Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
32  structures 20  species 0  interactions 26  sequences 18  architectures

Family: Endotoxin_C (PF03944)

Summary: delta endotoxin

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Delta endotoxin". More...

Delta endotoxin Edit Wikipedia article

delta endotoxin, N-terminal domain
PDB 1ji6 EBI.jpg
crystal structure of the insecticidal bacterial del endotoxin Cry3Bb1 bacillus thuringiensis[1]
delta endotoxin, middle domain
Pfam clanCL0568
delta endotoxin, C-terminal
Pfam clanCL0202
Cytolytic Delta-endotoxin Cyt1/2

Delta endotoxins (δ-endotoxins) are pore-forming toxins produced by Bacillus thuringiensis species of bacteria. They are useful for their insecticidal action and are the primary toxin produced by Bt corn. During spore formation the bacteria produce crystals of such proteins (hence the name Cry toxins) that are also known as parasporal bodies, next to the endospores; as a result some members are known as a parasporin. The Cyt (cytolytic) toxin group is a group of delta-endotoxins different from the Cry group.

Mechanism of action

When an insect ingests these proteins, they are activated by proteolytic cleavage. The N-terminus is cleaved in all of the proteins and a C-terminal extension is cleaved in some members. Once activated, the endotoxin binds to the gut epithelium and causes cell lysis by the formation of cation-selective channels, which leads to death.[2][1]


The activated region of the delta toxin is composed of three distinct structural domains: an N-terminal helical bundle domain (InterProIPR005639) involved in membrane insertion and pore formation; a beta-sheet central domain involved in receptor binding; and a C-terminal beta-sandwich domain (InterProIPR005638) that interacts with the N-terminal domain to form a channel.[1][2]


B. thuringiensis encodes many proteins of the delta endotoxin family (InterProIPR038979), with some strains encoding multiple types simultaneously.[3] A gene mostly found on plasmids,[4] delta-entotoxins sometimes show up in genomes of other species, albeit at a lower proportion than those found in B. Thuringiensis.[5] The gene names looks like Cry3Bb, which in this case indicates a Cry toxin of superfamily 3 family B subfamily b.[6]

Cry proteins that are interesting to cancer research are listed under a parasporin (PS) nomenclature in addition to the Cry nomenclature. They do not kill insects, but instead kill leukemia cells.[7][8][9] The Cyt toxins tend to form their own group distinct from Cry toxins.[10] Not all Cry -- crystal-form -- toxins directly share a common root.[11] Examples of non-three-domain toxins that nevertheless have a Cry name include Cry34/35Ab1 and related beta-sandwich binary (Bin-like) toxins, Cry6Aa, and many beta-sandwich parasporins.[12]

Specific delta-endotoxins that has been used for genetic engineering include Cry3Bb1 found in MON 863 and Cry1Ab found in MON 810, both of which are corn species. Cry3Bb1 is particularly useful because it kills the coleopteran insects such as the corn rootworm, an activity not seen in other Cry proteins.[1] Other common toxins include Cry2Ab and Cry1F in cotton and corn.[13] In addition, Cry1Ac is effective as a vaccine adjuvant in humans.[14]

Some insects populations have started to develop resistance towards delta endotoxin, with five resistant species found as of 2013. Plants with two kinds of delta endotoxins tend to make resistance happen slower, as the insects have to evolve to overcome both toxins at once. Planting non-Bt plants with the resistant plants will reduce the selection pressure for developing the toxin. Finally, two-toxin plants should not be planted with one-toxin plants, as one-toxin plants act as a stepping stone for adaption in this case.[13]


  1. ^ a b c d Galitsky N, Cody V, Wojtczak A, Ghosh D, Luft JR, Pangborn W, English L (August 2001). "Structure of the insecticidal bacterial delta-endotoxin Cry3Bb1 of Bacillus thuringiensis". Acta Crystallographica. Section D, Biological Crystallography. 57 (Pt 8): 1101–9. doi:10.1107/S0907444901008186. PMID 11468393.
  2. ^ a b Grochulski P, Masson L, Borisova S, Pusztai-Carey M, Schwartz JL, Brousseau R, Cygler M (December 1995). "Bacillus thuringiensis CryIA(a) insecticidal toxin: crystal structure and channel formation". Journal of Molecular Biology. 254 (3): 447–64. doi:10.1006/jmbi.1995.0630. PMID 7490762.
  3. ^ "Pesticidal crystal protein (IPR038979)". InterPro. Retrieved 12 April 2019.
  4. ^ Dean DH (1984). "Biochemical genetics of the bacterial insect-control agent Bacillus thuringiensis: basic principles and prospects for genetic engineering" (PDF). Biotechnology & Genetic Engineering Reviews. 2: 341–63. doi:10.1080/02648725.1984.10647804. PMID 6443645.
  5. ^ "Species: Pesticidal crystal protein (IPR038979)". InterPro.
  6. ^ "Bacillus thuringiensis Toxin Nomenclature". Bt toxin specificity database. Retrieved 12 April 2019.
  7. ^ Mizuki E, Park YS, Saitoh H, Yamashita S, Akao T, Higuchi K, Ohba M (July 2000). "Parasporin, a human leukemic cell-recognizing parasporal protein of Bacillus thuringiensis". Clinical and Diagnostic Laboratory Immunology. 7 (4): 625–34. doi:10.1128/CDLI.7.4.625-634.2000. PMC 95925. PMID 10882663.
  8. ^ Ohba M, Mizuki E, Uemori A (January 2009). "Parasporin, a new anticancer protein group from Bacillus thuringiensis". Anticancer Research. 29 (1): 427–33. PMID 19331182.
  9. ^ "List of Parasporins". Committee of Parasporin Classification and Nomenclature. Accessed Jan 4, 2013
  10. ^ Crickmore N. "Other Cry Seqences" (PDF). Retrieved 12 April 2019.
  11. ^ Crickmore N, Zeigler DR, Feitelson J, Schnepf E, Van Rie J, Lereclus D, et al. (September 1998). "Revision of the nomenclature for the Bacillus thuringiensis pesticidal crystal proteins" (PDF). Microbiology and Molecular Biology Reviews. 62 (3): 807–13. PMC 98935. PMID 9729610.
  12. ^ Kelker MS, Berry C, Evans SL, Pai R, McCaskill DG, Wang NX, et al. (2014-11-12). "Structural and biophysical characterization of Bacillus thuringiensis insecticidal proteins Cry34Ab1 and Cry35Ab1". PLOS ONE. 9 (11): e112555. Bibcode:2014PLoSO...9k2555K. doi:10.1371/journal.pone.0112555. PMC 4229197. PMID 25390338.
  13. ^ a b Tabashnik BE, Brévault T, Carrière Y (June 2013). "Insect resistance to Bt crops: lessons from the first billion acres". Nature Biotechnology. 31 (6): 510–21. doi:10.1038/nbt.2597. PMID 23752438.
  14. ^ Rodriguez-Monroy MA, Moreno-Fierros L (March 2010). "Striking activation of NALT and nasal passages lymphocytes induced by intranasal immunization with Cry1Ac protoxin". Scandinavian Journal of Immunology. 71 (3): 159–68. doi:10.1111/j.1365-3083.2009.02358.x. PMID 20415781.

Further reading

External links

This article incorporates text from the public domain Pfam and InterPro: IPR015790

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

delta endotoxin Provide feedback

This family contains insecticidal toxins produced by Bacillus species of bacteria. During spore formation the bacteria produce crystals of this protein. When an insect ingests these proteins they are activated by proteolytic cleavage. The N terminus is cleaved in all of the proteins and a C terminal extension is cleaved in some members. Once activated the endotoxin binds to the gut epithelium and causes cell lysis leading to death. This activated region of the delta endotoxin is composed of three structural domains. The N-terminal helical domain is involved in membrane insertion and pore formation. The second and third domains are involved in receptor binding.

Literature references

  1. Li J, Carroll J, Ellar DJ; , Nature 1991;353:815-821.: Crystal structure of insecticidal delta-endotoxin from Bacillus thuringiensis at 2.5 angstroms resolution. PUBMED:1658659 EPMC:1658659

  2. Schnepf E, Crickmore N, Van Rie J, Lereclus D, Baum J, Feitelson J, Zeigler DR, Dean DH; , Microbiol Mol Biol Rev 1998;62:775-806.: Bacillus thuringiensis and its pesticidal crystal proteins. PUBMED:9729609 EPMC:9729609

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005638

The crystal proteins of Bacillus thuringiensis have been extensively studied because of their pesticidal properties and their high natural levels of production [ PUBMED:9729610 ]. When an insect ingests these proteins, they are activated by proteolytic cleavage. The N terminus is cleaved in all of the proteins and a C-terminal extension is cleaved in some members. Once activated, the endotoxin binds to the gut epithelium and causes cell lysis by the formation of cation-selective channels, which leads to death. The activated region of the toxin is composed of three distinct structural domains: an N-terminal helical bundle domain ( INTERPRO ) involved in membrane insertion and pore formation; a beta-sheet central domain involved in receptor binding; and a C-terminal beta-sandwich domain ( INTERPRO ) that interacts with the N-terminal domain to form a channel [ PUBMED:7490762 , PUBMED:11468393 ].

This entry represents the conserved C-terminal domain.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

Loading domain graphics...

Pfam Clan

This family is a member of clan GBD (CL0202), which has the following description:

This large superfamily contains beta sandwich domains with a jelly roll topology. Many of these families are involved in carbohydrate recognition. Despite sharing little sequence similarity they do share a weak sequence motif, with a conserved bulge in the C-terminal beta sheet. The probable role of this bulge is in bending of the beta sheet that contains the bulge. This enables the curvature of the sheet forming the sugar binding site [1].

The clan contains the following 70 members:

7TMR-DISMED2 Agarase_CBM Allantoicase ANAPC10 Arabino_trans_C Bac_rhamnosid_N BcsB BetaGal_dom4_5 BPA_C Calpain_III CBM-like CBM27 CBM32 CBM46 CBM60 CBM65_1 CBM_11 CBM_15 CBM_17_28 CBM_26 CBM_35 CBM_4_9 CBM_6 CE2_N CIA30 Clenterotox Cry1Ac_D5 DUF4465 DUF4627 DUF5000 DUF5010_C DUF5077 DUF5625 DUF642 Endotoxin_C Ephrin_lbd Exop_C F5_F8_type_C FBA FlhE GH101_N GH115_C Glft2_N Glyco_hydro_2_N GxDLY HA70_C Laminin_B Laminin_N Lectin_like Lipl32 Lyase_N Malectin Malectin_like Muskelin_N NPCBM P_proprotein PA-IL PAW PCMD PepX_C PINIT PITH PPC PulA_N1 Sad1_UNC SGBP_B_XBD TcA_TcB_BD Thioredoxin_10 XRCC1_N YpM


We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

Representative proteomes UniProt
Jalview View  View  View  View  View  View  View 
HTML View  View           
PP/heatmap 1 View           

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

Representative proteomes UniProt

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

Representative proteomes UniProt
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...


This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Arne Eloffson
Previous IDs: endotoxin_C;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , de Maagd R
Number in seed: 80
Number in full: 26
Average length of the domain: 131.50 aa
Average identity of full alignment: 14 %
Average coverage of the sequence by the domain: 12.72 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.0 21.0
Trusted cut-off 21.0 21.0
Noise cut-off 20.9 20.9
Model length: 143
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

Sunburst controls


Weight segments by...

Change the size of the sunburst


Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Loading sunburst data...

Tree controls


The tree shows the occurrence of this domain across different species. More...


Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.


For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Endotoxin_C domain has been found. There are 32 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

Loading structure mapping...

AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
Q54HS7 View 3D Structure Click here