7NA9: BoNT/B-LC-JSG-C1

Name: PDB 7NA9: Crystal structure of BoNT/B-LC-JSG-C1
Published: 2021-12-22
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

Crystal structure of BoNT/B-LC-JSG-C1. Determined by X-ray diffraction at 1.76 Å resolution. Released 22 Dec 2021.

Method: X-ray diffraction
Resolution: 1.76 Å
Organisms: Clostridium botulinum, Vicugna pacos
Chains: 2
Atoms: 5,173
Mol. weight: 66.16 kDa
Ligands: ZN
Released: 22 Dec 2021

Explore 7NA9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7NA9 contains 28 α-helices and 38 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: 22 helices, 26 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	74	1	2
α-helix	82-100	19
α-helix	103-114	12
α-helix	116-118	3
β-strand	128-129	2	3
β-strand	137-142	6	1
β-strand	150-155	6	1
β-strand	158-161	4	1
β-strand	166	1	2
β-strand	171-173	3	1
β-strand	176-177	2	4
β-strand	180-181	2	4
α-helix	182-184	3
β-strand	191-194	4	1
β-strand	199-200	2	5
β-strand	202-203	2	6
α-helix	207-209	3
α-helix	214-216	3
β-strand	220-221	2	6
α-helix	224-239	16
α-helix	243-245	3
β-strand	248-249	2	7
β-strand	264-265	2	7
α-helix	266-272	7
α-helix	276-279	4
α-helix	282-305	24
β-strand	308-309	2	3
α-helix	317-327	11
β-strand	331-332	2	8
β-strand	338-339	2	8
α-helix	342-350	9
α-helix	351-355	5
α-helix	358-365	8
β-strand	381-383	3	5
β-strand	393	1	9
β-strand	397	1	9
α-helix	401-403	3
α-helix	407-412	6
β-strand	413	1	6
α-helix	418-420	3
β-strand	421-422	2	5
α-helix	426-437	12

Chain D: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	-1-1	3
β-strand	3-7	5	10
β-strand	11-13	3	11
β-strand	18-25	8	10
β-strand	34-39	6	12
α-helix	44-45	2
β-strand	46-51	6	12
β-strand	58-60	3	12
β-strand	68-73	6	10
α-helix	74-76	3
β-strand	78-83	6	10
α-helix	88-90	3
β-strand	92-98	7	12
α-helix	107-110	4
α-helix	113-115	3
β-strand	118-119	2	12
β-strand	123-125	3	12
β-strand	126-128	3	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Botulinum neurotoxin type B	A	protein	446	Clostridium botulinum	P10844 (AlphaFold model)
Jsg-C1	D	protein	134	Vicugna pacos

Sequence of entity 1 (A), FASTA

>7NA9_1 Botulinum neurotoxin type B (chains A)
GPLGSMPVTINNFNYNDPIDNNNIIMMEPPFARGTGRYYKAFKITDRIWIIPERYTFGYK
PEDFNKSSGIFNRDVCEYYDPDYLNTNDKKNIFLQTMIKLFNRIKSKPLGEKLLEMIING
IPYLGDRRVPLEEFNTNIASVTVNKLISNPGEVERKKGIFANLIIFGPGPVLNENETIDI
GIQNHFASREGFGGIMQMKFCPEYVSVFNNVQENKGASIFNRRGYFSDPALILMHELIHV
LHGLYGIKVDDLPIVPNEKKFFMQSTDAIQAEELYTFGGQDPSIITPSTDKSIYDKVLQN
FRGIVDRLNKVLVCISDPNININIYKNKFKDKYKFVEDSEGKYSIDVESFDKLYKSLMFG
FTETNIAENYKIKTRASYFSDSLPPVKIKNLLDNEIYTIEEGFNISDKDMEKEYRGQNKA
INKQAYEEISKEHLAVYKIQMCKSVK

Sequence of entity 2 (D), FASTA

>7NA9_2 JSG-C1 (chains D)
GPLGSQVQLVESGGGLVQTGGSLRLSCAASGRTFRRNTMGWFRQAPGKVREFVAAISWSG
DRTYCADSVKGRFTISRDNAKNTVDLLMNSLKPEDTAIYYCAADGTASVFNSYASADRNK
YNYWGQGTQVTVSS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

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

Primary citation

Probing the structure and function of the protease domain of botulinum neurotoxins using single-domain antibodies. Lam, K.H., Tremblay, J.M., Perry, K. et al. PLoS Pathog (2022) 18:e1010169-e1010169. DOI 10.1371/journal.ppat.1010169 · PubMed

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

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
1G9D 2.2 Å, Crystal structure of clostridium botulinum neurotoxin B complexed with an inhibitor…

Browse structure collections

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