7KZ7

Crystals Structure of the Mutated Protease Domain of Botulinum Neurotoxin X (X4130B1).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Phage-assisted evolution of botulinum neurotoxin proteases with reprogrammed specificity.

Blum, T.R.Liu, H.Packer, M.S.Xiong, X.Lee, P.G.Zhang, S.Richter, M.Minasov, G.Satchell, K.J.F.Dong, M.Liu, D.R.

(2021) Science 371: 803-810

  • DOI: https://doi.org/10.1126/science.abf5972
  • Primary Citation of Related Structures:  
    7KZ7

  • PubMed Abstract: 

    Although bespoke, sequence-specific proteases have the potential to advance biotechnology and medicine, generation of proteases with tailor-made cleavage specificities remains a major challenge. We developed a phage-assisted protease evolution system with simultaneous positive and negative selection and applied it to three botulinum neurotoxin (BoNT) light-chain proteases. We evolved BoNT/X protease into separate variants that preferentially cleave vesicle-associated membrane protein 4 (VAMP4) and Ykt6, evolved BoNT/F protease to selectively cleave the non-native substrate VAMP7, and evolved BoNT/E protease to cleave phosphatase and tensin homolog (PTEN) but not any natural BoNT protease substrate in neurons. The evolved proteases display large changes in specificity (218- to >11,000,000-fold) and can retain their ability to form holotoxins that self-deliver into primary neurons. These findings establish a versatile platform for reprogramming proteases to selectively cleave new targets of therapeutic interest.


  • Organizational Affiliation

    Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Botulinum neurotoxin type X445Clostridium botulinumMutation(s): 6 
Gene Names: CBB2_0680
EC: 3.4.24.69
UniProt
Find proteins for P0DPK1 (Clostridium botulinum)
Explore P0DPK1 
Go to UniProtKB:  P0DPK1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DPK1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.935α = 90
b = 86.775β = 90
c = 93.557γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-23
    Type: Initial release
  • Version 1.1: 2021-12-15
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description