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/ Functional specificity of a hox protein mediated by the recognition of minor groove structure. Functional specificity of a hox protein mediated by the recognition of minor groove structure. Cell (0092-8674) 2007 imex curation Joshi R., Passner JM., Rohs R., Jain R., Sosinsky A., Crickmore MA., Jacob V., Aggarwal AK., Honig B., Mann RS. Aneel.Aggarwal@mssm.edu 01-April-2008: Contacted by JYOTI. Only protein-protein interactions in vitro In vitro x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Joshi R., Passner JM., Rohs R., Jain R., Sosinsky A., Crickmore MA., Jacob V., Aggarwal AK., Honig B., Mann RS. Aneel.Aggarwal@mssm.edu Accepted 2008-MAR-18 by CDEROW. 01-April-2008: Contacted by JYOTI. Cell (0092-8674) 2007 Only protein-protein interactions imex curation Functional specificity of a hox protein mediated by the recognition of minor groove structure. Functional specificity of a hox protein mediated by the recognition of minor groove structure. Cell (0092-8674) 2007 imex curation Joshi R., Passner JM., Rohs R., Jain R., Sosinsky A., Crickmore MA., Jacob V., Aggarwal AK., Honig B., Mann RS. Aneel.Aggarwal@mssm.edu 01-April-2008: Contacted by JYOTI. Only protein-protein interactions in vitro In vitro emsa electrophoretic mobility shift assay Gel retardation assay band shift band shift Gel retardation assay emsa weight autoradiogra molecular weight estimation by autoradiography weight autoradiogra Joshi R., Passner JM., Rohs R., Jain R., Sosinsky A., Crickmore MA., Jacob V., Aggarwal AK., Honig B., Mann RS. Aneel.Aggarwal@mssm.edu Accepted 2008-MAR-18 by CDEROW. 01-April-2008: Contacted by JYOTI. Cell (0092-8674) 2007 Only protein-protein interactions imex curation actctatgatttatgggctg DNA sequence derived from the drosophila Fkh gene - Hox-Exd binding site dna deoxyribonucleic acid DNA deoxyribonucleic acid dna DNA deoxyribonucleic acid in vitro In vitro ACTCTATGATTTATGGGCTG AF3808EABDD335E8 actctaagattaatcggctg DNA sequence derived from the drosophila Fkh gene - Hox-Exd binding site dna deoxyribonucleic acid DNA deoxyribonucleic acid dna DNA deoxyribonucleic acid drome Drosophila melanogaster (Fruit fly) Fruit fly ACTCTAAGATTAATCGGCTG BF3908EABDC5F4E8 gatctcaatgtcaagattta DNA sequence derived from the drosophila Fkh gene - Hox-Exd binding site dna deoxyribonucleic acid DNA deoxyribonucleic acid dna DNA deoxyribonucleic acid chemical synthesis Chemical synthesis (Chemical synthesis) GATCTCAATGTCAAGATTTATGGCCAGCTGTGGGACGAGG DF0229CE8B0A8F0A tcagcccataaatcatagag DNA sequence derived from the drosophila Fkh gene - Hox-Exd binding site dna deoxyribonucleic acid DNA deoxyribonucleic acid dna DNA deoxyribonucleic acid in vitro In vitro TCAGCCCATAAATCATAGAG 2E13AE95033A037C exd_drome Homeobox protein extradenticle exd CG8933 protein protein drome Drosophila melanogaster (Fruit fly) Fruit fly MEDPNRMLAHTGGMMAPQGYGLSGQDDGQNAGSENEVRKQKDIGEILQQIMSISEQSLDEAQARKHTLNCHRMKPALFSVLCEIKEKTVLSIRNTQEEEPPDPQLMRLDNMLIAEGVAGPEKGGGGAAAASAAAASQGGSLSIDGADNAIEHSDYRAKLAQIRQIYHQELEKYEQACNEFTTHVMNLLREQSRTRPITPKEIERMVQIIHKKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYKKNIGKAQEEANLYAAKKAAGASPYSMAGPPSGTTTPMMSPAPPQDSMGYPMGSGGYDQQQPYDNSMGGYDPNLHQDLSP DIP protein P40427 original sequence version: 142 DIP protein P40427 original sequence version: 120 79E3DC8F1F6B711F scr_drome Homeotic protein Sex combs reduced Scr CG1030 protein protein drome Drosophila melanogaster (Fruit fly) Fruit fly MDPDCFAMSSYQFVNSLASCYPQQMNPQQNHPGAGNSSAGGSGGGAGGSGGVVPSGGTNGGQGSAGAATPGANDYFPAAAAYTPNLYPNTPQAHYANQAAYGGQGNPDMVDYTQLQPQRLLLQQQQQQQQQQHAHAAAAVAAQQQQQLAQQQHPQQQQQQQQANISCKYANDPVTPGGSGGGGVSGSNNNNNSANSNNNNSQSLASPQDLSTRDISPKLSPSSVVESVARSLNKGVLGGSLAAAAAAAGLNNNHSGSGVSGGPGNVNVPMHSPGGGDSDSESDSGNEAGSSQNSGNGKKNPPQIYPWMKRVHLGTSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNIVPYHMGPYGHPYHQFDIHPSQFAHLSA DIP protein P09077 original sequence version: 127 8A3A58A60E0B32BE tcagccgattaatcttagag DNA sequence derived from the drosophila Fkh gene - Hox-Exd binding site dna deoxyribonucleic acid DNA deoxyribonucleic acid dna DNA deoxyribonucleic acid drome Drosophila melanogaster (Fruit fly) Fruit fly TCAGCCGATTAATCTTAGAG 2E13BE940323677C gatctcaatgtcaagattaa DNA sequence derived from the drosophila Fkh gene - Hox-Exd binding site dna deoxyribonucleic acid DNA deoxyribonucleic acid dna DNA deoxyribonucleic acid chemical synthesis Chemical synthesis (Chemical synthesis) GATCTCAATGTCAAGATTAATCGCCAGCTGTGGGACGAGG DF022EA34B118EBA hth_drome Homeobox protein homothorax hth dtl Homeobox protein dorsotonals CG17117 protein protein drome Drosophila melanogaster (Fruit fly) Fruit fly MAQPRYDDGLHGYGMDSGAAAAAMYDPHAGHRPPGLQGLPSHHSPHMTHAAAAAATVGMHGYHSGAGGHGTPSHVSPVGNHLMGAIPEVHKRDKDAIYEHPLFPLLALIFEKCELATCTPREPGVQGGDVCSSESFNEDIAMFSKQIRSQKPYYTADPEVDSLMVQAIQVLRFHLLELEKVHELCDNFCHRYISCLKGKMPIDLVIDERDTTKPPELGSANGEGRSNADSTSHTDGASTPDVRPPSSSLSYGGAMNDDARSPGAGSTPGPLSQQPPALDTSDPDGKFLSSLNPSELTYDGRWCRREWSSPADARNADASRRLYSSVFLGSPDNFGTSASGDASNASIGSGEGTGEEDDDASGKKNQKKRGIFPKVATNILRAWLFQHLTHPYPSEDQKKQLAQDTGLTILQVNNWFINARRRIVQPMIDQSNRAVYTPHPGPSGYGHDAMGYMMDSQAHMMHRPPGDPGFHQGYPHYPPAEYYGQHL 7EA4D7D1EFB16F8A scr-exd-1 1 7 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 ecoli Escherichia coli (strain K12) 4 unspecified role unspecified role neutral component neutral component 9 unspecified role unspecified role neutral component neutral component 8 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 ecoli Escherichia coli (strain K12) 14 18 direct interaction direct interaction 2.6A Exd and Scr both bind the double stranded DNA in a head-to-tail orientation on overlapping DNA sites on opposite faces of the strand The DNA sequence in crystal structure 2R5Z is as above except that 3 base pairs are changed to the Hox-Exd/Pbx consensus sequence we generated cocrystals and solved the structures of Scr and Exd bound to 20 bp overhanging nucleotides containing either the fkh250 and fkh250con binding sites. gatctcaatgtcaagattaa-hth 2 10 unspecified role unspecified role bait bait region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 8 unspecified role unspecified role prey prey region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain P09077:p.Arg326Ala mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain R A Wed May 02 19:17:22 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'arg326ala' Tue Jun 30 19:41:29 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Arg326Ala' P09077:p.His312Ala mutation mutation certain certain sequence position certain certain certain sequence position certain H A Wed May 02 15:33:25 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'his312ala' Tue Jun 30 17:14:36 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.His312Ala' region his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined P09077:p.[His312Ala;Arg326Ala] mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain H A certain certain sequence position certain certain certain sequence position certain R A Wed May 02 15:28:48 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'his312ala,arg326ala' Tue Jun 30 17:58:35 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.[His312Ala;Arg326Ala]' ecoli Escherichia coli (strain K12) 11 unspecified role unspecified role ancillary ancillary region binding region binding-associated region binding region range range range range 7 unspecified role unspecified role ancillary ancillary region his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined ecoli Escherichia coli (strain K12) physical association physical association Binding of SCR and SCR mutants to fkh250 and fkh250con DNAs Kd of Scr His312Ala binding to Fkh250 = 15nM Kd of Scr His312Ala/Arg326Ala binding to Fkh250 = 55nM Kd of Scr Arg326Ala binding to Fkh250 = 48nM Kd of Scr binding to Fkh250=8nM Fig. 5 scr-exd-3 1 3 unspecified role unspecified role neutral component neutral component 6 unspecified role unspecified role neutral component neutral component 8 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 ecoli Escherichia coli (strain K12) 7 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 ecoli Escherichia coli (strain K12) physical association physical association 2.6A Exd and Scr both bind the double stranded DNA in a head-to-tail orientation on overlapping DNA sites on opposite faces of the strand The DNA sequence in crystal structure 2R5Z is as above except that 3 base pairs are changed to the Hox-Exd/Pbx consensus sequence we generated cocrystals and solved the structures of Scr and Exd bound to 20 bp overhanging nucleotides containing either the fkh250 and fkh250con binding sites. scr-exd-4 2 11 unspecified role unspecified role neutral component neutral component region binding region binding-associated region binding region range range range range 8 unspecified role unspecified role neutral component neutral component P09077:p.[His312Ala;Arg326Ala] mutation mutation mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain H A certain certain sequence position certain certain certain sequence position certain R A Wed May 02 17:30:16 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'his312ala,arg326ala' Tue Jun 30 16:46:47 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.[His312Ala;Arg326Ala]' region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain P09077:p.Arg326Ala mutation mutation certain certain sequence position certain certain certain sequence position certain R A Wed May 02 15:43:16 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'arg326ala' Tue Jun 30 15:53:35 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Arg326Ala' P09077:p.His312Ala mutation mutation certain certain sequence position certain certain certain sequence position certain H A Wed May 02 17:01:49 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'his312ala' Tue Jun 30 18:41:33 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.His312Ala' region his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined ecoli Escherichia coli (strain K12) 5 unspecified role unspecified role neutral component neutral component 7 unspecified role unspecified role neutral component neutral component region his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined direct interaction direct interaction Binding of SCR and SCR mutants to fkh250 and fkh250con DNAs Kd of Scr His312Ala/Arg326Ala binding to Fkh250con = 18nM Kd of Scr Arg326Ala binding to Fkh250con = 29nM Nucleic acid was 32P labelled Kd of Scr binding to Fkh250con=10nM Kd of Scr His312Ala binding to Fkh250con=12nM 5