6G5F: Botulinum neurotoxin type B

Name: PDB 6G5F: Crystal structure of an engineered Botulinum Neurotoxin type B mutant E1191M/S1199Y in complex with human synaptotagmin 1
Published: 2019-01-16
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

Crystal structure of an engineered Botulinum Neurotoxin type B mutant E1191M/S1199Y in complex with human synaptotagmin 1. Determined by X-ray diffraction at 2.5 Å resolution. Released 16 Jan 2019.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Clostridium botulinum, Homo sapiens
Chains: 3
Atoms: 11,000
Mol. weight: 304.98 kDa
Ligands: MLI
Released: 16 Jan 2019

Explore 6G5F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6G5F contains 55 α-helices and 84 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: 21 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	13-14	2
β-strand	19-23	5	1
α-helix	25-27	3
β-strand	34-40	7	1
β-strand	43-46	4	1
α-helix	56-59	4
β-strand	64-65	2	2
β-strand	72-73	2	3
β-strand	74	1	4
α-helix	82-100	19
α-helix	103-114	12
α-helix	116-118	3
β-strand	128-129	2	5
β-strand	137-141	5	1
α-helix	144	1
α-helix	148-149	2
β-strand	151-155	5	1
β-strand	158-161	4	1
β-strand	166	1	4
β-strand	171-173	3	1
β-strand	176-177	2	6
β-strand	180-181	2	6
α-helix	182-184	3
β-strand	191-194	4	1
β-strand	199-203	5	7
β-strand	220-221	2	7
α-helix	222-223	2
α-helix	224-240	17
α-helix	247-248	2
β-strand	249	1	8
β-strand	251	1	9
β-strand	258	1	10
β-strand	264	1	8
α-helix	266-272	7
α-helix	276-279	4
α-helix	282-305	24
β-strand	308-309	2	5
α-helix	317-327	11
β-strand	331-332	2	11
β-strand	338-339	2	11
α-helix	342-350	9
α-helix	351-355	5
α-helix	358-365	8
β-strand	378-383	6	7
β-strand	393	1	12
β-strand	397	1	12
α-helix	407-412	6
β-strand	413	1	7
α-helix	418-420	3
β-strand	421-422	2	7
β-strand	429-430	2	3
β-strand	433-438	6	13

Chain B: 33 helices, 53 β-strands

Element	Residues	Length	Sheet
β-strand	446-450	5	13
α-helix	451-453	3
β-strand	455	1	10
α-helix	456	1
β-strand	458	1	9
α-helix	460-462	3
α-helix	466-468	3
β-strand	471-473	3	14
α-helix	488-492	5
α-helix	502-505	4
β-strand	507-508	2	1
α-helix	509-511	3
β-strand	517	1	6
β-strand	524-525	2	2
β-strand	527-532	6	13
α-helix	537-542	6
β-strand	554-556	3	15
α-helix	559-564	6
β-strand	568-570	3	15
α-helix	575-581	7
α-helix	587-605	19
α-helix	624-628	5
α-helix	639-646	8
α-helix	647-651	5
α-helix	663-665	3
β-strand	666-668	3	14
α-helix	669-670	2
α-helix	675-707	33
α-helix	709-740	32
α-helix	745-748	4
α-helix	753-782	30
α-helix	783-787	5
α-helix	788-812	25
α-helix	821-831	11
α-helix	835-838	4
α-helix	840-842	3
α-helix	847-857	11
α-helix	860-863	4
β-strand	864-867	4	16
β-strand	868-870	3	17
β-strand	875-877	3	17
β-strand	884-887	4	18
β-strand	892-893	2	16
β-strand	898-902	5	16
β-strand	909-912	4	18
β-strand	926-933	8	16
α-helix	935-938	4
α-helix	942-947	6
β-strand	950-956	7	18
β-strand	961-967	7	18
β-strand	970-976	7	18
β-strand	982-988	7	18
β-strand	992	1	19
β-strand	1003-1009	7	16
β-strand	1013-1018	6	16
β-strand	1021-1027	7	16
β-strand	1039-1046	8	18
β-strand	1053-1062	10	16
α-helix	1068-1078	11
β-strand	1083	1	20
β-strand	1085	1	21
β-strand	1091	1	21
α-helix	1092	1
β-strand	1093	1	22
β-strand	1097-1102	6	23
β-strand	1108-1112	5	23
α-helix	1113	1
β-strand	1119-1123	5	23
β-strand	1126	1	24
β-strand	1135	1	19
β-strand	1137	1	24
β-strand	1144-1149	6	23
β-strand	1160	1	22
β-strand	1162	1	20
β-strand	1166-1173	8	23
β-strand	1176-1181	6	23
β-strand	1182-1183	2	25
β-strand	1190-1192	3	23
β-strand	1194-1197	4	23
β-strand	1204-1205	2	25
β-strand	1208-1211	4	23
β-strand	1221-1225	5	23
β-strand	1236-1243	8	23
β-strand	1254-1260	7	23
α-helix	1262-1265	4
β-strand	1280-1283	4	23

Chain P: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	38-52	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Botulinum neurotoxin type B	A, B	protein	1291	Clostridium botulinum	P10844 (AlphaFold model)
Synaptotagmin-1	P	protein	21	Homo sapiens	P21579 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6G5F_1 Botulinum neurotoxin type B (chains A, B)
MPVTINNFNYNDPIDNNNIIMMEPPFARGTGRYYKAFKITDRIWIIPERYTFGYKPEDFN
KSSGIFNRDVCEYYDPDYLNTNDKKNIFLQTMIKLFNRIKSKPLGEKLLEMIINGIPYLG
DRRVPLEEFNTNIASVTVNKLISNPGEVERKKGIFANLIIFGPGPVLNENETIDIGIQNH
FASREGFGGIMQMKFCPEYVSVFNNVQENKGASIFNRRGYFSDPALILMHQLIYVLHGLY
GIKVDDLPIVPNEKKFFMQSTDAIQAEELYTFGGQDPSIITPSTDKSIYDKVLQNFRGIV
DRLNKVLVCISDPNININIYKNKFKDKYKFVEDSEGKYSIDVESFDKLYKSLMFGFTETN
IAENYKIKTRASYFSDSLPPVKIKNLLDNEIYTIEEGFNISDKDMEKEYRGQNKAINKQA
YEEISKEHLAVYKIQMCKSVKAPGICIDVDNEDLFFIADKNSFSDDLSKNERIEYNTQSN
YIENDFPINELILDTDLISKIELPSENTESLTDFNVDVPVYEKQPAIKKIFTDENTIFQY
LYSQTFPLDIRDISLTSSFDDALLFSNKVYSFFSMDYIKTANKVVEAGLFAGWVKQIVND
FVIEANKSNTMDKIADISLIVPYIGLALNVGNETAKGNFENAFEIAGASILLEFIPELLI
PVVGAFLLESYIDNKNKIIKTIDNALTKRNEKWSDMYGLIVAQWLSTVNTQFYTIKEGMY
KALNYQAQALEEIIKYRYNIYSEKEKSNINIDFNDINSKLNEGINQAIDNINNFINGCSV
SYLMKKMIPLAVEKLLDFDNTLKKNLLNYIDENKLYLIGSAEYEKSKVNKYLKTIMPFDL
SIYTNDTILIEMFNKYNSEILNNIILNLRYKDNNLIDLSGYGAKVEVYDGVELNDKNQFK
LTSSANSKIRVTQNQNIIFNSVFLDFSVSFWIRIPKYKNDGIQNYIHNEYTIINCMKNNS
GWKISIRGNRIIWTLIDINGKTKSVFFEYNIREDISEYINRWFFVTITNNLNNAKIYING
KLESNTDIKDIREVIANGEIIFKLDGDIDRTQFIWMKYFSIFNTELSQSNIEERYKIQSY
SEYLKDFWGNPLMYNKEYYMFNAGNKNSYIKLKKDSPVGEILTRSKYNQNSKYINYRDLY
IGEKFIIRRKSNSQSINDDIVRKEDYIYLDFFNLNQEWRVYTYKYFKKEEMKLFLAPIYD
SDEFYNTIQIKEYDEQPTYSCQLLFKKDEESTDEIGLIGIHRFYESGIVFEEYKDYFCIS
KWYLKEVKRKPYNLKLGCNWQFIPKDEGWTE

Sequence of entity 2 (P), FASTA

>6G5F_2 Synaptotagmin-1 (chains P)
GEGKEDAFSKLKEKFMNELHK

Ligands and cofactors

ID	Name	Formula	Copies
MLI	Malonate ion	C3 H2 O4	1

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

Primary citation

Engineered botulinum neurotoxin B with improved binding to human receptors has enhanced efficacy in preclinical models. Elliott, M., Favre-Guilmard, C., Liu, S.M. et al. Sci Adv (2019) 5:eaau7196-eaau7196. DOI 10.1126/sciadv.aau7196 · PubMed

Other PDB entries of the same protein (UniProt P10844 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7NA9 1.76 Å, Crystal structure of BoNT/B-LC-JSG-C1
1EPW 1.9 Å, Crystal structure of clostridium neurotoxin type B
1S0E 1.9 Å, Crystal structure of botulinum neurotoxin type B at pH 6.0
5VMR 1.95 Å, Receptor binding domain of BoNT/B in complex with mini-protein binder Bot.2110.4
1G9B 2.0 Å, Crystal structure of clostridium botulinum neurotoxin B complexed with an inhibitor…
1S0B 2.0 Å, Crystal structure of botulinum neurotoxin type B at pH 4.0
1Z0H 2.0 Å, N-terminal helix reorients in recombinant C-fragment of Clostridium botulinum type B
6G5G 2.0 Å, Crystal structure of an engineered Botulinum Neurotoxin type B mutant E1191M/S1199Y in…
6G5K 2.0 Å, Crystal structure of the binding domain of Botulinum Neurotoxin type B in complex with…
1G9A 2.1 Å, Crystal structure of clostridium botulinum neurotoxin B complexed with an inhibitor…
2NM1 2.15 Å, Structure of BoNT/B in complex with its protein receptor
1F82 2.2 Å, Botulinum neurotoxin type B catalytic domain

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