List of known pesticidal protein structures


Links to structures in the PDB are given where:

  • The structure corresponds to a BPPRC sequence entry. Note, where two BPPRC entries represent identical amino acid sequences (e.g. App6Aa1 and App6Aa2), the structure PDB entry will be associated with both (regardless of which quaternary rank was described in any associated publication).

  • The structure corresponds to a mutant of a BPPRC sequence entry where a small number of mutations have been included to aid crystallisation and/or to elucidate function.

  • The structure represents either a full length or an activated form of the toxin (the structure may not represent the full-length sequence in the BPPRC database entry).

NOTE: Users are advised to check the correspondence between the PDB entry sequence and the BPPRC sequence (e.g. using both the BPPRC best match finder needle and blast alignments) and should take care in the interpretation of the data.

Name Old Name Accession PDBID Modified Comment Year DOI
App1Ba1 XaxA CBJ91797.1 6GY6 No In complex with App2Ba1 (XaxB)
2018 10.7554/eLife.38017
App1Ba1 XaxA CBJ91797.1 6GY8 No
2018 10.7554/eLife.38017
App1Ca1 YaxA 6EK7_A 6EL1 No
2018 10.1038/s41467-018-04139-2
App1Ca1 YaxA 6EK7_A 6EK7 No
2018 10.1038/s41467-018-04139-2
App2Aa1 PaxB WP_046395991 6EK4 No
2018 10.1038/s41467-018-04139-2
App2Ba1 XaxB CBJ91798.1 6GY7 No
2018 10.7554/eLife.38017
App2Ba1 XaxB CBJ91798.1 6GY6 No In Complex with App1Ba1 (XaxA)
2018 10.7554/eLife.38017
App3Aa1 YaxB WP_011816274 6EL1 No
2018 10.1038/s41467-018-04139-2
App6Aa1, App6Aa2 Cry6Aa1, Cry6Aa2 AAA22357, AAM46849 5KUC Trypsin activated. Sequence in the structure matches App6Aa1, App6Aa2
2016 10.1186/s12915-016-0295-9
App6Aa1, App6Aa2 Cry6Aa1, Cry6Aa2 AAA22357, AAM46849 5KUD Sequence in the structure matches App6Aa1, App6Aa2
2016 10.1186/s12915-016-0295-9
App6Aa1, App6Aa2 Cry6Aa1, Cry6Aa2 AAA22357, AAM46849 5GHE Activated, major chain. Sequence in the structure matches App6Aa1, App6Aa2
2016 10.1016/j.bbrc.2016.07.002
Cry Chimera None 6DJ4_A 6DJ4 Yes Chimera of Cry1Ab, 1Ac, 1F: does not associate with a single database entry. Described as Cry1A.105
2018 10.1016/j.yrtph.2018.09.003
Cry chimera None 6OWK_A 6OWK Yes Chimeric protein (named "Cry1B tryptic core variant" in publication). This is a disabled insecticidal protein mutant [A160N,N167D] of an artificial chimera Cry1B.867: a fusion of domains 1+2 of Cry1Be5 with domain 3 of Cry1Ka2 (residues 1-502 and 473-621 respectively with reference to the parental genes).
2019 10.1128/AEM.00579-19
Cry variant None 6WPC_A 6WPC Yes Non-natural Cry variant named Cry1A.2, tryptic core
2021 10.1371/journal.pone.0249150
Cry11Aa1, Cry11Aa3 CryIVD, Cry11Aa3 AAA22352, CAD30081 7QX6 Yes E583Q mutant, pH7 natural crystals. Sequence also matches Cry11Aa3 (CAD30081)
2022 10.1038/s41467-022-31746-x
Cry11Aa1, Cry11Aa3 CryIVD, Cry11Aa3 AAA22352, CAD30081 7QX5 Yes Y449F mutant pH7 natural crystals. Sequence also matches Cry11Aa3 (CAD30081)
2022 10.1038/s41467-022-31746-x
Cry11Aa1, Cry11Aa3 CryIVD, Cry11Aa3 AAA22352, CAD30081 7QX7 Yes F17Y mutant, pH7 natural crystals. Sequence also matches Cry11Aa3 (CAD30081)
2022 10.1038/s41467-022-31746-x
Cry11Aa1, Cry11Aa3 CryIVD, Cry11Aa3 AAA22352, CAD30081 7QX4 No pH7 natural crystals. Sequence also matches Cry11Aa3 (CAD30081)
2022 10.1038/s41467-022-31746-x
Cry11Ba1 Jeg80 CAA60504 7R1E No pH10.4 natural crystals
2022 10.1038/s41467-022-31746-x
Cry11Ba1 Jeg80 CAA60504 7QYD No pH6.5 natural crystals
2022 10.1038/s41467-022-31746-x
Cry1Aa None None 8W7N No Full length Cry1Aa protoxin by serial synchrotron rotation crystallography NOTE sequence in pdb file does not match sequence from supplementary figure 2 in the paper so the exact sequence is unclear.
2023 10.1016/j.bbrc.2023.149144
Cry1Aa6 CryIA(a) AAA86265 1CIY No
1997 10.1006/jmbi.1995.0630
Cry1Ac4 Cry1Ac4 AAA73077 4W8J Yes Full-length (133 kDa) protoxin: 14x Cys-Ser and F462V mutant of Cry1Ac4
2014 10.1002/pro.2536
Cry1Ac7, Cry1Ac8 Cry1Ac7, Cry1Ac8 AAB46989, AAC44841 4ARY No Bound to GalNAc
2013 10.1107/s090744490101040x
Cry1Ac7, Cry1Ac8 Cry1Ac7, Cry1Ac8 AAB46989, AAC44841 4ARX No
2013 10.1107/s090744490101040x
Cry1Ca18 Cry1Ca18 PQ691233 9H99 No pH7 Full length protoxin structure of natural crystals by XFEL
2026 10.1016/j.str.2026.01.014
Cry1Ca18 Cry1Ca18 PQ691233 9QXQ No pH9 Full length protoxin structure of natural crystals by XFEL
2026 10.1016/j.str.2026.01.014
Cry1Da1 Cry1Da1 CAA38099 6OVB Yes V108C, E128C, S282V, Y316S, I368P mutant of Cry1Da1
2019 10.1128/AEM.00579-19
Cry2Aa Cry2Aa multiple, see comments 1I5P No Sequence in the structure matches Cry2Aa1, Cry2Aa2, Cry2Aa9, Cry2Aa10, Cry2Aa19, Cry2Aa20, Cry2Aa21 (AAA22335, AF433645, AYN72228, AAA83516, AYN72229, AYN72230, AAO13750)
2001 10.1016/s0969-2126(01)00601-3
Cry3Aa Cry3Aa multiple, see comments 4QX0,
4QX1,
4QX2,
4QX3,
No XFEL structure from natural crystals. Sequence in structure matches Cry3Aa2, Cry3Aa3, Cry3Aa5, Cry3Aa6, Cry3Aa12 (AAA22541, CAA68482, AAA50255, AAC43266, ABY49136)
2014 10.1073/pnas.1413456111
Cry3Aa Cry3Aa multiple, see comments 6LFP Co-crystalised in vivo with an entrapped recombinant lipase. Sequence in structure matches Cry3Aa2, Cry3Aa3, Cry3Aa5, Cry3Aa6, Cry3Aa12 (AAA22541, CAA68482, AAA50255, AAC43266, ABY49136)
2020 10.1021/jacs.9b13462
Cry3Aa Cry3Aa multiple, see comments 1DLC No Sequence in structure matches Cry3Aa2, Cry3Aa3, Cry3Aa5, Cry3Aa6, Cry3Aa12 (AAA22541, CAA68482, AAA50255, AAC43266, ABY49136)
1994 10.1038/353815a0
Cry3Aa Cry3Aa multiple, see comments 7EAR Yes Positive charged mutant with multiple mutations (N391K, N395K, E423K, Q430K, D432K, E433K, T436K, T461K, D462K, E463K, E466K). Sequence in structure matches Cry3Aa2, Cry3Aa3, Cry3Aa5, Cry3Aa6, Cry3Aa12 (AAA22541, CAA68482, AAA50255, AAC43266, ABY49136) with above mutations
2021 10.1016/j.biomaterials.2021.120759
Cry3Bb1 Cry3Bb1 AAA22334 1JI6 No
2001 10.1107/s0907444901008186
Cry4Aa1 Cry4Aa1 CAA68485 2C9K No
2006 10.1128/JB.188.9.3391-3401.2006
Cry4Ba1 Cry4Ba1 CAA30312 4MOA Yes R203Q mutant
2014 10.1074/jbc.M114.627554
Cry4Ba1 Cry4Ba1 CAA30312 1W99 No
2005 10.1016/j.jmb.2005.02.013
Cry5Ba1 Cry5Ba1 AAA68598 4D8M No
2012 10.1021/bi301386q
Cry5Ba2 None ABW88931 8HHE No Activated protein
2022 10.3390/toxins14120823
Cry7Ca1 Cry7Ca1 ABR67863 5ZI1 Yes
2018 10.1002/pro.3561
Cry8Ba2 Cry8Ba2 MZ355710 9H9B No Compressed form, full length protoxin structure of natural crystals by XFEL
2026 10.1016/j.str.2026.01.014
Cry8Ba2 Cry8Ba2 MZ355710 9H9A No Extended form, full length protoxin structure of natural crystals by XFEL
2026 10.1016/j.str.2026.01.014
Cry8Ea1 Cry8Ea1 AY329081 3EB7 No
2008 10.1016/j.jsb.2009.07.004
Cyt1Aa1, Cyt1Aa2, Cyt1Aa5 Cyt1Aa1, Cyt1Aa2, Cyt1Aa5 CAA26943, CAA27868, CAD30079 3RON No Sequence in the structure matches Cyt1Aa1, Cyt1Aa2, Cyt1Aa5
2011 10.1016/j.jmb.2011.09.021
Cyt1Aa1, Cyt1Aa2, Cyt1Aa5 Cyt1Aa1, Cyt1Aa2, Cyt1Aa5 CAA26943, CAA27868, CAD30079 6T1C Yes Cys7Ser mutant. Sequence in the structure matches Cyt1Aa1, Cyt1Aa2, Cyt1Aa5 with mutation above
2020 10.1038/s41467-020-14894-w
Cyt1Aa1, Cyt1Aa2, Cyt1Aa5 Cyt1Aa1, Cyt1Aa2, Cyt1Aa5 CAA26943, CAA27868, CAD30079 6T1A No pH10. Sequence in the structure matches Cyt1Aa1, Cyt1Aa2, Cyt1Aa5
2020 10.1038/s41467-020-14894-w
Cyt1Aa1, Cyt1Aa2, Cyt1Aa5 Cyt1Aa1, Cyt1Aa2, Cyt1Aa5 CAA26943, CAA27868, CAD30079 6T19 No Sequence in the structure matches Cyt1Aa1, Cyt1Aa2, Cyt1Aa5
2020 10.1038/s41467-020-14894-w
Cyt1Aa1, Cyt1Aa2, Cyt1Aa5 Cyt1Aa1, Cyt1Aa2, Cyt1Aa5 CAA26943, CAA27868, CAD30079 6T14 No pH7. Sequence in the structure matches Cyt1Aa1, Cyt1Aa2, Cyt1Aa5
2020 10.1038/s41467-020-14894-w
Cyt2Aa1, Cyt2Aa2, Cyt2Aa4 Cyt2Aa1, Cyt2Aa2, Cyt2Aa4 multiple, see comments 1CBY No Sequence in structure matches Cyt2Aa1, Cyt2Aa2, Cyt2Aa4 (CAA78519, CAA78519, AAM09651)
1996 10.1006/jmbi.1996.0152
Cyt2Ba Cyt2Ba multiple, see comments 2RCI No Sequence in structure matches Cyt2Ba1, Cyt2Ba7, Cyt2Ba9, Cyt2Ba10, Cyt2Ba12, Cyt2Ba13, Cyt2Ba14, Cyt2Ba15 (ACX54359, AAF37222, CAD30094, ACX54358, ACX54360, ACI42304, ACI42305, AEL29854)
2008 10.1016/j.jmb.2011.09.021
Cyt5Aa1 Cyt5Aa1 WP_013316150 2MLW No
2015 10.1038/srep08791
Gpp34Ab1 Cry34Ab1 AAG41671 4JOX No
2013 10.1371/journal.pone.0112555
Mcf1Aa1 Mcf1 None 8P52 No
2023 10.1038/s41467-023-44069-2
Mcf1Aa1 C1397A d15C – Arf None None 8P50 Yes Complex of Mcf1Aa1 C1397A delta15C with Arf3
None 10.1038/s41467-023-44069-2
Mcf1Aa1 C1397A delta15C None None 8P51 Yes
2023 10.1038/s41467-023-44069-2
Mpf1Aa1 PluMACPF 2QP2_A 2QP2 No
2007 10.1126/science.1144706
Mpf2Ba1 None None 8B6W Mpf2Ba1 pore form (21-mer)
None 10.1038/s41467-023-39891-7
Mpf2Ba1 None None 8B6U Mpf2Ba1 monomeric form
None 10.1038/s41467-023-39891-7
Mpf2Ba1 None None 8B6V Mpf2Ba1 prepore form (22-mer)
None 10.1038/s41467-023-39891-7
Mpf3Aa1 GNIP1Aa AML23188 6FBM No
2019 10.1073/pnas.1815547116
Mpp-like None PDB: 2D42_A 2D42 No Structure of an Mpp-like protein from a Bt strain. No activity reported so currently not in the official nomenclature. Sequence: AIINLLRELEIYGMQYANSHQYTYGSSYSDDTNPIRIAGLDARIPDPIVTDPVNHIVLDRRIITNTTSNSLEGVFSFSNAYTSRTSSQTRDGVTAGTNITGKYFANLFFEQVGLSGRIAFEGAVTNENKYTLDATQDFRDSQTIRVPPFHRATGVYTLEQGAFEKMTVLECVVSGNGIIRYYRTLPDNSYTEIVQRVNIIDVLQANGTPGFTISKEQNRAYFTGEGTISGQIGLQTFIDVVIEPLPGHA
2006 10.1002/prot.20843
Mpp23Aa1 Cry23Aa1 AAF76375 4RHZ No Co-crystalised with Xpp37Aa1
2014 Unpublished
Mpp46Aa1 Cry46Aa1 BAC79010 2ZTB No
2009 10.1016/j.jmb.2008.12.002
Mpp51Aa1 Cry51Aa1 ABI14444 4PKM No
2015 10.1016/j.bbrc.2015.04.068
Mpp51Aa2 Cry51Aa2 BAD22577 5HD2 Yes L11M mutant
2016 10.1038/ncomms12213
Mpp5Ac1 Sip1Ab AKA64626 8HX3 No Described as Sip1Ab in publication
2023 10.1002/ps.7622
Mpp75Aa1 Cry75Aa1 ASY04853 7ML9 No
2021 10.1371/journal.pone.0258052
Mtx1Aa1 Mtx1 AAA22601 2VSA No
2008 10.1016/j.jmb.2008.05.067
Mtx1Aa1 Mtx1 AAA22601 2CB4 Yes Catalytic domain E195Q mutant
2006 10.1016/j.jmb.2006.01.025
Mtx1Aa1 Mtx1 AAA22601 2CB6 Yes Catalytic domain E195Q mutant
2006 10.1016/j.jmb.2006.01.025
Mtx1Aa1 Mtx1 AAA22601 2VSE No
2008 10.1016/j.jmb.2008.05.067
Pra1 from P. akhurstii K1 PirA None 7FCN
2023 10.1016/j.ibmb.2023.104014
Pra2Aa1 PirA 3X0T_A 3X0T No
2015 10.1073/pnas.1503129112
Prb1 from P. akhurstii K1 PirB None 7FDP
2023 10.1016/j.ibmb.2023.104014
Prb2Aa1 PirB 3X0U_A 3X0U No
2015 10.1073/pnas.1503129112
Tpp1Aa2 BinA2 WP_012291791 5G37 No Natural co-crystal with Tpp2Aa2, pH5
2016 10.1038/nature19825
Tpp1Aa2 BinA2 WP_012291791 5FOZ No Natural co-crystal with Tpp2Aa2, pH10
2016 10.1038/nature19825
Tpp1Aa2 BinA2 WP_012291791 5FOY No Natural co-crystal with Tpp2Aa2, pH7
2016 10.1038/nature19825
Tpp2Aa2 BinB2 WP_012291792 5G37 No Natural co-crystal with Tpp1Aa2, pH5
2016 10.1038/nature19825
Tpp2Aa2 BinB2 WP_012291792 5FOZ No Natural co-crystal with Tpp1Aa2, pH10
2016 10.1038/nature19825
Tpp2Aa2 BinB2 WP_012291792 5FOY No Natural co-crystal with Tpp1Aa2, pH7
2016 10.1038/nature19825
Tpp2Aa3 BinB3 WP_036216621 3WA1 No
2014 10.1002/prot.24636
Tpp35Ab1 Cry35Ab1 AAG41672 4JP0 No
2014 10.1371/journal.pone.0112555
Tpp49Aa1 Cry49Aa1 CAH56541 8BEX No XFEL structure of natural crystals, pH3
2023 10.1073/pnas.2203241120
Tpp49Aa1 Cry49Aa1 CAH56541 8BEY No XFEL structure of natural crystals, pH7
2023 10.1073/pnas.2203241120
Tpp49Aa1 Cry49Aa1 CAH56541 8BEZ No XFEL structure of natural crystals, pH11
2023 10.1073/pnas.2203241120
Tpp78Aa1 Cry78Aa1 ATY50144 7Y78 No Residues 13-359
2022 10.1038/s42003-022-03754-6
Tpp78Aa1 Cry78Aa1 ATY50144 7Y79 Yes Residues 155-359 (lacking N-terminal domain)
2022 10.1038/s42003-022-03754-6
Tpp80Aa1 Cry80Aa1 QCT24227 8BAD No
2022 10.3390/toxins14120863
Txp1Aa1, Txp1Aa2 Txp40A24, Txp40b ABB29480, Q306L3 7xbj No Sequence in structure matches Txp1Aa1, Txp1Aa2
2023
Vip3Aa None multiple, see comments 6VLS No Trypsin activated fragment: truncated, non-active. Sequence in structure matches Vip3Aa7, Vip3Aa10, Vip3Aa11, Vip3Aa12, Vip3Aa15, Vip3Aa21, Vip3Aa33, Vip3Aa34, Vip3Aa36, Vip3Aa37, Vip3Aa43, Vip3Aa44, Vip3Aa55, Vip3Aa64 (AAK95326, AAN60738, AAR36859, AAM22456, AAP51131, ABD84410, ACY38212, ACY38213, ADF43020, ADJ18213, ADY76643, ADW66453, AIA96502, ASK51084)
2020 10.3390/toxins12070438
Vip3Aa90 None AAW65132 6TFK Described in publication and PDB as Vip3Aa16 but protein used was Vip3Aa90. Note in structure residue 121 is shown as Leu but it is, in fact, Ile. Trypsin activated
2020 10.1038/s41467-020-17758-5
Vip3Aa90 None AAW65132 6TFJ Described in publication and PDB as Vip3Aa16 but protein used was Vip3Aa90. Note in structure residue 121 is shown as Leu but it is, in fact, Ile.
2020 10.1038/s41467-020-17758-5
Vip3Bc1 Vip3Bc1 ATD53733 6YRF No
2020 10.1038/s41467-021-23146-4
Vip3Bc1 Vip3Bc1 ATD53733 7NTX No Trypsin activated
2020 10.1038/s41467-021-23146-4
Vip3Bc1 Vip3Bc1 ATD53733 6YRG No Trypsin activated (residues at tip of pore region constructed by homology modelling)
2020 10.1038/s41467-021-23146-4
Vip3Bc1 Vip3Bc1 ATD53733 6V1V Yes Multiple mutant form
2019 10.1002/pro.3803
Vip3Cb1 None LQ835767 9EFI No Protoxin structure
2025
Vip3Cb1 None LQ835767 9EFG No Vip3Cb1 activated toxin
2025
Vpa2Aa3 Vip2Aa3 AEH05931 1QS2 No With bound NAD
1999 10.1038/13300
Vpa2Aa3 Vip2Aa3 AEH05931 1QS1 No
1999 10.1038/13300
Vpb1Ac1 Vip1Ac1 AEH05932 6SMS No
2021 Unpublished
Vpb4Da2 Vpb4Da2 AZJ95709 7MJR Yes Q530Y-E531Y-K532Y mutant. Sequences matches Vpb4Da1 (AJT49287) and Vpb4Da2 with mutant above
2021 10.1371/journal.pone.0260532
Xpp37Aa1 Cry37Aa1 AAF76376 4RHZ No Co-crystalised with Mpp23Aa1
2015 Unpublished