4ISR: Binding domain of Botulinum neurotoxin DC

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

Binding domain of Botulinum neurotoxin DC in complex with rat synaptotagmin II. Determined by X-ray diffraction at 2.59 Å resolution. Released 14 Aug 2013.

Method: X-ray diffraction
Resolution: 2.59 Å
Organisms: Clostridium botulinum, Rattus norvegicus
Chains: 6
Atoms: 11,056
Mol. weight: 158.92 kDa
Released: 14 Aug 2013

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

Secondary structure: helices and β-sheets

4ISR contains 29 α-helices and 108 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, 36 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	894	1	3
β-strand	896-897	2	1
β-strand	905-908	4	1
β-strand	914	1	3
β-strand	916-920	5	2
α-helix	925-927	3
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	4
β-strand	1095	1	5
β-strand	1101	1	5
α-helix	1102	1
β-strand	1103	1	6
β-strand	1107-1112	6	7
β-strand	1118-1123	6	7
β-strand	1126-1131	6	7
β-strand	1144-1150	7	7
β-strand	1157	1	6
β-strand	1159	1	4
β-strand	1163-1170	8	7
β-strand	1173-1179	7	7
β-strand	1190-1196	7	7
α-helix	1200-1206	7
β-strand	1209-1215	7	7
β-strand	1220-1227	8	7
β-strand	1234-1245	12	7
β-strand	1255-1264	10	7
α-helix	1268-1270	3
α-helix	1274-1276	3
β-strand	1278-1282	5	7

Chain B: 8 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	864-867	4
β-strand	868-874	7	8
β-strand	879-881	3	8
β-strand	888-892	5	9
β-strand	894	1	10
β-strand	896-897	2	8
β-strand	905-908	4	8
β-strand	914	1	10
β-strand	916-920	5	9
α-helix	923-929	7
β-strand	933-943	11	8
α-helix	949-951	3
β-strand	952-958	7	9
β-strand	963-969	7	9
β-strand	972-978	7	9
β-strand	984-990	7	9
β-strand	1004-1011	8	8
β-strand	1015-1020	6	8
β-strand	1023-1029	7	8
β-strand	1041-1048	8	9
β-strand	1063-1072	10	8
α-helix	1078-1087	10
β-strand	1093	1	11
β-strand	1095	1	12
β-strand	1101	1	12
α-helix	1102	1
β-strand	1103	1	13
β-strand	1107-1112	6	14
β-strand	1118-1123	6	14
β-strand	1126-1131	6	14
β-strand	1144-1150	7	14
β-strand	1157	1	13
β-strand	1159	1	11
β-strand	1163-1170	8	14
β-strand	1173-1179	7	14
β-strand	1190-1196	7	14
α-helix	1200-1206	7
β-strand	1209-1215	7	14
β-strand	1220-1227	8	14
β-strand	1234-1245	12	14
β-strand	1255-1264	10	14
α-helix	1268-1270	3
α-helix	1274-1276	3
β-strand	1278-1282	5	14

Chain C: 9 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	865-867	3
β-strand	868-874	7	15
β-strand	879-881	3	15
β-strand	888-892	5	16
β-strand	894	1	17
β-strand	896-897	2	15
β-strand	905-908	4	15
β-strand	914	1	17
β-strand	916-920	5	16
α-helix	926-931	6
β-strand	933-943	11	15
α-helix	949-951	3
β-strand	952-959	8	16
β-strand	962-969	8	16
β-strand	972-978	7	16
β-strand	984-990	7	16
β-strand	1004-1011	8	15
β-strand	1015-1020	6	15
β-strand	1023-1029	7	15
β-strand	1041-1048	8	16
α-helix	1049-1050	2
β-strand	1063-1072	10	15
α-helix	1078-1087	10
β-strand	1093	1	18
β-strand	1095	1	19
β-strand	1101	1	19
α-helix	1102	1
β-strand	1103	1	20
β-strand	1107-1112	6	21
α-helix	1113-1115	3
β-strand	1118-1123	6	21
β-strand	1126-1131	6	21
β-strand	1144-1150	7	21
β-strand	1157	1	20
β-strand	1159	1	18
β-strand	1163-1170	8	21
β-strand	1173-1179	7	21
β-strand	1190-1196	7	21
α-helix	1200-1206	7
β-strand	1209-1215	7	21
β-strand	1220-1227	8	21
β-strand	1234-1245	12	21
β-strand	1255-1264	10	21
α-helix	1274-1276	3
β-strand	1278-1282	5	21

Chains D and E: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	43-54	12

Chain F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	44-54	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neurotoxin	A, B, C	protein	431	Clostridium botulinum	Q9LBR1
Synaptotagmin-2	D, E, F	protein	21	Rattus norvegicus	P29101 (AlphaFold model)

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

>4ISR_1 Neurotoxin (chains A, B, C)
MHHHHHHYFSINDSKILSLQNKKNTLMDTSGYNAEVRVEGNVQLNPIFPFDFKLGSSGDD
RGKVIVTQNENIVYNAMYESFSISFWIRINKWVSNLPGYTIIDSVKNNSGWSIGIISNFL
VFTLKQNENSEQDINFSYDISKNAAGYNKWFFVTITTNMMGNMMIYINGKLIDTIKVKEL
TGINFSKTITFQMNKIPNTGLITSDSDNINMWIRDFYIFAKELDDKDINILFNSLQYTNV
VKDYWGNDLRYDKEYYMINVNYMNRYMSKKGNGIVFNTRKNNNDFNEGYKIIIKRIRGNT
NDTRVRGENVLYFNTTIDNKQYSLGMYKPSRNLGTDLVPLGALDQPMDEIRKYGSFIIQP
CNTFDYYASQLFLSSNATTNRLGILSIGSYSFKLGDDYWFNHEYLIPVIKIEHYASLLES
TSTHWVFVPAS

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

>4ISR_2 Synaptotagmin-2 (chains D, E, F)
GESQEDMFAKLKDKFFNEINK

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
3N7M 2.6 Å, Crystal structure of W1252A mutant of HCR D/C VPI 5995
4ISQ 2.65 Å, Binding domain of Botulinum neurotoxin DC in complex with human synaptotagmin I
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

About this viewer

MolViewer shows 4ISR directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.