3RMX: HCR/D F1240A mutant

Name: PDB 3RMX: Crystal structure of HCR/D F1240A mutant
Published: 2011-06-01
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

Crystal structure of HCR/D F1240A mutant. Determined by X-ray diffraction at 2.75 Å resolution. Released 1 Jun 2011.

Method: X-ray diffraction
Resolution: 2.75 Å
Organism: Clostridium botulinum
Chains: 4
Atoms: 13,363
Mol. weight: 192.64 kDa
Released: 1 Jun 2011

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

Secondary structure: helices and β-sheets

3RMX contains 43 α-helices and 157 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, 41 β-strands

Element	Residues	Length	Sheet
α-helix	865-867	3
β-strand	868-871	4	1
β-strand	872-874	3	2
β-strand	879-881	3	2
β-strand	888-891	4	3
β-strand	897	1	1
β-strand	904-907	4	1
β-strand	913-917	5	3
β-strand	931-939	9	1
α-helix	941-945	5
β-strand	949-956	8	3
β-strand	961-967	7	3
β-strand	971-976	6	3
β-strand	984-987	4	3
β-strand	1003-1009	7	1
β-strand	1014	1	4
β-strand	1015-1019	5	1
β-strand	1022-1025	4	1
β-strand	1028	1	4
β-strand	1040-1044	5	3
β-strand	1055-1063	9	1
α-helix	1069-1079	11
β-strand	1084	1	5
β-strand	1086	1	6
β-strand	1092	1	6
α-helix	1093	1
β-strand	1094	1	7
β-strand	1098-1103	6	8
β-strand	1109-1112	4	9
β-strand	1114	1	10
β-strand	1117	1	10
β-strand	1119-1122	4	9
α-helix	1123	1
β-strand	1135-1139	5	8
α-helix	1147	1
β-strand	1148	1	7
α-helix	1149	1
β-strand	1150	1	5
β-strand	1155-1160	6	8
β-strand	1165-1174	10	8
β-strand	1189-1194	6	8
α-helix	1201-1203	3
β-strand	1205-1209	5	8
β-strand	1218-1222	5	8
β-strand	1228-1235	8	8
β-strand	1245-1251	7	8
α-helix	1256-1259	4
α-helix	1261-1263	3
β-strand	1265-1268	4	8
β-strand	1271	1	11
β-strand	1274	1	11

Chain B: 12 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	863-866	4
β-strand	868-871	4	12
β-strand	872-874	3	13
β-strand	879-881	3	13
β-strand	888-891	4	14
β-strand	897	1	12
β-strand	904-907	4	12
β-strand	914-917	4	14
β-strand	931-939	9	12
α-helix	941-945	5
β-strand	949-956	8	14
β-strand	961-967	7	14
β-strand	970-976	7	14
β-strand	982-988	7	14
β-strand	1003-1009	7	12
β-strand	1015-1019	5	12
β-strand	1022-1026	5	12
β-strand	1040-1043	4	14
β-strand	1055-1063	9	12
α-helix	1069-1079	11
β-strand	1084	1	15
β-strand	1086	1	16
α-helix	1091	1
β-strand	1092	1	16
α-helix	1093	1
β-strand	1094	1	17
β-strand	1098-1103	6	18
β-strand	1109-1112	4	19
β-strand	1119-1122	4	19
α-helix	1123	1
β-strand	1135-1139	5	18
α-helix	1147	1
β-strand	1148	1	17
α-helix	1149	1
β-strand	1150	1	15
β-strand	1154-1161	8	18
β-strand	1164-1170	7	18
β-strand	1188-1189	2	20
β-strand	1191-1194	4	18
α-helix	1201-1203	3
β-strand	1204-1209	6	18
α-helix	1210-1211	2
β-strand	1218-1222	5	18
β-strand	1228-1229	2	18
β-strand	1230-1235	6	20
β-strand	1245-1251	7	20
α-helix	1254-1257	4
α-helix	1261-1263	3
β-strand	1265-1268	4	18

Chain C: 11 helices, 42 β-strands

Element	Residues	Length	Sheet
α-helix	863-866	4
β-strand	868-871	4	21
β-strand	872-874	3	22
β-strand	879-881	3	22
β-strand	888-891	4	23
β-strand	897	1	21
β-strand	904-907	4	21
β-strand	914-917	4	23
β-strand	931-939	9	21
α-helix	941-944	4
β-strand	949-955	7	23
β-strand	961	1	24
β-strand	962-967	6	23
β-strand	970-973	4	23
β-strand	976	1	24
β-strand	985	1	23
β-strand	988	1	23
α-helix	991-993	3
β-strand	1003-1009	7	21
β-strand	1014	1	25
β-strand	1017-1019	3	21
β-strand	1022-1025	4	21
β-strand	1028	1	25
β-strand	1040-1043	4	23
β-strand	1055-1063	9	21
α-helix	1066-1068	3
α-helix	1072-1078	7
β-strand	1084	1	26
β-strand	1086	1	27
β-strand	1092	1	27
α-helix	1093	1
β-strand	1094	1	28
β-strand	1098-1103	6	29
β-strand	1109-1112	4	30
β-strand	1114	1	31
β-strand	1117	1	31
β-strand	1119-1122	4	30
α-helix	1123	1
β-strand	1135-1139	5	29
α-helix	1147	1
β-strand	1148	1	28
α-helix	1149	1
β-strand	1150	1	26
β-strand	1154-1161	8	29
β-strand	1164-1170	7	29
β-strand	1188-1194	7	29
β-strand	1205-1209	5	29
β-strand	1218-1222	5	29
β-strand	1228-1235	8	29
β-strand	1245-1251	7	29
α-helix	1256-1259	4
α-helix	1261-1263	3
β-strand	1265-1268	4	29

Chain D: 10 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	863-866	4
β-strand	868-874	7	32
β-strand	879-881	3	32
β-strand	888-891	4	33
β-strand	897	1	32
β-strand	904-907	4	32
β-strand	914-917	4	33
β-strand	931-939	9	32
α-helix	941-944	4
β-strand	949-956	8	33
β-strand	961-967	7	33
β-strand	970-976	7	33
β-strand	982-988	7	33
β-strand	1002-1009	8	32
β-strand	1014-1019	6	32
β-strand	1022-1028	7	32
β-strand	1040-1043	4	33
β-strand	1055-1063	9	32
α-helix	1069-1079	11
β-strand	1084	1	34
β-strand	1086	1	35
β-strand	1092	1	35
α-helix	1093	1
β-strand	1094	1	36
β-strand	1098-1103	6	37
β-strand	1106	1	37
β-strand	1109-1112	4	38
β-strand	1119-1122	4	38
α-helix	1123	1
β-strand	1135-1139	5	37
α-helix	1147	1
β-strand	1148	1	36
α-helix	1149	1
β-strand	1150	1	34
β-strand	1154-1161	8	37
β-strand	1164-1167	4	37
β-strand	1168-1174	7	39
β-strand	1188-1193	6	39
α-helix	1201-1203	3
β-strand	1204-1209	6	37
β-strand	1218-1222	5	37
β-strand	1228-1229	2	37
β-strand	1230-1235	6	39
β-strand	1245-1251	7	39
α-helix	1254-1256	3
α-helix	1261-1263	3
β-strand	1265-1268	4	37

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Botulinum neurotoxin type D	A, B, C, D	protein	415	Clostridium botulinum	P19321

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

>3RMX_1 Botulinum neurotoxin type D (chains A, B, C, D)
NSINDSKILSLQNKKNALVDTSGYNAEVRVGDNVQLNTIYTNDFKLSSSGDKIIVNLNNN
ILYSAIYENSSVSFWIKISKDLTNSHNEYTIINSIEQNSGWKLCIRNGNIEWILQDVNRK
YKSLIFDYSESLSHTGYTNKWFFVTITNNIMGYMKLYINGELKQSQKIEDLDEVKLDKTI
VFGIDENIDENQMLWIRDFNIFSKELSNEDINIVYEGQILRNVIKDYWGNPLKFDTEYYI
INDNYIDRYIAPESNVLVLVQYPDRSKLYTGNPITIKSVSDKNPYSRILNGDNIILHMLY
NSRKYMIIRDTDTIYATQGGECSQNCVYALKLQSNLGNYGIGIFSIKNIVSKNKYCSQIF
SSFRENTMLLADIYKPWRASFKNAYTPVAVTNYETKLLSTSSFWKFISRDPGWVE

Primary citation

Novel Ganglioside-mediated Entry of Botulinum Neurotoxin Serotype D into Neurons. Kroken, A.R., Karalewitz, A.P., Fu, Z. et al. J Biol Chem (2011) 286:26828-26837. DOI 10.1074/jbc.M111.254086 · PubMed

Other PDB entries of the same protein (UniProt P19321), best resolution first:

2FPQ 1.65 Å, Crystal Structure of Botulinum Neurotoxin Type D Light Chain
3OGG 1.65 Å, Crystal structure of the receptor binding domain of botulinum neurotoxin D
3OBR 1.72 Å, Crystal structure of Botulinum neurotoxin serotype D binding domain
3N7J 2.0 Å, Crystal structure of botulinum neurotoxin serotype D binding domain
3OBT 2.0 Å, Crystal structure of Botulinum neurotoxin serotype D ligand binding domain in complex…
3RMY 2.3 Å, Crystal structure of HCR/D W1238A mutant
5BQN 2.3 Å, Crystal structure of the LHn fragment of botulinum neurotoxin type D, mutant H233Y E230Q
5BQM 3.1 Å, Crystal structure of SXN101959, a Clostridium botulinum neurotoxin type D derivative and…

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