8HHE

Crystal structure of Cry5B from Bacillus thuringiensis at 4.5 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.50 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Insights from the Structure of an Active Form of Bacillus thuringiensis Cry5B.

Li, J.Wang, L.Kotaka, M.Lee, M.M.Chan, M.K.

(2022) Toxins (Basel) 14

  • DOI: https://doi.org/10.3390/toxins14120823
  • Primary Citation of Related Structures:  
    8HHE

  • PubMed Abstract: 

    The crystal protein Cry5B, a pore-forming protein produced by the soil bacterium Bacillus thuringiensis , has been demonstrated to have excellent anthelmintic activity. While a previous structure of the three-domain core region of Cry5B(112-698) had been reported, this structure lacked a key N-terminal extension critical to function. Here we report the structure of Cry5B(27-698) containing this N-terminal extension. This new structure adopts a distinct quaternary structure compared to the previous Cry5B(112-698) structure, and also exhibits a change in the conformation of residues 112-140 involved in linking the N-terminal extension to the three-domain core by forming a random coil and an extended α-helix. A role for the N-terminal extension is suggested based on a computational model of the tetramer with the conformation of residues 112-140 in its alternate α-helix conformation. Finally, based on the Cry5B(27-698) structure, site-directed mutagenesis studies were performed on Tyr495, which revealed that having an aromatic group or bulky group at this residue 495 is important for Cry5B toxicity.


  • Organizational Affiliation

    School of Life Sciences and Center of Novel Biomaterials, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Crystaline entomocidal protoxin
A, B
808Bacillus thuringiensis YBT-1518Mutation(s): 0 
Gene Names: YBT1518_04070
UniProt
Find proteins for B7SB31 (Bacillus thuringiensis YBT-1518)
Explore B7SB31 
Go to UniProtKB:  B7SB31
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB7SB31
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.50 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.401α = 90
b = 114.401β = 90
c = 263.35γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CNSrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The University Grants Committee, Research Grants Council (RGC)Hong KongGRF 14176017

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-07
    Type: Initial release
  • Version 1.1: 2023-01-04
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description