6G5F

Crystal structure of an engineered Botulinum Neurotoxin type B mutant E1191M/S1199Y in complex with human synaptotagmin 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Engineered botulinum neurotoxin B with improved binding to human receptors has enhanced efficacy in preclinical models.

Elliott, M.Favre-Guilmard, C.Liu, S.M.Maignel, J.Masuyer, G.Beard, M.Boone, C.Carre, D.Kalinichev, M.Lezmi, S.Mir, I.Nicoleau, C.Palan, S.Perier, C.Raban, E.Zhang, S.Dong, M.Stenmark, P.Krupp, J.

(2019) Sci Adv 5: eaau7196-eaau7196

  • DOI: 10.1126/sciadv.aau7196
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Although botulinum neurotoxin serotype A (BoNT/A) products are common treatments for various disorders, there is only one commercial BoNT/B product, whose low potency, likely stemming from low affinity toward its human receptor synaptotagmin 2 (hSyt2 ...

    Although botulinum neurotoxin serotype A (BoNT/A) products are common treatments for various disorders, there is only one commercial BoNT/B product, whose low potency, likely stemming from low affinity toward its human receptor synaptotagmin 2 (hSyt2), has limited its therapeutic usefulness. We express and characterize two full-length recombinant BoNT/B1 proteins containing designed mutations E1191M/S1199Y (rBoNT/B1 MY ) and E1191Q/S1199W (rBoNT/B1 QW ) that enhance binding to hSyt2. In preclinical models including human-induced pluripotent stem cell neurons and a humanized transgenic mouse, this increased hSyt2 affinity results in high potency, comparable to that of BoNT/A. Last, we solve the cocrystal structure of rBoNT/B1 MY in complex with peptides of hSyt2 and its homolog hSyt1. We demonstrate that neuronal surface receptor binding limits the clinical efficacy of unmodified BoNT/B and that modified BoNT/B proteins have promising clinical potential.


    Organizational Affiliation

    Synthetic Biology and Bioengineering Research Center, KRIBB, Daejeon, 34141, Republic of Korea.,Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, 34134, Republic of Korea.,Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; baumeist@biochem.mpg.de.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea. sglee@kribb.re.kr.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, 3800, Australia.,Brigham and Women's Hospital Division of Rheumatology, Immunology and Allergy and Harvard Medical School, Boston, MA, 02115, USA. I.vanRhijn@uu.nl.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea.,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584CL, Utrecht, The Netherlands. I.vanRhijn@uu.nl.,Ipsen Bioinnovation, 102 Park Drive, Milton Park, Abingdon OX14 4RY, UK.,Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia. Jamie.rossjohn@monash.edu.,Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.,Institute of Organic Chemistry, Justus-Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany.,Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, 3800, Australia. Jamie.rossjohn@monash.edu.,Department of Urology, Boston Children's Hospital, Department of Microbiology and Immunobiology and Department of Surgery, Harvard Medical School, Boston, MA 02115, USA.,Brigham and Women's Hospital Division of Rheumatology, Immunology and Allergy and Harvard Medical School, Boston, MA, 02115, USA.,Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.,Department of Microbiology and Immunology, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA, 30322, USA.,Faculty of Chemistry, Philipps-University Marburg, Hans-Meerwein-Straße 4, 35032, Marburg, Germany.,Synthetic Biology and Bioengineering Research Center, KRIBB, Daejeon, 34141, Republic of Korea. sglee@kribb.re.kr.,National Institute of Child Health and Human Development, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, USA.,Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, Université Paul Sabatier, 31077, Toulouse, France.,Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032, Marburg, Germany.,Department of Biochemistry and Biophysics, Stockholm University, Stockholm SE-106 91, Sweden.,Stratingh Institute for Chemistry, University of Groningen, 9747AG, Groningen, The Netherlands.,Department of Biophysics, Ruhr University Bochum, 44801 Bochum, Germany.,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584CL, Utrecht, The Netherlands.,Ipsen Innovation, 5 Avenue du Canada, 91940 Les Ulis, France.,Institute of Infection and Immunity, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK. Jamie.rossjohn@monash.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Botulinum neurotoxin type B
A, B
1291Clostridium botulinumMutation(s): 4 
Gene Names: botB
Find proteins for P10844 (Clostridium botulinum)
Go to UniProtKB:  P10844
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Synaptotagmin-1
P
21Homo sapiensMutation(s): 0 
Gene Names: SYT1 (SVP65, SYT)
Find proteins for P21579 (Homo sapiens)
Go to Gene View: SYT1
Go to UniProtKB:  P21579
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MLI
Query on MLI

Download SDF File 
Download CCD File 
B
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.202 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 176.078α = 90.00
b = 356.419β = 90.00
c = 103.939γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden--

Revision History 

  • Version 1.0: 2019-01-16
    Type: Initial release
  • Version 1.1: 2019-02-20
    Type: Data collection, Database references