5L21: BoNT/A receptor binding domain

Name: PDB 5L21: Crystal structure of BoNT/A receptor binding domain in complex with VHH C2
Published: 2017-08-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

Crystal structure of BoNT/A receptor binding domain in complex with VHH C2. Determined by X-ray diffraction at 1.68 Å resolution. Released 9 Aug 2017.

Method: X-ray diffraction
Resolution: 1.68 Å
Organisms: Clostridium botulinum (strain Hall / ATCC 3502 / NCTC 13319 / Type A), Vicugna pacos
Chains: 2
Atoms: 5,003
Mol. weight: 63.2 kDa
Released: 9 Aug 2017

Explore 5L21 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5L21 contains 14 α-helices and 62 β-strands across 2 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, 50 β-strands

Element	Residues	Length	Sheet
α-helix	872-875	4
β-strand	879-880	2	1
β-strand	881-884	4	2
β-strand	887-890	4	2
β-strand	897-900	4	3
β-strand	905-906	2	1
β-strand	914-917	4	1
β-strand	924-927	4	3
α-helix	930-932	3
β-strand	935-936	2	4
β-strand	941-948	8	1
α-helix	950-952	3
α-helix	955-957	3
β-strand	962-969	8	3
β-strand	972-979	8	3
β-strand	982-988	7	3
β-strand	994-1000	7	3
β-strand	1004	1	5
β-strand	1015-1021	7	1
β-strand	1026-1031	6	1
β-strand	1034-1040	7	1
β-strand	1047-1048	2	4
β-strand	1052-1058	7	3
β-strand	1066-1075	10	1
α-helix	1081-1091	11
β-strand	1096	1	6
β-strand	1098	1	7
β-strand	1104	1	7
α-helix	1105	1
β-strand	1106	1	8
β-strand	1110-1111	2	9
β-strand	1112-1115	4	10
β-strand	1122-1125	4	9
β-strand	1134-1137	4	9
β-strand	1142-1145	4	5
β-strand	1149-1152	4	5
α-helix	1158-1159	2
β-strand	1160-1164	5	9
β-strand	1173	1	8
β-strand	1175	1	6
β-strand	1179-1186	8	9
β-strand	1189-1194	6	9
β-strand	1195	1	11
β-strand	1204-1205	2	9
β-strand	1207-1209	3	9
α-helix	1210	1
α-helix	1211-1213	3
β-strand	1218	1	11
β-strand	1220-1223	4	9
β-strand	1226	1	12
β-strand	1232	1	12
β-strand	1235	1	13
β-strand	1237-1240	4	9
β-strand	1246-1255	10	9
β-strand	1258-1264	7	9
α-helix	1265-1273	9
β-strand	1281	1	13
β-strand	1282-1285	4	10
β-strand	1288	1	14
β-strand	1291	1	14

Chain B: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	15
β-strand	10-12	3	16
β-strand	18-25	8	15
α-helix	33-35	3
β-strand	38-43	6	16
α-helix	49-51	3
β-strand	53-58	6	16
β-strand	65-66	2	16
α-helix	68-70	3
β-strand	74-79	6	15
β-strand	84-89	6	15
α-helix	94-96	3
β-strand	98-104	7	16
β-strand	107-108	2	16
β-strand	109	1	15
β-strand	112-116	5	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Botulinum neurotoxin type A	A	protein	428	Clostridium botulinum (strain Hall / ATCC 3502 / NCTC 13319 / Type A)	P0DPI1 (AlphaFold model)
VHH-C2	B	protein	119	Vicugna pacos

Sequence of entity 1 (A), FASTA

>5L21_1 Botulinum neurotoxin type A (chains A)
GPMNIINTSILNLRYESNHLIDLSRYASKINIGSKVNFDPIDKNQIQLFNLESSKIEVIL
KNAIVYNSMYENFSTSFWIRIPKYFNSISLNNEYTIINCMENNSGWKVSLNYGEIIWTLQ
DTQEIKQRVVFKYSQMINISDYINRWIFVTITNNRLNNSKIYINGRLIDQKPISNLGNIH
ASNNIMFKLDGCRDTHRYIWIKYFNLFDKELNEKEIKDLYDNQSNSGILKDFWGDYLQYD
KPYYMLNLYDPNKYVDVNNVGIRGYMYLKGPRGSVMTTNIYLNSSLYRGAKFIIKKYASG
NKDNIVRNNDRVYINVVVKNKEYRLATNASQAGVEKILSALEIPDVGNLSQVVVMKSKND
QGITNKCKMNLQDNNGNDIGFIGFHQFNNIAKLVASNWYNRQIERSSRTLGCSWEFIPVD
DGWGERPL

Sequence of entity 2 (B), FASTA

>5L21_2 VHH-C2 (chains B)
QVQLVESGGGLAQPGGSLRLSCEASGFGTWFRFDENTVNWYRQPPGKSREFDELVARYPK
SGIVTYLDSVKGRFTISRDNAKKMAFLQMDNLKPEDTAVYYCNVGEFWGQGTQVTISSE

Primary citation

A camelid single-domain antibody neutralizes botulinum neurotoxin A by blocking host receptor binding. Yao, G., Lam, K.H., Weisemann, J. et al. Sci Rep (2017) 7:7438-7438. DOI 10.1038/s41598-017-07457-5 · PubMed

Other PDB entries of the same protein (UniProt P0DPI1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3BON 1.2 Å, Structure of the C. botulinum neurotoxin serotype A with Zn2+ cofactor bound
4EL4 1.2 Å, Crystal structure of the catalytic domain of botulinum neurotoxin BoNT/A C134S/C165S…
3BOK 1.25 Å, Structure of the C. botulinum neurotoxin serotype A apo-enzyme
3BOO 1.4 Å, Structure of the C. botulinum neurotoxin serotype A with an inhibitory peptide bound
5MK6 1.45 Å, Crystal structure of the receptor-binding domain of botulinum neurotoxin A1 (crystal…
3C8B 1.47 Å, Crystal structure of the catalytic domain of botulinum neurotoxin serotype A with…
3DDA 1.5 Å, Crystal structure of the catalytic domain of Botulinum neurotoxin serotype a with a…
3QW7 1.5 Å, Crystal structure of the protease domain of Botulinum Neurotoxin Serotype A with a…
3C8A 1.52 Å, Crystal structure of the catalytic domain of botulinum neurotoxin serotype A with…
3C89 1.58 Å, Crystal structure of the catalytic domain of botulinum neurotoxin serotype A with…
2VU9 1.6 Å, Crystal structure of botulinum neurotoxin serotype a binding domain in complex with GT1B
3C88 1.6 Å, Crystal structure of the catalytic domain of botulinum neurotoxin serotype A with…

Browse structure collections

About this viewer

MolViewer shows 5L21 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.