4PKM | pdb_00004pkm

Crystal Structure of Bacillus thuringiensis Cry51Aa1 Protoxin at 1.65 Angstroms Resolution

• PDB DOI: https://doi.org/10.2210/pdb4PKM/pdb

• Classification: TOXIN
• Organism(s): Bacillus thuringiensis F14-1
• Expression System: Bacillus thuringiensis BMB171
• Mutation(s): No 


• Deposited: 2014-05-15 Released: 2015-06-03 
• Deposition Author(s): Xu, C., Chinte, U., Chen, L., Yao, Q., Zhou, D., Meng, Y., Li, L., Rose, J., Bi, L.J., Yu, Z., Sun, M., Wang, B.C.
• Funding Organization(s): National Basic Research Program of China (973 Program)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.199 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

Crystal structure of Cry51Aa1: A potential novel insecticidal aerolysin-type beta-pore-forming toxin from Bacillus thuringiensis.

Xu, C., Chinte, U., Chen, L., Yao, Q., Meng, Y., Zhou, D., Bi, L.J., Rose, J., Adang, M.J., Wang, B.C., Yu, Z., Sun, M.

(2015) Biochem Biophys Res Commun 462: 184-189

• PubMed: 25957471 
• DOI: https://doi.org/10.1016/j.bbrc.2015.04.068
• Primary Citation Related Structures: 
  4PKM


• PubMed Abstract: 
  

  The structures of several Bacillus thuringiensis (Bt) insecticidal crystal proteins have been determined by crystallographic methods and a close relationship has been explicated between specific toxicities and conserved three-dimensional architectures. In this study, as a representative of the coleopteran- and hemipteran-specific Cry51A group, the complete structure of Cry51Aa1 protoxin has been determined by X-ray crystallography at 1.65 Å resolution. This is the first report of a coleopteran-active Bt insecticidal toxin with high structural similarity to the aerolysin-type β-pore forming toxins (β-PFTs). Moreover, study of featured residues and structural elements reveal their possible roles in receptor binding and pore formation events. This study provides new insights into the action of aerolysin-type β-PFTs from a structural perspective, and could be useful for the control of coleopteran and hemipteran insect pests in agricultures.

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Organizational Affiliation: 
• State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China; Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA.
Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA; SER-CAT, University of Georgia and the Advanced Photon Source, Argonne National Laboratory, Argonne, IL, 60439, USA.
Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA.
Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai, 200438, PR China.
State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China.
National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, PR China.
Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA; Department of Entomology, University of Georgia, Athens, GA, 30602, USA.
Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA; SER-CAT, University of Georgia and the Advanced Photon Source, Argonne National Laboratory, Argonne, IL, 60439, USA. Electronic address: [e-mail].
State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China. Electronic address: [e-mail].
State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.42 kDa 
• Atom Count: 2,796 
• Modeled Residue Count: 305 
• Deposited Residue Count: 309 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cry51Aa1	A	309	Bacillus thuringiensis F14-1	Mutation(s): 0  Gene Names: cry51Aa1
UniProt
Find proteins for A7IZR5 (Bacillus thuringiensis) Explore A7IZR5  Go to UniProtKB:  A7IZR5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
GLY	D [auth A], E [auth A], F [auth A]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.199 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.703	α = 90
b = 54.703	β = 90
c = 209.98	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	phasing
Coot	model building
HKL-2000	data scaling
ARP	model building
PHENIX	refinement
PHASES	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-06-03 
Deposition Author(s): Xu, C., Chinte, U., Chen, L., Yao, Q., Zhou, D., Meng, Y., Li, L., Rose, J., Bi, L.J., Yu, Z., Sun, M., Wang, B.C.

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Funding Organization	Location	Grant Number
National Basic Research Program of China (973 Program)	China	2013CB127504

Revision History  

• Version 1.0: 2015-06-03
  Type: Initial release
  
• Version 1.1: 2015-06-17
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Advisory, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Refinement description