5VMR: Receptor binding domain of BoNT/B

Receptor binding domain of BoNT/B in complex with mini-protein binder Bot.2110.4. Determined by X-ray diffraction at 1.95 Å resolution. Released 20 Sept 2017.

Method: X-ray diffraction
Resolution: 1.95 Å
Organisms: Clostridium botulinum, unidentified
Chains: 4
Atoms: 8,308
Mol. weight: 114.93 kDa
Released: 20 Sept 2017

Explore 5VMR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5VMR contains 25 α-helices and 88 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: 10 helices, 43 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
α-helix	913-914	2
β-strand	918	1	4
β-strand	926-933	8	1
α-helix	935-938	4
α-helix	939-941	3
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	5
β-strand	1085	1	6
β-strand	1091	1	6
α-helix	1092	1
β-strand	1093	1	7
β-strand	1097-1098	2	8
β-strand	1099-1102	4	9
β-strand	1108-1112	5	8
α-helix	1113	1
β-strand	1119-1123	5	8
α-helix	1124-1125	2
β-strand	1126	1	10
β-strand	1137	1	10
β-strand	1145-1149	5	8
β-strand	1160	1	7
β-strand	1162	1	5
β-strand	1166-1173	8	8
β-strand	1176-1181	6	8
β-strand	1182-1183	2	11
β-strand	1190-1192	3	8
α-helix	1193	1
β-strand	1194-1197	4	8
β-strand	1204-1205	2	11
β-strand	1208-1211	4	8
β-strand	1221	1	9
β-strand	1222-1226	5	8
β-strand	1234-1244	11	8
β-strand	1253-1260	8	8
α-helix	1263-1266	4
β-strand	1280-1283	4	9

Chain B: 9 helices, 45 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
α-helix	913-914	2
β-strand	918	1	4
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
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	1098	1	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	1254-1260	7	18
α-helix	1263-1266	4
β-strand	1280-1283	4	19
β-strand	1286	1	22
β-strand	1289	1	22

Chain C: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	3-14	12
α-helix	18-28	11
α-helix	32-38	7

Chain D: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	3-14	12
α-helix	18-28	11
α-helix	32-35	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Botulinum neurotoxin type B	A, B	protein	438	Clostridium botulinum	P10844 (AlphaFold model)
Bot.2110.4	C, D	protein	43	unidentified

Sequence of entity 1 (A, B), FASTA

>5VMR_1 Botulinum neurotoxin type B (chains A, B)
GPLGSEILNNIILNLRYKDNNLIDLSGYGAKVEVYDGVELNDKNQFKLTSSANSKIRVTQ
NQNIIFNSVFLDFSVSFWIRIPKYKNDGIQNYIHNEYTIINCMKNNSGWKISIRGNRIIW
TLIDINGKTKSVFFEYNIREDISEYINRWFFVTITNNLNNAKIYINGKLESNTDIKDIRE
VIANGEIIFKLDGDIDRTQFIWMKYFSIFNTELSQSNIEERYKIQSYSEYLKDFWGNPLM
YNKEYYMFNAGNKNSYIKLKKDSPVGEILTRSKYNQNSKYINYRDLYIGEKFIIRRKSNS
QSINDDIVRKEDYIYLDFFNLNQEWRVYTYKYFKKEEEKLFLAPISDSDEFYNTIQIKEY
DEQPTYSCQLLFKKDEESTDEIGLIGIHRFYESGIVFEEYKDYFCISKWYLKEVKRKPYN
LKLGCNWQFIPKDEGWTE

Sequence of entity 2 (C, D), FASTA

>5VMR_2 Bot.2110.4 (chains C, D)
PDMFCALKIKFFLEIGDEDAARKAAKKCGYSEEQAERIIKKNL

Primary citation

Massively parallel de novo protein design for targeted therapeutics. Chevalier, A., Silva, D.A., Rocklin, G.J. et al. Nature (2017) 550:74-79. DOI 10.1038/nature23912 · 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
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…

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