3RSJ: HCRF

Name: PDB 3RSJ: Structure of HCRF in complex with Ganglioside GD1a
Published: 2011-08-17
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

Structure of HCRF in complex with Ganglioside GD1a. Determined by X-ray diffraction at 2.0 Å resolution. Released 17 Aug 2011.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Clostridium botulinum
Chains: 4
Atoms: 13,922
Mol. weight: 194.96 kDa
Released: 17 Aug 2011

Explore 3RSJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3RSJ contains 21 α-helices and 159 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: 5 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	867-869	3
β-strand	870-873	4	1
β-strand	874-876	3	2
β-strand	881-883	3	2
β-strand	890-895	6	3
β-strand	898-899	2	1
β-strand	906-910	5	1
β-strand	915-920	6	3
β-strand	934-941	8	1
α-helix	943-945	3
α-helix	948-950	3
β-strand	955-962	8	3
β-strand	966-973	8	3
β-strand	976-982	7	3
β-strand	988-994	7	3
β-strand	998	1	4
β-strand	1008-1015	8	1
β-strand	1020-1025	6	1
β-strand	1028-1034	7	1
β-strand	1046-1052	7	3
β-strand	1059-1068	10	1
α-helix	1074-1083	10
β-strand	1089	1	5
β-strand	1091	1	6
β-strand	1097	1	6
β-strand	1099	1	7
β-strand	1103-1108	6	8
β-strand	1114-1118	5	9
β-strand	1123-1128	6	9
β-strand	1131-1134	4	4
β-strand	1138-1141	4	4
β-strand	1148-1153	6	8
β-strand	1165	1	7
β-strand	1167	1	5
β-strand	1171-1178	8	8
β-strand	1181-1187	7	8
β-strand	1195-1202	8	8
β-strand	1212-1219	8	8
β-strand	1222-1229	8	8
β-strand	1234-1240	7	8
β-strand	1244	1	9
β-strand	1245-1248	4	8
α-helix	1249-1253	5
β-strand	1266-1269	4	8

Chain B: 6 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	870-873	4	10
β-strand	874-877	4	11
β-strand	880-883	4	11
β-strand	890-895	6	12
β-strand	897-899	3	10
β-strand	907-910	4	10
β-strand	915-920	6	12
β-strand	934-941	8	10
α-helix	943-945	3
α-helix	948-950	3
β-strand	955-961	7	12
β-strand	967-973	7	12
β-strand	976-982	7	12
β-strand	988-994	7	12
β-strand	998	1	13
β-strand	1008-1015	8	10
β-strand	1020-1025	6	10
β-strand	1028-1034	7	10
β-strand	1046-1052	7	12
β-strand	1059-1068	10	10
α-helix	1071-1073	3
α-helix	1074-1083	10
β-strand	1089	1	14
β-strand	1091	1	15
β-strand	1097	1	15
α-helix	1098	1
β-strand	1099	1	16
β-strand	1103-1108	6	17
β-strand	1114-1118	5	18
β-strand	1123-1128	6	18
β-strand	1131-1134	4	13
β-strand	1138-1141	4	13
β-strand	1148-1153	6	17
β-strand	1165	1	16
β-strand	1167	1	14
β-strand	1171-1178	8	17
β-strand	1181-1187	7	17
β-strand	1195-1202	8	17
β-strand	1212-1219	8	17
β-strand	1222-1229	8	17
β-strand	1234-1240	7	17
β-strand	1244	1	18
β-strand	1245-1248	4	17
α-helix	1249-1251	3
β-strand	1266-1269	4	17
β-strand	1272	1	19
β-strand	1275	1	19

Chain C: 4 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	870-873	4	20
β-strand	874-876	3	21
β-strand	881-883	3	21
β-strand	890-895	6	22
β-strand	898-899	2	20
β-strand	907-910	4	20
β-strand	915-920	6	22
β-strand	934-941	8	20
α-helix	943-945	3
α-helix	948-950	3
β-strand	955-961	7	22
β-strand	967-973	7	22
β-strand	976-982	7	22
β-strand	988-994	7	22
β-strand	998	1	23
β-strand	1008-1015	8	20
β-strand	1020-1025	6	20
β-strand	1028-1034	7	20
β-strand	1046-1052	7	22
β-strand	1059-1068	10	20
α-helix	1074-1083	10
β-strand	1089	1	24
β-strand	1091	1	25
β-strand	1097	1	25
β-strand	1099	1	26
β-strand	1103-1108	6	27
β-strand	1114-1118	5	28
β-strand	1122	1	27
β-strand	1123-1128	6	28
β-strand	1131-1134	4	23
β-strand	1138-1141	4	23
β-strand	1148-1153	6	27
β-strand	1165	1	26
β-strand	1167	1	24
β-strand	1170-1178	9	27
β-strand	1181-1187	7	27
β-strand	1195-1202	8	27
β-strand	1212-1219	8	27
β-strand	1222-1229	8	27
β-strand	1234-1240	7	27
β-strand	1244	1	28
β-strand	1245-1248	4	27
α-helix	1250-1253	4
β-strand	1266-1269	4	27

Chain D: 6 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	867-869	3
β-strand	870-873	4	29
β-strand	874-877	4	30
β-strand	880-883	4	30
β-strand	890-895	6	31
β-strand	898-899	2	29
β-strand	906-910	5	29
β-strand	915-920	6	31
β-strand	934-941	8	29
α-helix	943-945	3
α-helix	948-950	3
β-strand	955-961	7	31
β-strand	967-973	7	31
β-strand	976-982	7	31
β-strand	988-994	7	31
β-strand	998	1	32
β-strand	1008-1015	8	29
β-strand	1020-1025	6	29
β-strand	1028-1034	7	29
β-strand	1046-1052	7	31
β-strand	1059-1068	10	29
α-helix	1074-1083	10
β-strand	1089	1	33
β-strand	1091	1	34
β-strand	1097	1	34
α-helix	1098	1
β-strand	1099	1	35
β-strand	1103-1108	6	36
β-strand	1114-1118	5	37
β-strand	1123-1128	6	37
β-strand	1131-1134	4	32
β-strand	1138-1141	4	32
β-strand	1148-1153	6	36
β-strand	1165	1	35
β-strand	1167	1	33
β-strand	1171-1178	8	36
β-strand	1181-1187	7	36
β-strand	1195-1202	8	36
β-strand	1212-1219	8	36
β-strand	1222-1229	8	36
β-strand	1234-1240	7	36
β-strand	1244	1	37
β-strand	1245-1248	4	36
α-helix	1251-1253	3
β-strand	1266-1269	4	36

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
BoNT/F	A, B, C, D	protein	413	Clostridium botulinum	A7GBG3 (AlphaFold model)

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

>3RSJ_1 BoNT/F (chains A, B, C, D)
IKDNSILDMRYENNKFIDISGYGSNISINGDVYIYSTNRNQFGIYSSKPSEVNIAQNNDI
IYNGRYQNFSISFWVRIPKYFNKVNLNNEYTIIDCIRNNNSGWKISLNYNKIIWTLQDTA
GNNQKLVFNYTQMISISDYINKWIFVTITNNRLGNSRIYINGNLIDEKSISNLGDIHVSD
NILFKIVGCNDTRYVGIRYFKVFDTELGKTEIETLYSDEPDPSILKDFWGNYLLYNKRYY
LLNLLRTDKSITQNSNFLNINQQRGVYQKPNIFSNTRLYTGVEVIIRKNGSTDISNTDNF
VRKNDLAYINVVDRDVEYRLYADISIAKPEKIIKLIRTSNSNNSLGQIIVMDSIGNNCTM
NFQNNNGGNIGLLGFHSNNLVASSWYYNNIRKNTSSNGCFWSFISKEHGWQEN

Primary citation

Unique ganglioside recognition strategies for clostridial neurotoxins. Benson, M.A., Fu, Z., Kim, J.J. et al. J Biol Chem (2011) 286:34015-34022. DOI 10.1074/jbc.M111.272054 · PubMed

Other PDB entries of the same protein (UniProt A7GBG3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3FIE 2.1 Å, Crystal structure of Clostridium botulinum neurotoxin serotype F catalytic domain with…
3FUQ 2.1 Å, Glycosylated SV2 and Gangliosides as Dual Receptors for Botulinum Neurotoxin Serotype F
3FII 2.17 Å, Crystal structure of Clostridium botulinum neurotoxin serotype F catalytic domain with…

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