6UHT: BoNT/B receptor-binding domain

Crystal structure of BoNT/B receptor-binding domain in complex with VHH JLI-G10. Determined by X-ray diffraction at 2.2 Å resolution. Released 4 Mar 2020.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Clostridium botulinum, Vicugna pacos
Chains: 4
Atoms: 9,563
Mol. weight: 135.15 kDa
Released: 4 Mar 2020

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

Secondary structure: helices and β-sheets

6UHT contains 26 α-helices and 110 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: 8 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	864-867	4	1
β-strand	868-870	3	2
β-strand	875-877	3	2
β-strand	884-887	4	3
β-strand	892-893	2	1
β-strand	898-902	5	1
β-strand	909-912	4	3
β-strand	926-933	8	1
α-helix	935-938	4
α-helix	939-941	3
α-helix	942-947	6
β-strand	949-956	8	3
β-strand	961-967	7	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	1053-1062	10	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	1097-1098	2	7
β-strand	1099-1102	4	8
β-strand	1108-1112	5	7
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
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	1234-1243	10	7
β-strand	1249	1	11
β-strand	1252	1	11
β-strand	1254-1260	7	7
α-helix	1262-1266	5
β-strand	1280-1283	4	8

Chain B: 8 helices, 44 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	898-902	5	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	949-956	8	14
β-strand	961-967	7	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
β-strand	1039-1046	8	14
β-strand	1053-1062	10	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
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	1249	1	22
β-strand	1252	1	22
β-strand	1254-1260	7	18
α-helix	1262-1266	5
β-strand	1280-1283	4	19

Chain C: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	23
β-strand	10-13	4	24
β-strand	17-23	7	23
β-strand	34-41	8	24
β-strand	48-54	7	24
β-strand	60-62	3	24
α-helix	64-66	3
β-strand	70-74	5	23
β-strand	80-86	7	23
α-helix	90-92	3
β-strand	94-102	9	24
α-helix	108-110	3
α-helix	111-113	3
β-strand	116-117	2	24
β-strand	121-126	6	24

Chain D: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	-1-1	3
β-strand	2-7	6	25
β-strand	10-12	3	26
β-strand	18-26	9	25
α-helix	29-31	3
β-strand	34-41	8	26
β-strand	48-54	7	26
β-strand	60-62	3	26
α-helix	64-66	3
β-strand	70-74	5	25
β-strand	80-85	6	25
α-helix	90-92	3
β-strand	94-102	9	26
α-helix	108-110	3
α-helix	111-113	3
β-strand	116-117	2	26
β-strand	121-125	5	26

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Botulinum neurotoxin type B	A, B	protein	438	Clostridium botulinum	P10844 (AlphaFold model)
Jli-G10	C, D	protein	140	Vicugna pacos

Sequence of entity 1 (A, B), FASTA

>6UHT_1 Botulinum neurotoxin type B (chains A, B)
GPLGSEILNNIILNLRYKDNNLIDLSGYGAKVEVYDGVELNDKNQFKLTSSANSKIRVTQ
NQNIIFNSVFLDFSVSFWIRIPKYKNDGIQNYIHNEYTIINCMKNNSGWKISIRGNRIIW
TLIDINGKTKSVFFEYNIREDISEYINRWFFVTITNNLNNAKIYINGKLESNTDIKDIRE
VIANGEIIFKLDGDIDRTQFIWMKYFSIFNTELSQSNIEERYKIQSYSEYLKDFWGNPLM
YNKEYYMFNAGNKNSYIKLKKDSPVGEILTRSKYNQNSKYINYRDLYIGEKFIIRRKSNS
QSINDDIVRKEDYIYLDFFNLNQEWRVYTYKYFKKEEEKLFLAPISDSDEFYNTIQIKEY
DEQPTYSCQLLFKKDEESTDEIGLIGIHRFYESGIVFEEYKDYFCISKWYLKEVKRKPYN
LKLGCNWQFIPKDEGWTE

Sequence of entity 2 (C, D), FASTA

>6UHT_2 JLI-G10 (chains C, D)
GPLGSQVQLVESGGGLVQAGGSLRLSCAASILTYDLDYYYIGWVRQAPGKEREGVSCISS
TDGATYYADSVKGRFTISRNNAKNTVYLQMNNLKPEDTAIYYCAAAPLAGRYCPASHEYG
YWGQGTQVTVSSAHHSEDPS

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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