6UC6: BoNT/B receptor-binding domain

Crystal structure of BoNT/B receptor-binding domain in complex with VHH JLI-H11. Determined by X-ray diffraction at 2.32 Å resolution. Released 4 Mar 2020.

Method: X-ray diffraction
Resolution: 2.32 Å
Organisms: Clostridium botulinum, Vicugna pacos
Chains: 4
Atoms: 9,263
Mol. weight: 138.13 kDa
Released: 4 Mar 2020

Explore 6UC6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6UC6 contains 31 α-helices and 105 β-strands across 4 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: 9 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	864-867	4	1
β-strand	868-871	4	2
β-strand	874-877	4	2
β-strand	884-887	4	3
β-strand	892-893	2	1
β-strand	898-901	4	1
β-strand	908-912	5	3
β-strand	926-933	8	1
α-helix	935-938	4
α-helix	942-947	6
β-strand	950-957	8	3
β-strand	960-967	8	3
β-strand	970-976	7	3
β-strand	982-988	7	3
β-strand	1003-1009	7	1
β-strand	1013-1018	6	1
β-strand	1021-1027	7	1
β-strand	1040-1046	7	3
β-strand	1054-1062	9	1
α-helix	1068-1079	12
β-strand	1083	1	4
β-strand	1085	1	5
β-strand	1091	1	5
α-helix	1092	1
β-strand	1093	1	6
β-strand	1098	1	7
β-strand	1099-1102	4	8
β-strand	1108-1112	5	7
α-helix	1113	1
β-strand	1119-1123	5	7
α-helix	1124-1125	2
β-strand	1126	1	9
β-strand	1137	1	9
β-strand	1145-1149	5	7
β-strand	1160	1	6
α-helix	1161	1
β-strand	1162	1	4
β-strand	1166-1173	8	7
β-strand	1176-1181	6	7
β-strand	1182-1183	2	10
β-strand	1190-1192	3	7
α-helix	1193	1
β-strand	1194-1197	4	7
β-strand	1204-1205	2	10
β-strand	1208-1211	4	7
β-strand	1221	1	8
β-strand	1222-1226	5	7
β-strand	1234-1244	11	7
β-strand	1253-1260	8	7
α-helix	1263-1266	4
β-strand	1280-1283	4	8

Chain B: 10 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	864-867	4	12
β-strand	868-870	3	13
β-strand	875-877	3	13
β-strand	884-887	4	14
β-strand	892-893	2	12
β-strand	898-901	4	12
β-strand	909-912	4	14
β-strand	926-933	8	12
α-helix	935-938	4
α-helix	939-941	3
α-helix	942-947	6
β-strand	949-957	9	14
β-strand	960-967	8	14
β-strand	970-976	7	14
β-strand	982-988	7	14
β-strand	1003-1009	7	12
β-strand	1013-1018	6	12
β-strand	1021-1027	7	12
α-helix	1039	1
β-strand	1040-1046	7	14
β-strand	1054-1062	9	12
α-helix	1068-1079	12
β-strand	1083	1	15
β-strand	1085	1	16
β-strand	1091	1	16
α-helix	1092	1
β-strand	1093	1	17
β-strand	1097-1098	2	18
β-strand	1099-1102	4	19
β-strand	1108-1112	5	18
α-helix	1113	1
β-strand	1119-1123	5	18
α-helix	1124-1125	2
β-strand	1126	1	20
β-strand	1137	1	20
β-strand	1145-1149	5	18
β-strand	1160	1	17
α-helix	1161	1
β-strand	1162	1	15
β-strand	1166-1173	8	18
β-strand	1176-1181	6	18
β-strand	1182-1183	2	21
β-strand	1190-1192	3	18
β-strand	1194-1197	4	18
β-strand	1204-1205	2	21
β-strand	1208-1211	4	18
β-strand	1221	1	19
β-strand	1222-1226	5	18
β-strand	1234-1243	10	18
β-strand	1254-1260	7	18
α-helix	1262-1266	5
β-strand	1280-1283	4	19

Chain C: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	11
β-strand	10-12	3	7
β-strand	18-25	8	11
α-helix	29-31	3
β-strand	33-39	7	7
α-helix	44-45	2
β-strand	46-51	6	7
β-strand	58-60	3	7
α-helix	62-64	3
β-strand	65	1	11
β-strand	68-73	6	11
α-helix	74-76	3
β-strand	78-83	6	11
α-helix	88-90	3
β-strand	92-99	8	7
α-helix	105-107	3
α-helix	112-115	4
β-strand	119-123	5	7

Chain D: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	22
β-strand	10-12	3	18
β-strand	18-25	8	22
α-helix	29-31	3
β-strand	33-39	7	18
β-strand	46-51	6	18
β-strand	58-60	3	18
α-helix	62-64	3
β-strand	68-73	6	22
β-strand	78-83	6	22
α-helix	88-90	3
β-strand	92-99	8	18
α-helix	105-107	3
α-helix	112-115	4
β-strand	119-123	5	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Botulinum neurotoxin type B	A, B	protein	438	Clostridium botulinum	P10844 (AlphaFold model)
Jli-H11	C, D	protein	154	Vicugna pacos

Sequence of entity 1 (A, B), FASTA

>6UC6_1 Botulinum neurotoxin type B (chains A, B)
GPLGSEILNNIILNLRYKDNNLIDLSGYGAKVEVYDGVELNDKNQFKLTSSANSKIRVTQ
NQNIIFNSVFLDFSVSFWIRIPKYKNDGIQNYIHNEYTIINCMKNNSGWKISIRGNRIIW
TLIDINGKTKSVFFEYNIREDISEYINRWFFVTITNNLNNAKIYINGKLESNTDIKDIRE
VIANGEIIFKLDGDIDRTQFIWMKYFSIFNTELSQSNIEERYKIQSYSEYLKDFWGNPLM
YNKEYYMFNAGNKNSYIKLKKDSPVGEILTRSKYNQNSKYINYRDLYIGEKFIIRRKSNS
QSINDDIVRKEDYIYLDFFNLNQEWRVYTYKYFKKEEEKLFLAPISDSDEFYNTIQIKEY
DEQPTYSCQLLFKKDEESTDEIGLIGIHRFYESGIVFEEYKDYFCISKWYLKEVKRKPYN
LKLGCNWQFIPKDEGWTE

Sequence of entity 2 (C, D), FASTA

>6UC6_2 JLI-H11 (chains C, D)
MHHHHHHMASMTGGQQMGRGSQVQLVESGGGLVQPGESLRLSCGASGMSLDYYAIAWYRQ
APGKEREGVSCISVSGSSAQYLDSVRGRFIISKDNTKSTAYLQMNSLKPEDTAVYYCAAL
ADCAGYASLTFDFDSWGQGTQVAVSSAHHSEDPS

Primary citation

Structural Insights into Rational Design of Single-Domain Antibody-Based Antitoxins against Botulinum Neurotoxins. Lam, K., Tremblay, J.M., Vazquez-Cintron, E. et al. Cell Rep (2020) 30:2526. DOI 10.1016/j.celrep.2020.01.107

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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