IntAct European Bioinformatics Institute IntAct intact http://www.ebi.ac.uk/ http://www.ebi.ac.uk/intact/query/${ac} EBI-[0-9]+|IA:[0-9]+ INTerAction database (IntAct) provides an open source database and toolkit for the storage, presentation and analysis of molecular interactions. http://www.ebi.ac.uk/intact European Bioinformatics Institute; Wellcome Trust Genome Campus; Hinxton, Cambridge; CB10 1SD; United Kingdom http://www.ebi.ac.uk/intact/ http://www.ebi.ac.uk/ qi-2010-2 Crystal structure of the Caenorhabditis elegans apoptosome reveals an octameric assembly of CED-4. in vitro In vitro molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column predetermined predetermined participant predetermined Qi S., Pang Y., Hu Q., Liu Q., Li H., Zhou Y., He T., Liang Q., Liu Y., Yuan X., Luo G., Li H., Wang J., Yan N., Shi Y. Apoptosis - Interactions involving proteins with a function related to apoptosis nyan@tsinghua.edu.cn, shi-lab@tsinghua.edu.cn Cell (0092-8674) 2010 Only protein-protein interactions imex curation qi-2010-1 Crystal structure of the Caenorhabditis elegans apoptosome reveals an octameric assembly of CED-4. in vitro In vitro x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Qi S., Pang Y., Hu Q., Liu Q., Li H., Zhou Y., He T., Liang Q., Liu Y., Yuan X., Luo G., Li H., Wang J., Yan N., Shi Y. Apoptosis - Interactions involving proteins with a function related to apoptosis nyan@tsinghua.edu.cn, shi-lab@tsinghua.edu.cn Cell (0092-8674) 2010 Only protein-protein interactions imex curation qi-2010-3 Crystal structure of the Caenorhabditis elegans apoptosome reveals an octameric assembly of CED-4. in vitro In vitro cosedimentation cosedimentation predetermined predetermined participant predetermined Qi S., Pang Y., Hu Q., Liu Q., Li H., Zhou Y., He T., Liang Q., Liu Y., Yuan X., Luo G., Li H., Wang J., Yan N., Shi Y. Apoptosis - Interactions involving proteins with a function related to apoptosis Sedimentation equilibrium analysis nyan@tsinghua.edu.cn, shi-lab@tsinghua.edu.cn Cell (0092-8674) 2010 Only protein-protein interactions imex curation qi-2010-4 Crystal structure of the Caenorhabditis elegans apoptosome reveals an octameric assembly of CED-4. in vitro In vitro biochemical biochemical predetermined predetermined participant predetermined Qi S., Pang Y., Hu Q., Liu Q., Li H., Zhou Y., He T., Liang Q., Liu Y., Yuan X., Luo G., Li H., Wang J., Yan N., Shi Y. Apoptosis - Interactions involving proteins with a function related to apoptosis Capillary electrophoresis nyan@tsinghua.edu.cn, shi-lab@tsinghua.edu.cn Cell (0092-8674) 2010 Only protein-protein interactions imex curation qi-2010-5 Crystal structure of the Caenorhabditis elegans apoptosome reveals an octameric assembly of CED-4. in vitro In vitro itc isothermal titration calorimetry ITC ITC itc predetermined predetermined participant predetermined Qi S., Pang Y., Hu Q., Liu Q., Li H., Zhou Y., He T., Liang Q., Liu Y., Yuan X., Luo G., Li H., Wang J., Yan N., Shi Y. Apoptosis - Interactions involving proteins with a function related to apoptosis Sedimentation equilibrium analysis nyan@tsinghua.edu.cn, shi-lab@tsinghua.edu.cn Cell (0092-8674) 2010 Only protein-protein interactions imex curation qi-2010-6 Crystal structure of the Caenorhabditis elegans apoptosome reveals an octameric assembly of CED-4. in vitro In vitro comigration in sds comigration in sds page comigration in sds weight by comassie molecular weight estimation by coomasie staining weight by comassie Qi S., Pang Y., Hu Q., Liu Q., Li H., Zhou Y., He T., Liang Q., Liu Y., Yuan X., Luo G., Li H., Wang J., Yan N., Shi Y. Apoptosis - Interactions involving proteins with a function related to apoptosis Crystals were harvested, washed, and applied to SDS-PAGE followed by coomassie blue staining nyan@tsinghua.edu.cn, shi-lab@tsinghua.edu.cn Cell (0092-8674) 2010 Only protein-protein interactions imex curation qi-2010-7 Crystal structure of the Caenorhabditis elegans apoptosome reveals an octameric assembly of CED-4. in vitro In vitro molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column anti tag western anti tag western blot anti tag western Qi S., Pang Y., Hu Q., Liu Q., Li H., Zhou Y., He T., Liang Q., Liu Y., Yuan X., Luo G., Li H., Wang J., Yan N., Shi Y. Apoptosis - Interactions involving proteins with a function related to apoptosis nyan@tsinghua.edu.cn, shi-lab@tsinghua.edu.cn Cell (0092-8674) 2010 Only protein-protein interactions imex curation q9xyf4-pro_0000004672 Dronc NEDD2-like caspase Nc CG8091 protein protein drome Drosophila melanogaster (Fruit fly) Fruit fly DEYD 321 324 q9xyf4-pro_0000004671 Caspase Nc subunit 1 Dronc NEDD2-like caspase Nc CG8091 protein protein drome Drosophila melanogaster (Fruit fly) Fruit fly DTPSPEASEGPCVSKLRNEPLGALTPYVGVVDGPEVKKSKKIHGGDSAILGTYKMQSRFNRGVLLMVNIMDYPDQNRRRIGAEKDSKSLIHLFQELNFTIFPYGNVNQDQFFKLLTMVTSSSYVQNTECFVMVLMTHGNSVEGKEKVEFCDGSVVDMQKIKDHFQTAKCPYLVNKPKVLMFPFCRG 135 320 ced3_caeel Cell death protein 3 ced-3 Caspase ced-3 C48D1.2 protein protein caeel Caenorhabditis elegans MMRQDRRSLLERNIMMFSSHLKVDEILEVLIAKQVLNSDNGDMINSCGTVREKRREIVKAVQRRGDVAFDAFYDALRSTGHEGLAEVLEPLARSVDSNAVEFECPMSPASHRRSRALSPAGYTSPTRVHRDSVSSVSSFTSYQDIYSRARSRSRSRALHSSDRHNYSSPPVNAFPSQPSSANSSFTGCSSLGYSSSRNRSFSKASGPTQYIFHEEDMNFVDAPTISRVFDEKTMYRNFSSPRGMCLIINNEHFEQMPTRNGTKADKDNLTNLFRCMGYTVICKDNLTGRGMLLTIRDFAKHESHGDSAILVILSHGEENVIIGVDDIPISTHEIYDLLNAANAPRLANKPKIVFVQACRGERRDNGFPVLDSVDGVPAFLRRGWDNRDGPLFNFLGCVRPQVQQVWRKKPSQADILIAYATTAQYVSWRNSARGSWFIQAVCEVFSTHAKDMDVVELLTEVNKKVACGFQTSQGSNILKQMPEMTSRLLKKFYFWPEARNSAV p30429-2 Cell death protein 4 Short C35D10.9 ced-4 protein protein caeel Caenorhabditis elegans MLCEIECRALSTAHTRLIHDFEPRDALTYLEGKNIFTEDHSELISKMSTRLERIANFLRIYRRQASELGPLIDFFNYNNQSHLADFLEDYIDFAINEPDLLRPVVIAPQFSRQMLDRKLLLGNVPKQMTCYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWAQELRLRCLVTTRDVEISNAASQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMFFKSCEPKTFEKMAQLNNKLESRGLVGVECITPYSYKSLAMALQRCVEVLSDEDRSALAFAVVMPPGVDIPVKLWSCVIPVDICSNEEEQLDDEVADRLKRLSKRGALLSGKRMPVLTFKIDHIIHMFLKHVVDAQTIANGISILEQRLLEIGNNNVSVPERHIPSHFQKFRRSSASEMYPKTTEETVIRPEDFPKFMQLHQKFYDSLKNFACC Major transcript. ac-devd-cho Ac-Asp-Glu-Val-Asp-CHO small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) nc-1 Dimerisation of Nc (Dronc) 909567 n/a 909574 unspecified role unspecified role neutral component neutral component Stoichiometry: 2.0 n/a 909575 unspecified role unspecified role neutral component neutral component Stoichiometry: 2.0 direct interaction direct interaction false false false Supp. Fig. 5C Expression system of Nc not given. The two chains of mature Nc form a homodimer. ced3 Interaction between internal chains of ced3 909567 n/a 909576 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 n/a 909576 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false P42573:p.Cys358Ala mutation mutation certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 909586 909584 direct interaction direct interaction false false false Supp. Fig. 5C ced3-ced4 Interaction between internal chains of ced-3 and ced-4 909567 n/a 909577 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) n/a 909576 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) n/a 909576 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false P42573:p.Cys358Ala mutation mutation certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Supp. Fig. 5D ced4 Crystallisation of ced4 909568 n/a 909577 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) Stoichiometry: 8.0 direct interaction direct interaction false false false 3.55A Rworking 27.5%, Rfree 31.1% Supp. Table 1 The assembly contains eight molecules of CED-4, arranged as a tetramer of an asymmetric dimer. Each CED-4 contains an ATP molecule and a Mg2+ ion, both buried in the assembly and inaccessible to water molecules. ced3-2 Interaction between internal chains of ced3 909569 n/a 909576 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false P42573:p.Cys358Ala mutation mutation certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 n/a 909576 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 direct interaction direct interaction false false false Supp. Fig. 5D ced3-ced4-2 Interaction between internal chains of ced-3 and ced-4 909570 n/a 909576 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false P42573:p.Cys358Ala mutation mutation certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 n/a 909576 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 n/a 909577 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) Stoichiometry: 4.0 physical association physical association false false false Supp. Fig. 5E ced3-ced4-3 Interaction between internal chains of ced-3 and ced-4 909571 n/a 909576 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false P42573:p.Cys358Ala mutation mutation certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 n/a 909576 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 n/a 909577 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) Stoichiometry: 4.0 physical association physical association false false false Supp. Fig. 5F ced3-ced4-4 Interaction between internal chains of ced-3 and ced-4 909572 n/a 909576 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) n/a 909577 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) n/a 909576 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false P42573:p.Cys358Ala mutation mutation certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) physical association physical association false false false Supp. Fig. 6A Although ced-3 was not visible in a ced-3:ced-4 crystal, subsequent analysis of the crystals showed both proteins to be present. ced3-devd Dimerisation of ced-3 induced by Ac-DEVD-CHO 909573 n/a 909576 unspecified role unspecified role neutral component neutral component c-terminal his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 n/a 909578 unspecified role unspecified role neutral component neutral component direct interaction direct interaction false false false Supp. Fig. 6A