6RIM

Crystal structure of the catalytic domain of the Weissela oryzae botulinum like toxin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Crystal structure of the catalytic domain of the Weissella oryzae botulinum-like toxin.

Kosenina, S., Masuyer, G., Zhang, S., Dong, M., Stenmark, P.

(2019) FEBS Lett 593: 1403-1410

  • DOI: https://doi.org/10.1002/1873-3468.13446
  • Primary Citation of Related Structures:  
    6RIM

  • PubMed Abstract: 

    Botulinum neurotoxins (BoNTs) are the most potent toxins known. So far, eight serotypes have been identified that all act as zinc-dependent endopeptidases targeting SNARE proteins and inhibiting the release of neurotransmitters. Recently, the first botulinum toxin-like protein was identified outside the Clostridial genus, designated BoNT/Wo in the genome of Weissella oryzae. Here, we report the 1.6 Å X-ray crystal structure of the light chain of BoNT/Wo (LC/Wo). LC/Wo presents the core fold common to BoNTs but has an unusually wide, open and negatively charged catalytic pocket, with an additional Ca 2+ ion besides the zinc ion and a unique ß-hairpin motif. The structural information will help establish the substrate profile of BoNT/Wo and help our understanding of how BoNT evolved.

    • Organizational Affiliation: 

    Department of Biochemistry and Biophysics, Stockholm University, Sweden.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative botulinum-like toxin Wo
A, B, C, D, E
A, B, C, D, E, F, G, H
498Weissella oryzaeMutation(s): 0 
Gene Names: WOSG25_110680
EC: 3.4.24.69
UniProt
Find proteins for A0A069CUU9 (Weissella oryzae (strain DSM 25784 / JCM 18191 / LMG 30913 / SG25))
Explore A0A069CUU9 
Go to UniProtKB:  A0A069CUU9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A069CUU9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
I [auth A]
K [auth B]
M [auth C]
O [auth D]
Q [auth E]
I [auth A],
K [auth B],
M [auth C],
O [auth D],
Q [auth E],
S [auth F],
U [auth G],
W [auth H]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA
Download Ideal Coordinates CCD File 
J [auth A]
L [auth B]
N [auth C]
P [auth D]
R [auth E]
J [auth A],
L [auth B],
N [auth C],
P [auth D],
R [auth E],
T [auth F],
V [auth G],
X [auth H]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.908α = 101.71
b = 105.208β = 90
c = 179.621γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2018-03406

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-29
    Type: Initial release
  • Version 1.1: 2019-06-05
    Changes: Data collection, Derived calculations
  • Version 1.2: 2019-07-03
    Changes: Data collection, Database references
  • Version 1.3: 2019-08-21
    Changes: Data collection
  • Version 1.4: 2024-10-23
    Changes: Data collection, Database references, Derived calculations, Structure summary