17
β-strand	1004	1	19
β-strand	1015-1021	7	15
β-strand	1026-1031	6	15
β-strand	1034-1040	7	15
β-strand	1047-1048	2	18
β-strand	1049-1058	10	17
β-strand	1067-1075	9	15
α-helix	1081-1091	11
β-strand	1096	1	20
β-strand	1098	1	21
β-strand	1104	1	21
α-helix	1105	1
β-strand	1111-1115	5	22
β-strand	1122-1125	4	22
β-strand	1134-1137	4	22
β-strand	1143-1145	3	19
β-strand	1149-1151	3	19
β-strand	1159-1164	6	22
β-strand	1175	1	20
β-strand	1178-1185	8	22
β-strand	1190-1194	5	22
β-strand	1195	1	23
β-strand	1203-1205	3	22
β-strand	1207-1209	3	22
α-helix	1211-1213	3
β-strand	1218	1	23
β-strand	1220-1224	5	22
β-strand	1235-1240	6	22
β-strand	1246-1255	10	22
β-strand	1258-1264	7	22
α-helix	1266-1269	4
α-helix	1277-1280	4
β-strand	1282-1286	5	22

Chain B: 47 helices, 71 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3
β-strand	18-22	5	24
β-strand	29-36	8	24
β-strand	39-41	3	24
α-helix	55-57	3
α-helix	59	1
β-strand	64	1	25
α-helix	72-91	20
α-helix	93-104	12
α-helix	106-109	4
β-strand	110-113	4	26
β-strand	116-118	3	26
β-strand	119	1	27
β-strand	123-125	3	24
β-strand	131-132	2	24
β-strand	136-139	4	24
β-strand	144	1	25
β-strand	149-152	4	24
α-helix	155-159	5
β-strand	166-169	4	24
β-strand	174-176	3	28
β-strand	177-178	2	29
β-strand	181-182	2	29
α-helix	183-184	2
α-helix	185-200	16
α-helix	204-206	3
β-strand	210-215	6	30
β-strand	224-228	5	30
α-helix	229-235	7
α-helix	239-242	4
α-helix	254-268	15
α-helix	269-273	5
α-helix	281-291	11
α-helix	295-300	6
α-helix	303-310	8
α-helix	322-325	4
β-strand	330-332	3	28
β-strand	340	1	31
β-strand	343	1	31
β-strand	354-355	2	28
α-helix	356	1
α-helix	357-361	5
β-strand	368-373	6	32
β-strand	379-385	7	32
β-strand	391-393	3	30
β-strand	402	1	33
α-helix	425-429	5
α-helix	432-435	4
α-helix	436-438	3
β-strand	441	1	27
β-strand	459-463	5	32
α-helix	468-474	7
β-strand	483-485	3	34
α-helix	488-493	6
β-strand	499-501	3	34
α-helix	505-513	9
α-helix	518-519	2
α-helix	523-541	19
β-strand	545-549	5	35
β-strand	552-556	5	35
α-helix	558-562	5
α-helix	573-580	8
α-helix	582-585	4
β-strand	596	1	33
α-helix	600-603	4
α-helix	604-608	5
α-helix	611-640	30
α-helix	641-645	5
α-helix	646-679	34
α-helix	685-724	40
α-helix	725-729	5
α-helix	730-754	25
α-helix	760-769	10
α-helix	782-787	6
α-helix	792-800	9
β-strand	804-807	4	36
β-strand	808-813	6	37
β-strand	816-821	6	37
β-strand	828-831	4	38
β-strand	836-839	4	36
β-strand	844-848	5	36
β-strand	855-858	4	38
α-helix	860-863	4
β-strand	870-878	9	36
β-strand	886-893	8	38
β-strand	896-903	8	38
β-strand	906-912	7	38
β-strand	918-923	6	38
β-strand	932-939	8	36
β-strand	944-949	6	36
β-strand	952-958	7	36
β-strand	970-973	4	38
β-strand	980-988	9	36
α-helix	994-1005	12
β-strand	1019	1	39
β-strand	1024	1	40
β-strand	1026-1028	3	41
β-strand	1035	1	41
β-strand	1037-1041	5	40
β-strand	1044-1048	5	40
β-strand	1058-1059	2	40
α-helix	1060	1
β-strand	1062-1065	4	40
β-strand	1073	1	39
β-strand	1078-1080	3	42
β-strand	1081-1084	4	40
β-strand	1090-1094	5	40
β-strand	1099	1	43
β-strand	1100-1103	4	40
α-helix	1110-1111	2
β-strand	1112-1115	4	42
β-strand	1125-1128	4	42
β-strand	1131-1132	2	42
β-strand	1134-1135	2	43
β-strand	1145-1146	2	43
α-helix	1153-1156	4
β-strand	1157	1	42
β-strand	1158-1160	3	41

Chain C: 19 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	177-182	6	44
α-helix	183-193	11
β-strand	199-206	8	45
β-strand	209-217	9	45
β-strand	221	1	46
β-strand	227	1	44
β-strand	231-236	6	46
β-strand	237-244	8	45
β-strand	247-250	4	45
β-strand	251	1	47
β-strand	256-261	6	46
β-strand	263-267	5	48
β-strand	277	1	49
β-strand	282-288	7	48
β-strand	299-304	6	46
β-strand	307	1	47
α-helix	314-330	17
β-strand	341-344	4	48
α-helix	346-347	2
β-strand	348	1	49
α-helix	351-356	6
β-strand	358-361	4	44
β-strand	364-366	3	44
β-strand	369	1	50
β-strand	375	1	50
β-strand	381-388	8	44
α-helix	403-408	6
β-strand	412-417	6	44
α-helix	418-421	4
α-helix	422-426	5
α-helix	427-432	6
α-helix	438-440	3
β-strand	441-442	2	51
β-strand	449-450	2	52
β-strand	451-452	2	51
β-strand	456-462	7	52
β-strand	468-473	6	52
β-strand	479-483	5	52
β-strand	486-495	10	52
β-strand	504-519	16	52
β-strand	522-529	8	52
β-strand	534-540	7	52
α-helix	541-546	6
α-helix	548-564	17
α-helix	572-584	13
β-strand	586-589	4	52
β-strand	592-597	6	52
α-helix	599-608	10
α-helix	613-633	21
α-helix	642-649	8
α-helix	655-668	14
α-helix	671-674	4
α-helix	682-695	14
α-helix	704-713	10
β-strand	715-716	2	48
β-strand	725-731	7	44
β-strand	734-740	7	44

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Botulinum neurotoxin type A	A	protein	1296	Clostridium botulinum A str. Hall	P0DPI0 (AlphaFold model)
NtnH	B	protein	1161	Clostridium botulinum A	C1FUH8 (AlphaFold model)
OrfX2	C	protein	750	Clostridium botulinum A	C1FUH4 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9ARL_1 Botulinum neurotoxin type A (chains A)
MPFVNKQFNYKDPVNGVDIAYIKIPNAGQMQPVKAFKIHNKIWVIPERDTFTNPEEGDLN
PPPEAKQVPVSYYDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTSIVRGIPFWGG
STIDTELKVIDTNCINVIQPDGSYRSEELNLVIIGPSADIIQFECKSFGHEVLNLTRNGY
GSTQYIRFSPDFTFGFEESLEVDTNPLLGAGKFATDPAVTLAHQLIHAGHRLYGIAINPN
RVFKVNTNAYYEMSGLEVSFEELRTFGGHDAKFIDSLQENEFRLYYYNKFKDIASTLNKA
KSIVGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKMLTEIYTEDNFVKFFKV
LNAKTFLNFDKAVFKINIVPKVNYTIYDGFNLRNTNLAANFNGQNTEINNMNFTKLKNFT
GLFEFYKLLCVRGIITSKTKSLDKGYNKALNDLCIKVNNWDLFFSPSEDNFTNDLNKGEE
ITSDTNIEAAEENISLDLIQQYYLTFNFDNEPENISIENLSSDIIGQLELMPNIERFPNG
KKYELDKYTMFHYLRAQEFEHGKSRIALTNSVNEALLNPSRVYTFFSSDYVKKVNKATEA
AMFLGWVEQLVYDFTDETSEVSTTDKIADITIIIPYIGPALNIGNMLYKDDFVGALIFSG
AVILLEFIPEIAIPVLGTFALVSYIANKVLTVQTIDNALSKRNEKWDEVYKYIVTNWLAK
VNTQIDLIRKKMKEALENQAEATKAIINYQYNQYTEEEKNNINFNIDDLSSKLNESINKA
MININKFLNQCSVSYLMNSMIPYGVKRLEDFDASLKDALLKYIYDNRGTLIGQVDRLKDK
VNNTLSTDIPFQLSKYVDNQRLLSTFTEYIKNIINTSILNLRYESNHLIDLSRYASKINI
GSKVNFDPIDKNQIQLFNLESSKIEVILKNAIVYNSMYENFSTSFWIRIPKYFNSISLNN
EYTIINCMENNSGWKVSLNYGEIIWTLQDTQEIKQRVVFKYSQMINISDYINRWIFVTIT
NNRLNNSKIYINGRLIDQKPISNLGNIHASNNIMFKLDGCRDTHRYIWIKYFNLFDKELN
EKEIKDLYDNQSNSGILKDFWGDYLQYDKPYYMLNLYDPNKYVDVNNVGIRGYMYLKGPR
GSVMTTNIYLNSSLYRGTKFIIKKYASGNKDNIVRNNDRVYINVVVKNKEYRLATNASQA
GVEKILSALEIPDVGNLSQVVVMKSKNDQGITNKCKMNLQDNNGNDIGFIGFHQFNNIAK
LVASNWYNRQIERSSRTLGCSWEFIPVDDGWGERPL

Sequence of entity 2 (B), FASTA

>9ARL_2 NtnH (chains B)
MKINNNFNIDSLIDNRDVAIVRGRKTDTFFKVFQVAPNIWVAPERYYGESLNINEDQKSD
GGIYDSNFLLTNDEKDEFLQATVKILQRINNNVIGAKLLSLISTAIPFPYEYKPGDYRQT
NYLVSKDNQHYYTANLVIFGPGTNIVENNAVYYKKEDSENGMGTMSEIWFQPFLTYKYDQ
FYVDPALELIKCLIKSLYYLYGIKPSDDLSIPYRLRSEFNSLEYSELDMVDFLISGGTDY
KLLNTNPYWFTDNYFINAPKNFEKYKNDYETKIKNNNDIANSIKLYLEQKFKTNVQDIWE
LNLSYFSTEFEIMMPEIFNNALNHYHRKEYYVIDYFKNYNINGFINGQIKTILLLSKYNK
NIINKPELIVNLINENNSVLMKSNIYGDGLKGTIGNFYAVYKIPYNIGDEYHINSSDSCL
DNVDIKEIDNIPPINDADIYPYRKNCDPFTPVYNITETKEINTTIPFPVNYLQAQVTNSN
DINLSSDFLKVISSKDRSLVYSFLDNTIDYLDSIKYDGPIDTDKKYYLWLKEIFRNYSFD
MTETQEVNTLCGFNKVVPWLGKALNILNTGNSFIEEFKTLGPISLINKKENITMPKIEID
EIPNSMLNLSFKDLSENLFNIFSKNNSYFEKIYYDFLDQWWTQYYSQYFDLICMAKRSVL
AQESLIKKIIQKKLSYLIGNSNISSDNLALMNLTTTNTLRDISNESQIAMNNVNNFLNNV
AICVFQTNIYPKFISFMEQCINNINKNTREFIQKCTNITENEKLQLINQNIFSSLDFDFL
NIENLKSLFNSETGLLIKEETSPYELVLYAFQEPGNNAIGDASGKNTSIEYSKDIGLVYG
INSDALYLNGSNQSISFSNDFFENGLTNSFSIYFWLRNLGKDTIKSKLIGSKEDNCGWEI
YFQDTGLVFNMIDSNGNEKNIYLSDVSNNSWHYITISVDRLKEQLLIFIDDNLVANESIK
EILNIYSSNIISLLSENNPSYIEGLTILNKPTTSQEVLSNYFKVLNNSYIRDSSEERLEY
NKTYQLYNYVFSENPIYEIKQNNNIYLTINNTNNLNLQVSKFKLLSINPNKQYVQKLDEV
IISVLDNMEKYIDISEDNRLQLIDNKNNAKKMIISNDIFISNCLTLSYNGKYICLSMKDE
NHNWMICNNDMSKYLYLWSFK

Sequence of entity 3 (C), FASTA

>9ARL_3 OrfX2 (chains C)
MNNLKPFIYYDWEKTILKNTKENYSINEIIPKTFFMELHGTKITNSTLNGTWKSWNLTNE
GEGSYPVLKCIIDDGYLDMNFGASSEKIPLKNVWIKLCMKINPNSDGTYSIPEKSSSFYI
KDNSLKISKDNLILDKYLNKLMLSYFKNNIKNIEMFINKSRIQTKVVGDLSLLGWNTENS
VSFRTMNEFIKKDNLYPKDFKAVYSYRKMTFTATGTFDSWEMTTGADGRNIRFKCPIKYA
VYDLDGDVFNSSTENFLLIQVDLTYFDSKTTINDPTGENDGKQFNLKIKTNDDKLKNVLI
VTYNLTDTDGSMSSEDKDFLSLAFRNWFNENIQQFEQIFAYILLDETAKIPEYQWLKPTQ
ISYGSASVETANDEPDLDASIFSAMSMVENNTNSTPSHAVDNRMLQLTKTQAAFGISFPL
FIEHFLKQALLSSQFISVDDIVADINTLTITNNKQIIFGKVENSDGKNVDSSLKPGKLKL
SLQNNLIVLELFDLTWEQGRGVTGHFDFRQEYELALESKSGKQIPILKVHDEPEIEYYVE
EAQWKTNEDMIVSAVVGTVFSMILGASMKLAGSALSKAGKLIRSKATTIKGRKKIYINRS
NVRQLRKDSGATEIELERINRRNSSIAAEDARLISNNGTTSIQTLGDMKKKPMSTGQRIA
IGAKKIAGTAVMFGAVGLGMNFGEMLINYINAMENNDYSAIPGINSFMQQCIGAMQWPDK
DSELKVTFGKLQGIYLLGGTLEKNNKTDNK

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 P0DPI0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8RVI 1.6 Å, Structure of the binding domain of BoNT/A mutant H1253K in complex with the GM1a…
6XCF 1.68 Å, Structure of the C. botulinum neurotoxin serotype A light chain protease in complex with…
6XCB 1.74 Å, Structure of the C. botulinum neurotoxin serotype A light chain protease in complex with…
8RVH 1.8 Å, Structure of the binding domain of BoNT/A mutant Y1117V/H1253K in complex with the GD1a…
6XCC 1.9 Å, Structure of the C. botulinum neurotoxin serotype A light chain protease in complex with…
8RVG 1.9 Å, Structure of the binding domain of BoNT/A mutant Y1117V in complex with the GD1a…
6XCD 1.92 Å, Structure of the C. botulinum neurotoxin serotype A light chain protease in complex with…
2IMA 1.94 Å, Clostridium botulinum Neurotoxin Serotype A Light Chain Inhibited by…
2ISG 2.0 Å, Botulinum Neurotoxin A Light Chain WT Crystal Form B
2ISH 2.0 Å, Botulinum Neurotoxin A Light Chain WT Crystal Form C
2ISE 2.2 Å, Botulinum Neurotoxin A Light Chain WT Crystal Form A
7KYF 2.33 Å, Botulism Neurooxin Light Chain A app form

Browse structure collections

About this viewer

MolViewer shows 9ARL directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.