4KBB: Botulinum neurotoxin B binding domain

Structure of Botulinum neurotoxin B binding domain in complex with both synaptotagmin II and GD1a. Determined by X-ray diffraction at 2.3 Å resolution. Released 3 Jul 2013.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: Clostridium botulinum, Mus musculus
Chains: 4
Atoms: 7,875
Mol. weight: 127.62 kDa
Ligands: MG
Released: 3 Jul 2013

Explore 4KBB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4KBB contains 20 α-helices and 90 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, 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	898-901	4	1
β-strand	909-912	4	3
β-strand	926-933	8	1
α-helix	935-938	4
α-helix	942-947	6
β-strand	949-957	9	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
α-helix	1038-1039	2
β-strand	1040-1046	7	3
β-strand	1054-1062	9	1
α-helix	1068-1077	10
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
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
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	1222-1225	4	7
β-strand	1236-1244	9	7
β-strand	1253-1260	8	7
α-helix	1262-1266	5
β-strand	1280-1283	4	8
β-strand	1286	1	11
β-strand	1289	1	11

Chain B: 9 helices, 46 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	922	1	15
β-strand	926-933	8	12
α-helix	935-938	4
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
β-strand	1035	1	15
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	16
β-strand	1085	1	17
β-strand	1091	1	17
α-helix	1092	1
β-strand	1093	1	18
β-strand	1097-1098	2	19
β-strand	1099-1102	4	20
β-strand	1108-1112	5	19
α-helix	1113	1
β-strand	1119-1123	5	19
α-helix	1124-1125	2
β-strand	1126	1	21
β-strand	1137	1	21
β-strand	1145-1149	5	19
β-strand	1160	1	18
β-strand	1162	1	16
β-strand	1166-1173	8	19
β-strand	1176-1181	6	19
β-strand	1182-1183	2	22
β-strand	1190-1192	3	19
α-helix	1193	1
β-strand	1194-1197	4	19
β-strand	1204-1205	2	22
β-strand	1208-1211	4	19
β-strand	1221	1	20
β-strand	1222-1225	4	19
β-strand	1236-1244	9	19
β-strand	1253-1260	8	19
α-helix	1262-1266	5
β-strand	1280-1283	4	20
β-strand	1286	1	23
β-strand	1289	1	23

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	46-57	12

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	43-57	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Botulinum neurotoxin type B	A, B	protein	459	Clostridium botulinum	P10844 (AlphaFold model)
Synaptotagmin-2	C, D	protein	68	Mus musculus	P46097 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4KBB_1 Botulinum neurotoxin type B (chains A, B)
MGSSHHHHHHSSGLVPRGSHMASMNSEILNNIILNLRYKDNNLIDLSGYGAKVEVYDGVE
LNDKNQFKLTSSANSKIRVTQNQNIIFNSVFLDFSVSFWIRIPKYKNDGIQNYIHNEYTI
INCMKNNSGWKISIRGNRIIWTLIDINGKTKSVFFEYNIREDISEYINRWFFVTITNNLN
NAKIYINGKLESNTDIKDIREVIANGEIIFKLDGDIDRTQFIWMKYFSIFNTELSQSNIE
ERYKIQSYSEYLKDFWGNPLMYNKEYYMFNAGNKNSYIKLKKDSPVGEILTRSKYNQNSK
YINYRDLYIGEKFIIRRKSNSQSINDDIVRKEDYIYLDFFNLNQEWRVYTYKYFKKEEEK
LFLAPISDSDEFYNTIQIKEYDEQPTYSCQLLFKKDEESTDEIGLIGIHRFYESGIVFEE
YKDYFCISKWYLKEVKRKPYNLKLGCNWQFIPKDEGWTE

Sequence of entity 2 (C, D), FASTA

>4KBB_2 Synaptotagmin-2 (chains C, D)
EGWTENQEPNVAPATTTATMPLAPVAPADNSTESTGPGESQEDMFAKLKEKFFNEINKIV
LEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

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

Primary citation

Structure of dual receptor binding to botulinum neurotoxin B. Berntsson, R.P., Peng, L., Dong, M. et al. Nat Commun (2013) 4:2058-2058. DOI 10.1038/ncomms3058 · 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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