8HX3

crystal structure of secreted coleopteran active protein (Sip)

• PDB DOI: https://doi.org/10.2210/pdb8HX3/pdb

• Classification: TOXIN
• Organism(s): Bacillus thuringiensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-01-03 Released: 2023-07-12 
• Deposition Author(s): Chen, Z., Jiang, K., Gao, X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 0.278 
• R-Value Work: 0.240 
• R-Value Observed: 0.241 

Literature

Structural insight into Bacillus thuringiensis Sip1Ab reveals its similarity to ETX_MTX2 family beta-pore-forming toxin.

Chen, Z., Shi, Y., Wang, D., Liu, X., Jiao, X., Gao, X., Jiang, K.

(2023) Pest Manag Sci 79: 4264-4273

• PubMed: 37341620 
• DOI: https://doi.org/10.1002/ps.7622
• Primary Citation of Related Structures:  
  8HX3


• PubMed Abstract: 
  

  Microbially derived, protein-based biopesticides are an important approach for sustainable pest management. The secreted insecticidal proteins (Sips) produced by the bacterium Bacillus thuringiensis exhibit potent insecticidal activity against coleopteran pests and are, therefore, attractive as candidate biopesticides. However, the modes-of-action of Sips are unclear as comprehensive structural information for these proteins is lacking. Using X-ray crystallography, we elucidated the structure of monomeric Sip1Ab at 2.28 Å resolution. Structural analyses revealed that Sip1Ab has the three domains and conserved fold characteristic of other aerolysin-like beta-pore-forming toxins (β-PFTs). Based on the sequence and structural similarities between Sip1Ab and other ETX_MTX2 subfamily toxins, we suggested the mechanism of these proteins and proposed that it is common to them all. The atomic-level structural data for Sip1Ab generated by the present study could facilitate future structural and mechanistic research on Sips as well as their application in sustainable insect pest management. © 2023 Society of Chemical Industry.

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Organizational Affiliation: 

State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 72.6 kDa 
• Atom Count: 5,297 
• Modelled Residue Count: 634 
• Deposited Residue Count: 634 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Secreted coleopteran active protein	A, B	317	Bacillus thuringiensis	Mutation(s): 0  Gene Names: sip
UniProt
Find proteins for A0A2Z0MQV7 (Bacillus thuringiensis) Explore A0A2Z0MQV7  Go to UniProtKB:  A0A2Z0MQV7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth B], E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 0.278 
• R-Value Work: 0.240 
• R-Value Observed: 0.241 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.02	α = 90
b = 233.987	β = 90
c = 111.904	γ = 90

Software Package:

Software Name	Purpose
CRANK2	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-12 
Deposition Author(s): Chen, Z., Jiang, K., Gao, X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31901943

Revision History  

• Version 1.0: 2023-07-12
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Database references