4ISQ: Binding domain of Botulinum neurotoxin DC

Name: PDB 4ISQ: Binding domain of Botulinum neurotoxin DC in complex with human synaptotagmin I
Published: 2013-08-14
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

Binding domain of Botulinum neurotoxin DC in complex with human synaptotagmin I. Determined by X-ray diffraction at 2.65 Å resolution. Released 14 Aug 2013.

Method: X-ray diffraction
Resolution: 2.65 Å
Organisms: Clostridium botulinum, Homo sapiens
Chains: 6
Atoms: 10,970
Mol. weight: 160.27 kDa
Released: 14 Aug 2013

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

Secondary structure: helices and β-sheets

4ISQ contains 29 α-helices and 107 β-strands across 6 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, 34 β-strands

Element	Residues	Length	Sheet
α-helix	864-867	4
β-strand	868-874	7	1
β-strand	879-881	3	1
β-strand	888-892	5	2
β-strand	896-897	2	1
β-strand	905-908	4	1
β-strand	916-920	5	2
α-helix	924-927	4
β-strand	933-943	11	1
α-helix	949-951	3
β-strand	952-959	8	2
β-strand	962-969	8	2
β-strand	972-978	7	2
β-strand	984-990	7	2
β-strand	1004-1011	8	1
β-strand	1015-1020	6	1
β-strand	1023-1029	7	1
β-strand	1041-1048	8	2
α-helix	1049-1050	2
β-strand	1063-1072	10	1
α-helix	1078-1087	10
β-strand	1093	1	3
β-strand	1095	1	4
β-strand	1101	1	4
α-helix	1102	1
β-strand	1103	1	5
β-strand	1107-1112	6	6
α-helix	1113-1115	3
β-strand	1118-1123	6	6
β-strand	1126-1131	6	6
β-strand	1144-1150	7	6
β-strand	1157	1	5
β-strand	1159	1	3
β-strand	1163-1170	8	6
β-strand	1173-1179	7	6
β-strand	1190-1196	7	6
α-helix	1200-1206	7
β-strand	1209-1215	7	6
β-strand	1220-1227	8	6
β-strand	1234-1245	12	6
β-strand	1255-1264	10	6
α-helix	1274-1276	3
β-strand	1278-1282	5	6

Chain B: 9 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	864-867	4
β-strand	868-874	7	7
β-strand	879-881	3	7
β-strand	888-892	5	8
β-strand	894	1	9
β-strand	896-897	2	7
α-helix	898	1
β-strand	905-907	3	7
β-strand	914	1	9
β-strand	916-920	5	8
α-helix	923-929	7
β-strand	933-943	11	7
α-helix	949-951	3
β-strand	952-958	7	8
β-strand	963-969	7	8
β-strand	972-980	9	8
β-strand	983-990	8	8
β-strand	1004-1011	8	7
β-strand	1015-1020	6	7
β-strand	1023-1029	7	7
β-strand	1041-1048	8	8
β-strand	1063-1072	10	7
α-helix	1078-1087	10
β-strand	1093	1	10
β-strand	1095	1	11
β-strand	1101	1	11
α-helix	1102	1
β-strand	1103	1	12
β-strand	1107-1112	6	13
α-helix	1113-1115	3
β-strand	1118-1123	6	13
β-strand	1126-1131	6	13
β-strand	1144-1150	7	13
β-strand	1157	1	12
β-strand	1159	1	10
β-strand	1163-1169	7	13
β-strand	1174-1179	6	13
β-strand	1190-1196	7	13
α-helix	1200-1206	7
β-strand	1209-1215	7	13
β-strand	1220-1227	8	13
β-strand	1234-1245	12	13
β-strand	1255-1264	10	13
α-helix	1274-1276	3
β-strand	1278-1282	5	13

Chain C: 8 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	864-866	3
β-strand	868-874	7	14
β-strand	879-881	3	14
β-strand	888-892	5	15
β-strand	894	1	16
β-strand	896-897	2	14
β-strand	905-908	4	14
β-strand	914	1	16
β-strand	916-920	5	15
α-helix	925-930	6
β-strand	933-943	11	14
α-helix	949-951	3
β-strand	952-958	7	15
β-strand	963-969	7	15
β-strand	972-978	7	15
β-strand	984-990	7	15
β-strand	1004-1011	8	14
β-strand	1015-1020	6	14
β-strand	1023-1029	7	14
β-strand	1041-1048	8	15
β-strand	1063-1072	10	14
α-helix	1078-1087	10
β-strand	1093	1	17
β-strand	1095	1	18
β-strand	1101	1	18
α-helix	1102	1
β-strand	1103	1	19
β-strand	1107-1112	6	20
β-strand	1115	1	20
β-strand	1118-1123	6	20
β-strand	1126-1131	6	20
α-helix	1132	1
β-strand	1144-1150	7	20
β-strand	1157	1	19
β-strand	1159	1	17
β-strand	1163-1169	7	20
β-strand	1174-1179	6	20
β-strand	1190-1196	7	20
α-helix	1200-1206	7
β-strand	1209-1215	7	20
β-strand	1220-1227	8	20
β-strand	1234-1245	12	20
β-strand	1255-1264	10	20
α-helix	1274-1276	3
β-strand	1278-1282	5	20

Chains D, E and F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	37-47	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neurotoxin	A, B, C	protein	431	Clostridium botulinum	Q9LBR1
Synaptotagmin-1	D, E, F	protein	21	Homo sapiens	P21579 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>4ISQ_1 Neurotoxin (chains A, B, C)
MHHHHHHYFSINDSKILSLQNKKNTLMDTSGYNAEVRVEGNVQLNPIFPFDFKLGSSGDD
RGKVIVTQNENIVYNAMYESFSISFWIRINKWVSNLPGYTIIDSVKNNSGWSIGIISNFL
VFTLKQNENSEQDINFSYDISKNAAGYNKWFFVTITTNMMGNMMIYINGKLIDTIKVKEL
TGINFSKTITFQMNKIPNTGLITSDSDNINMWIRDFYIFAKELDDKDINILFNSLQYTNV
VKDYWGNDLRYDKEYYMINVNYMNRYMSKKGNGIVFNTRKNNNDFNEGYKIIIKRIRGNT
NDTRVRGENVLYFNTTIDNKQYSLGMYKPSRNLGTDLVPLGALDQPMDEIRKYGSFIIQP
CNTFDYYASQLFLSSNATTNRLGILSIGSYSFKLGDDYWFNHEYLIPVIKIEHYASLLES
TSTHWVFVPAS

Sequence of entity 2 (D, E, F), FASTA

>4ISQ_2 Synaptotagmin-1 (chains D, E, F)
GEGKEDAFSKLKEKFMNELHK

Primary citation

Crystal Structures of Botulinum Neurotoxin DC in Complex with Its Protein Receptors Synaptotagmin I and II. Berntsson, R.P., Peng, L., Svensson, L.M. et al. Structure (2013) 21:1602-1611. DOI 10.1016/j.str.2013.06.026 · PubMed

Other PDB entries of the same protein (UniProt Q9LBR1), best resolution first:

3N7L 2.0 Å, Crystal structure of botulinum neurotoxin serotype D/C VPI 5993 binding domain
4ISR 2.59 Å, Binding domain of Botulinum neurotoxin DC in complex with rat synaptotagmin II
3N7M 2.6 Å, Crystal structure of W1252A mutant of HCR D/C VPI 5995
4FVV 2.7 Å, Crystal structure of HCR/D-Sa-GBL1/C
3AZW 2.99 Å, Crystal structure of the receptor binding domain
3AZV 3.1 Å, Crystal structure of the receptor binding domain

Browse structure collections

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