7UIB: BoNT/E receptor binding domain

Name: PDB 7UIB: Crystal structure of BoNT/E receptor binding domain in complex with SV2, VHH, and sialic acid
Published: 2023-04-05
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

Crystal structure of BoNT/E receptor binding domain in complex with SV2, VHH, and sialic acid. Determined by X-ray diffraction at 2.77 Å resolution. Released 5 Apr 2023.

Method: X-ray diffraction
Resolution: 2.77 Å
Organisms: Vicugna pacos, Homo sapiens, Clostridium botulinum
Chains: 6
Atoms: 10,570
Mol. weight: 151.18 kDa
Ligands: NAG, SLB
Released: 5 Apr 2023

Explore 7UIB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7UIB contains 19 α-helices and 149 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: 5 helices, 45 β-strands

Element	Residues	Length	Sheet
β-strand	851-854	4	25
β-strand	855-858	4	26
β-strand	861-864	4	26
β-strand	871-876	6	27
β-strand	879-880	2	25
β-strand	887-891	5	25
β-strand	896-901	6	27
β-strand	909-910	2	28
β-strand	915-922	8	25
β-strand	926	1	29
β-strand	937-943	7	27
β-strand	949-955	7	27
β-strand	958-964	7	27
β-strand	970-976	7	27
β-strand	982	1	30
β-strand	990-997	8	25
β-strand	1002-1007	6	25
β-strand	1010-1016	7	25
β-strand	1023-1024	2	28
β-strand	1028-1034	7	27
β-strand	1041-1050	10	25
α-helix	1056-1065	10
β-strand	1071	1	31
β-strand	1073	1	32
β-strand	1079	1	32
β-strand	1081	1	33
β-strand	1086-1090	5	34
β-strand	1096-1100	5	34
β-strand	1105	1	35
β-strand	1106-1111	6	34
α-helix	1112-1113	2
β-strand	1114-1115	2	30
β-strand	1118-1119	2	30
α-helix	1120	1
β-strand	1126-1131	6	34
β-strand	1141	1	33
β-strand	1143	1	31
β-strand	1147-1155	9	34
β-strand	1158-1161	4	34
β-strand	1162-1164	3	35
β-strand	1173-1174	2	34
β-strand	1175-1177	3	35
β-strand	1186-1193	8	34
β-strand	1196-1203	8	34
β-strand	1208-1215	8	34
β-strand	1218-1222	5	34
α-helix	1224-1227	4
α-helix	1235-1238	4
β-strand	1240-1243	4	34
β-strand	1249	1	29

Chain B: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	17-25	9	1
β-strand	32-39	8	3
β-strand	46-52	7	3
β-strand	57-60	4	3
β-strand	65	1	1
β-strand	68-72	5	1
β-strand	78-84	7	1
α-helix	88-90	3
β-strand	92-100	9	3
α-helix	113-115	3
β-strand	118-119	2	3
β-strand	123-125	3	3
β-strand	126-127	2	2

Chain C: 3 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	489	1
β-strand	490-493	4	4
β-strand	496-497	2	5
β-strand	501-507	7	6
β-strand	509-512	4	4
β-strand	515-517	3	5
α-helix	519	1
β-strand	520-527	8	6
β-strand	530-532	3	4
β-strand	535-539	5	5
β-strand	540-542	3	6
β-strand	545-547	3	6
β-strand	550-552	3	4
β-strand	555-559	5	5
α-helix	563-565	3
β-strand	566-567	2	6
β-strand	570-572	3	4
β-strand	575-577	3	5

Chain D: 5 helices, 49 β-strands

Element	Residues	Length	Sheet
β-strand	851-854	4	13
β-strand	855-858	4	14
β-strand	861-864	4	14
β-strand	871-876	6	15
β-strand	879-881	3	13
β-strand	884-891	8	13
β-strand	896-901	6	15
β-strand	909-910	2	16
β-strand	915-922	8	13
β-strand	926	1	17
β-strand	937-943	7	15
β-strand	949-955	7	15
β-strand	958-964	7	15
β-strand	970-976	7	15
β-strand	982	1	18
β-strand	990-997	8	13
β-strand	1002-1007	6	13
β-strand	1010-1016	7	13
β-strand	1023-1024	2	16
β-strand	1028-1034	7	15
β-strand	1041-1050	10	13
α-helix	1056-1065	10
β-strand	1071	1	19
β-strand	1073	1	20
β-strand	1079	1	20
β-strand	1081	1	21
β-strand	1086-1090	5	22
β-strand	1093	1	22
β-strand	1096	1	23
β-strand	1099-1100	2	22
β-strand	1105	1	24
β-strand	1106-1107	2	22
β-strand	1111	1	23
α-helix	1112-1113	2
β-strand	1114-1115	2	18
β-strand	1118-1119	2	18
β-strand	1126-1131	6	22
β-strand	1141	1	21
β-strand	1143	1	19
β-strand	1147-1155	9	22
β-strand	1158-1161	4	22
β-strand	1162-1164	3	24
β-strand	1173-1174	2	22
β-strand	1175-1177	3	24
β-strand	1186-1193	8	22
β-strand	1196-1203	8	22
β-strand	1208-1215	8	22
β-strand	1218-1222	5	22
α-helix	1224-1227	4
α-helix	1235-1238	4
β-strand	1240-1243	4	22
α-helix	1244-1245	2
β-strand	1246	1	17
β-strand	1249	1	17

Chain E: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	11	1	8
β-strand	19-25	7	7
β-strand	32-39	8	9
α-helix	44-45	2
β-strand	46-51	6	9
β-strand	58-60	3	9
β-strand	69-73	5	7
β-strand	78-82	5	7
α-helix	88-90	3
β-strand	92-100	9	9
α-helix	113-115	3
β-strand	118-119	2	9
β-strand	123-125	3	9
β-strand	126	1	8

Chain F: 1 helix, 15 β-strands

Element	Residues	Length	Sheet
β-strand	490-493	4	10
β-strand	496-497	2	11
β-strand	501-507	7	12
β-strand	509-512	4	10
β-strand	515-517	3	11
β-strand	520-527	8	12
β-strand	530-532	3	10
β-strand	535-539	5	11
β-strand	540-542	3	12
β-strand	545-547	3	12
β-strand	550-552	3	10
β-strand	555-559	5	11
α-helix	563-565	3
β-strand	566-567	2	12
β-strand	570-572	3	10
β-strand	575-577	3	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
VHH-G6	B, E	protein	129	Vicugna pacos
SV2	C, F	protein	105	Homo sapiens	Q496J9 (AlphaFold model)
Neurotoxin type E	A, D	protein	407	Clostridium botulinum	Q00496 (AlphaFold model)

Sequence of entity 1 (B, E), FASTA

>7UIB_1 VHH-G6 (chains B, E)
QLQLVETGGGLVKPGGSLRLSCVVSGFTFDDYRMAWVRQAPGKELEWVSSIDSWSINTYY
EDSVKGRFTISTDNAKNTLYLQMSSLKPEDTAVYYCAAEDRLGVPTINAHPSKYDYNYWG
QGTQVTVSS

Sequence of entity 2 (C, F), FASTA

>7UIB_2 SV2 (chains C, F)
VERDKYANFTINFTMENQIHTGMEYDNGRFIGVKFKSVTFKDSVFKECYFEDVTSSNTFF
RNCTFINTVFYNTDLFEYKFVNSRLINSTFLHNKEGTSPSASGGS

Sequence of entity 3 (A, D), FASTA

>7UIB_3 Neurotoxin type E (chains A, D)
RIKSSSVLNMRYKNDKYVDTSGYDSNININGDVYKYPTNKNQFGIYNDKLSEVNISQNDY
IIYDNKYKNFSISFWVRIPNYDNKIVNVNNEYTIINCMRDNNSGWKVSLNHNEIIWTLQD
NAGINQKLAFNYGNANGISDYINKWIFVTITNDRLGDSKLYINGNLIDQKSILNLGNIHV
SDNILFKIVNCSYTRYIGIRYFNIFDKELDETEIQTLYSNEPNTNILKDFWGNYLLYDKE
YYLLNVLKPNNFIDRRKDSTLSINNIRSTILLANRLYSGIKVKIQRVNNSSTNDNLVRKN
DQVYINFVASKTHLFPLYADTATTNKEKTIKISSSGNRFNQVVVMNSVGNNCTMNFKNNN
GNNIGLLGFKADTVVASTWYYTHMRDHTNSNGCFWNFISEEHGWQEK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4
SLB	N-acetyl-beta-neuraminic acid	C11 H19 N O9	2

Water and common crystallization additives (SO4, PG4) are not listed.

Primary citation

Structural basis for botulinum neurotoxin E recognition of synaptic vesicle protein 2. Liu, Z., Lee, P.G., Krez, N. et al. Nat Commun (2023) 14:2338-2338. DOI 10.1038/s41467-023-37860-8 · PubMed

Other PDB entries of the same protein (UniProt Q496J9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5JLV 2.0 Å, Receptor binding domain of Botulinum neurotoxin A in complex with human glycosylated SV2C
6ES1 2.0 Å, Crystal structure of the binding domain from botulinum neurotoxin A2 bound to…
4JRA 2.3 Å, Crystal structure of the botulinum neurotoxin a receptor-binding domain in complex with…
5MOY 2.3 Å, Crystal structure of the BoNT/A2 receptor-binding domain in complex with the luminal…
7UIA 2.59 Å, Crystal structure of BoNT/E receptor binding domain in complex with SV2 and VHH

Browse structure collections

About this viewer

MolViewer shows 7UIB 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.