3RMY: HCR/D W1238A mutant

Name: PDB 3RMY: Crystal structure of HCR/D W1238A mutant
Published: 2011-06-01
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

Crystal structure of HCR/D W1238A mutant. Determined by X-ray diffraction at 2.3 Å resolution. Released 1 Jun 2011.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Clostridium botulinum
Chains: 4
Atoms: 13,352
Mol. weight: 192.76 kDa
Released: 1 Jun 2011

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

Secondary structure: helices and β-sheets

3RMY contains 43 α-helices and 148 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, 40 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	914-917	4	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	970-976	7	3
β-strand	982	1	3
β-strand	985-988	4	3
β-strand	1003-1009	7	1
β-strand	1014-1019	6	1
β-strand	1022-1023	2	1
β-strand	1027-1028	2	1
β-strand	1040-1043	4	3
β-strand	1055-1063	9	1
α-helix	1069-1079	11
β-strand	1084	1	4
β-strand	1086	1	5
β-strand	1092	1	5
α-helix	1093	1
β-strand	1094	1	6
β-strand	1098-1103	6	7
β-strand	1106	1	7
β-strand	1109-1112	4	8
β-strand	1114	1	9
β-strand	1117	1	9
β-strand	1119-1122	4	8
α-helix	1123	1
β-strand	1135-1139	5	7
α-helix	1147	1
β-strand	1148	1	6
α-helix	1149	1
β-strand	1150	1	4
β-strand	1154-1161	8	7
β-strand	1164-1170	7	7
β-strand	1188-1194	7	7
α-helix	1201-1203	3
β-strand	1205-1209	5	7
β-strand	1218-1222	5	7
β-strand	1228-1233	6	7
β-strand	1247-1251	5	7
α-helix	1255-1257	3
α-helix	1261-1263	3
β-strand	1265-1268	4	7

Chain B: 10 helices, 38 β-strands

Element	Residues	Length	Sheet
α-helix	863-866	4
β-strand	868-871	4	10
β-strand	872-874	3	11
β-strand	879-881	3	11
β-strand	888-891	4	12
β-strand	897	1	10
β-strand	904-907	4	10
β-strand	914-917	4	12
β-strand	931-939	9	10
α-helix	941-945	5
β-strand	949-955	7	12
β-strand	961-967	7	12
β-strand	970-976	7	12
β-strand	982-987	6	12
β-strand	1003-1009	7	10
β-strand	1014-1019	6	10
β-strand	1022-1028	7	10
β-strand	1040-1043	4	12
β-strand	1055-1063	9	10
α-helix	1069-1079	11
β-strand	1084	1	13
β-strand	1086	1	14
β-strand	1092	1	14
α-helix	1093	1
β-strand	1094	1	15
β-strand	1098-1103	6	16
β-strand	1106	1	16
β-strand	1109-1112	4	17
β-strand	1114	1	18
β-strand	1117	1	18
β-strand	1119-1122	4	17
α-helix	1123	1
β-strand	1135-1139	5	16
α-helix	1147	1
β-strand	1148	1	15
α-helix	1149	1
β-strand	1150	1	13
β-strand	1154-1160	7	16
β-strand	1165-1170	6	16
β-strand	1188-1194	7	16
α-helix	1201-1203	3
β-strand	1205-1209	5	16
β-strand	1218-1222	5	16
β-strand	1228-1235	8	16
β-strand	1245-1251	7	16
α-helix	1255-1257	3
α-helix	1261-1263	3
β-strand	1265-1268	4	16

Chain C: 12 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	865-867	3
β-strand	868-871	4	19
β-strand	872-874	3	20
β-strand	879-881	3	20
β-strand	888-891	4	21
β-strand	897	1	19
β-strand	904-907	4	19
β-strand	914-917	4	21
β-strand	931-939	9	19
α-helix	941-944	4
β-strand	949-956	8	21
β-strand	961-967	7	21
β-strand	970-976	7	21
β-strand	982-988	7	21
β-strand	1003-1009	7	19
β-strand	1014-1019	6	19
β-strand	1022-1028	7	19
α-helix	1036-1038	3
β-strand	1040-1043	4	21
β-strand	1055-1063	9	19
α-helix	1069-1080	12
β-strand	1084	1	22
β-strand	1086	1	23
α-helix	1091	1
β-strand	1092	1	23
α-helix	1093	1
β-strand	1094	1	24
β-strand	1098-1103	6	25
β-strand	1109-1115	7	25
β-strand	1117-1122	6	25
α-helix	1123	1
β-strand	1135-1139	5	25
α-helix	1147	1
β-strand	1148	1	24
α-helix	1149	1
β-strand	1150	1	22
β-strand	1154-1161	8	25
β-strand	1164-1174	11	25
β-strand	1188-1194	7	25
α-helix	1201-1203	3
β-strand	1205-1209	5	25
β-strand	1218-1222	5	25
β-strand	1228-1235	8	25
β-strand	1245-1251	7	25
α-helix	1255-1257	3
α-helix	1261-1263	3
β-strand	1265-1268	4	25

Chain D: 11 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	863-866	4
β-strand	868-871	4	26
β-strand	872-874	3	27
β-strand	879-881	3	27
β-strand	888-891	4	28
β-strand	897	1	26
β-strand	904-907	4	26
β-strand	914-917	4	28
β-strand	931-939	9	26
α-helix	941-944	4
β-strand	949-955	7	28
β-strand	961-967	7	28
β-strand	970-976	7	28
β-strand	982-985	4	28
β-strand	1003-1010	8	26
β-strand	1014-1019	6	26
β-strand	1022-1025	4	26
β-strand	1040-1043	4	28
β-strand	1055-1063	9	26
α-helix	1069-1080	12
β-strand	1084	1	29
β-strand	1086	1	30
β-strand	1092	1	30
α-helix	1093	1
β-strand	1094	1	31
β-strand	1098-1103	6	32
β-strand	1109-1112	4	33
β-strand	1119-1122	4	33
α-helix	1123	1
β-strand	1135-1139	5	32
α-helix	1147	1
β-strand	1148	1	31
α-helix	1149	1
β-strand	1150	1	29
β-strand	1154-1161	8	32
β-strand	1164-1174	11	32
β-strand	1188-1194	7	32
α-helix	1201-1203	3
β-strand	1205-1209	5	32
β-strand	1218-1222	5	32
β-strand	1228-1235	8	32
α-helix	1238-1240	3
β-strand	1245-1251	7	32
α-helix	1256-1259	4
α-helix	1261-1263	3
β-strand	1265-1268	4	32

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

>3RMY_1 Botulinum neurotoxin type D (chains A, B, C, D)
NSINDSKILSLQNKKNALVDTSGYNAEVRVGDNVQLNTIYTNDFKLSSSGDKIIVNLNNN
ILYSAIYENSSVSFWIKISKDLTNSHNEYTIINSIEQNSGWKLCIRNGNIEWILQDVNRK
YKSLIFDYSESLSHTGYTNKWFFVTITNNIMGYMKLYINGELKQSQKIEDLDEVKLDKTI
VFGIDENIDENQMLWIRDFNIFSKELSNEDINIVYEGQILRNVIKDYWGNPLKFDTEYYI
INDNYIDRYIAPESNVLVLVQYPDRSKLYTGNPITIKSVSDKNPYSRILNGDNIILHMLY
NSRKYMIIRDTDTIYATQGGECSQNCVYALKLQSNLGNYGIGIFSIKNIVSKNKYCSQIF
SSFRENTMLLADIYKPARFSFKNAYTPVAVTNYETKLLSTSSFWKFISRDPGWVE

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…
5BQN 2.3 Å, Crystal structure of the LHn fragment of botulinum neurotoxin type D, mutant H233Y E230Q
3RMX 2.75 Å, Crystal structure of HCR/D F1240A mutant
5BQM 3.1 Å, Crystal structure of SXN101959, a Clostridium botulinum neurotoxin type D derivative and…

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