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/ Structure-based analysis of HU-DNA binding. Structure-based analysis of HU-DNA binding. J. Mol. Biol. (0022-2836) 2007 imex curation Swinger K.K., Rice P.A. price@uchicago.edu 02-Aug-2013: Contacted by IntAct-Help. 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 Swinger K.K., Rice P.A. price@uchicago.edu Accepted 2013-JUN-27 by PPORRAS 02-Aug-2013: Contacted by IntAct-Help. J. Mol. Biol. (0022-2836) 2007 Only protein-protein interactions imex curation Structure-based analysis of HU-DNA binding. Structure-based analysis of HU-DNA binding. J. Mol. Biol. (0022-2836) 2007 imex curation Swinger K.K., Rice P.A. price@uchicago.edu 02-Aug-2013: Contacted by IntAct-Help. Only protein-protein interactions in vitro In vitro emsa electrophoretic mobility shift assay Gel retardation assay band shift band shift Gel retardation assay emsa predetermined predetermined participant predetermined Swinger K.K., Rice P.A. Interactions of AHU with dna duplexes 9/10/11 were not captured as the bands for specific interactions were masked by a smear by non-specific binding. Therefore, no kD values could be calculated either. price@uchicago.edu Accepted 2013-JUN-27 by PPORRAS 02-Aug-2013: Contacted by IntAct-Help. J. Mol. Biol. (0022-2836) 2007 Only protein-protein interactions imex curation dna_17097674_ahu-duplex-1-rev dna from 17097674 AHU-duplex-1 reverse ss dna single stranded deoxyribonucleic acid ss DNA ss dna chemical synthesis Chemical synthesis (Chemical synthesis) ATGCAAACAACGTACGTTGTTTAACATTCGTTGCAACAAAATGC dna_17097674_ahu-duplex-6-rev dna from 17097674 AHU-duplex-6 reverse ss dna single stranded deoxyribonucleic acid ss DNA ss dna chemical synthesis Chemical synthesis (Chemical synthesis) ATGCAAACAACGTACGTTGTTCAACATACGTTGCAACAAAATGC dna_17097674_ahu-duplex-8-forw dna from 17097674 AHU-duplex-8 forward ss dna single stranded deoxyribonucleic acid ss DNA ss dna chemical synthesis Chemical synthesis (Chemical synthesis) TACGTTTGTTGCATGCATACACCGTGTTGCAACGTTGTTTTACG ihfa_ecoli Integration host factor subunit alpha ihfA hid himA b1712 JW1702 protein protein ecoli Escherichia coli (strain K12) MALTKAEMSEYLFDKLGLSKRDAKELVELFFEEIRRALENGEQVKLSGFGNFDLRDKNQRPGRNPKTGEDIPITARRVVTFRPGQKLKSRVENASPKDE DIP protein P0A6X7 original sequence version: 45 278AC82BCD79D754 dna_17097674_ihf-duplex-cog-site dna_17097674_ihf-duplex-cog-site ds dna double stranded deoxyribonucleic acid ds DNA ds dna chemical synthesis Chemical synthesis (Chemical synthesis) GGCCAAAAAAGCATTGCTTATCAATTTGTTGCACC dna_2ht0-2 crystallised dna from 2ht0 stand-2 ds dna double stranded deoxyribonucleic acid ds DNA ds dna chemical synthesis Chemical synthesis (Chemical synthesis) TGATAAGCAATGCTTTTTTGGC dna_17097674_ahu-duplex-2-rev dna from 17097674 AHU-duplex-2 reverse ss dna single stranded deoxyribonucleic acid ss DNA ss dna chemical synthesis Chemical synthesis (Chemical synthesis) CCCGCCATGCAAACAACGTACGTTGTTTAACTATTCGTACGTTGTTTATGCCCGCCC ihfb_ecoli Integration host factor subunit beta ihfB himD hip b0912 JW0895 protein protein ecoli Escherichia coli (strain K12) MTKSELIERLATQQSHIPAKTVEDAVKEMLEHMASTLAQGERIEIRGFGSFSLHYRAPRTGRNPKTGDKVELEGKYVPHFKPGKELRDRANIYG 7558D89EF469EA26 7558D89EF469EA26 dna_17097674_ahu-duplex-4-forw dna from 17097674 AHU-duplex-4 forward ss dna single stranded deoxyribonucleic acid ss DNA ss dna chemical synthesis Chemical synthesis (Chemical synthesis) TACGTTTGTTGCATGCATACAAATTGTTGCAACGTTGTTTTACG dna_2ht0-1 crystallised dna from 2ht0 stand-1 ds dna double stranded deoxyribonucleic acid ds DNA ds dna chemical synthesis Chemical synthesis (Chemical synthesis) CGGTGCAACAAAT dna_17097674_ahu-duplex-3-rev dna from 17097674 AHU-duplex-3 reverse ss dna single stranded deoxyribonucleic acid ss DNA ss dna chemical synthesis Chemical synthesis (Chemical synthesis) ATGCAAACAACGTACGTTGTTTAACTTACGTTGCAACAAAATGC dna_17097674_ahu-duplex-3-forw dna from 17097674 AHU-duplex-3 forward ss dna single stranded deoxyribonucleic acid ss DNA ss dna chemical synthesis Chemical synthesis (Chemical synthesis) TACGTTTGTTGCATGCATTCAAATTGTTGCAACGTTGTTTTACG dna_17097674_ahu-duplex-4-rev dna from 17097674 AHU-duplex-4 reverse ds dna double stranded deoxyribonucleic acid ds DNA ds dna chemical synthesis Chemical synthesis (Chemical synthesis) ATGCAAACAACGTACGTTGTTTAACATACGTTGCAACAAAATGC dna_17097674_ahu-duplex-6-forw dna from 17097674 AHU-duplex-6 forward ss dna single stranded deoxyribonucleic acid ss DNA ss dna chemical synthesis Chemical synthesis (Chemical synthesis) TACGTTTGTTGCATGCATACAAGTTGTTGCAACGTTGTTTTACG dna_17097674_ahu-duplex-5-rev dna from 17097674 AHU-duplex-5 reverse ss dna single stranded deoxyribonucleic acid ss DNA ss dna chemical synthesis Chemical synthesis (Chemical synthesis) ATGCAAACAACGTACGTTGTTTAACATACGTTGCAACAAAATGC dna_2ht0-4 crystallised dna from 2ht0 stand-4 ds dna double stranded deoxyribonucleic acid ds DNA ds dna chemical synthesis Chemical synthesis (Chemical synthesis) GCTTATCAATTTGTTGCACC dna_2ht0-3 crystallised dna from 2ht0 stand-3 ds dna double stranded deoxyribonucleic acid ds DNA ds dna chemical synthesis Chemical synthesis (Chemical synthesis) GGCCAAAAAAGCATT dna_17097674_ihf-duplex-4-rev dna from 17097674 IHF-duplex-4 reverse ss dna single stranded deoxyribonucleic acid ss DNA ss dna chemical synthesis Chemical synthesis (Chemical synthesis) ATGCAAACAACGTACGTTGTTTAACATACGTTGCAACAAAATGC dna_17097674_ahu-duplex-1-forw dna from 17097674 AHU-duplex-1 forward ss dna single stranded deoxyribonucleic acid ss DNA ss dna chemical synthesis Chemical synthesis (Chemical synthesis) TACGTTTGTTGCATGCTTACAAATTGTTGCAACGTTGTTTTACG dna_17097674_ahu-duplex-5-forw dna from 17097674 AHU-duplex-5 forward ss dna single stranded deoxyribonucleic acid ss DNA ss dna chemical synthesis Chemical synthesis (Chemical synthesis) TACGTTTGTTGCATGCATACAATTTGTTGCAACGTTGTTTTACG dna_17097674_ahu-duplex-7-forw dna from 17097674 AHU-duplex-7 forward ss dna single stranded deoxyribonucleic acid ss DNA ss dna chemical synthesis Chemical synthesis (Chemical synthesis) TACGTTTGTTGCATGCATATCAAATTGTTGCAACGTTGTTTTACG dna_17097674_ahu-duplex-7-rev dna from 17097674 AHU-duplex-7 reverse ss dna single stranded deoxyribonucleic acid ss DNA ss dna chemical synthesis Chemical synthesis (Chemical synthesis) ATGCAAACAACGTACGTTGTTTAACTATACGTTGCAACAAAATGC dna_17097674_ihf-duplex-4-forw dna from 17097674 IHF-duplex-4 forward ss dna single stranded deoxyribonucleic acid ss DNA ss dna chemical synthesis Chemical synthesis (Chemical synthesis) TACGTTTGTTGCATGCATACAAATTGTTGCAACGTTGTTTTACG dna_17097674_ahu-duplex-8-rev dna from 17097674 AHU-duplex-8 reverse ss dna single stranded deoxyribonucleic acid ss DNA ss dna chemical synthesis Chemical synthesis (Chemical synthesis) ATGCAAACAACGTACGTTGTGGCACATACGTTGCAACAAAATGC dna_17097674_ahu-duplex-2-forw dna from 17097674 AHU-duplex-2 forward ss dna single stranded deoxyribonucleic acid ss DNA ss dna chemical synthesis Chemical synthesis (Chemical synthesis) GGGCGGTACGTTTGTTGCATGCTTATCAATTTGTTGCATGCAACAAATACGGGCGGG dbh_noss1 DNA-binding protein HU hup hanA asr3935 protein protein noss1 Nostoc sp. (strain PCC 7120 / UTEX 2576) MNKGELVDAVAEKASVTKKQADAVLTAALETIIEAVSSGDKVTLVGFGSFESRERKAREGRNPKTNEKMEIPATRVPAFSAGKLFREKVAPPKA 045BD1FAE4F85DDF ihfa-ihfb-1 1 18 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) 19 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) 12 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) 6 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) 10 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) 8 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) physical association physical association Fig. 1a, 4b, Table 3 All = 0.24; R = 0.24; Rwork = 0.24; Rfree = 0.28 2.0 A DNA sequences imported from PDBe entry. It's not clear from the paper if the 4 strands were used like this in the crystal as strands 1 and 2 and strands 3 and 4 are forming one stand each of 2 different duplexes as described in Table 3 for the EMSA experiment. The 'Ps' (phosphates?) were removed from the PDBe entry. ihfa-ihfb-1 2 25 unspecified role unspecified role bait bait dna binding binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain chemical synthesis Chemical synthesis (Chemical synthesis) 20 unspecified role unspecified role bait bait dna binding binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain chemical synthesis Chemical synthesis (Chemical synthesis) 6 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) 10 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) 40 38 physical association physical association Fig. 5, Table 3 dbh-dna-2 2 27 unspecified role unspecified role bait bait dna binding binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain chemical synthesis Chemical synthesis (Chemical synthesis) 9 unspecified role unspecified role bait bait dna binding binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain chemical synthesis Chemical synthesis (Chemical synthesis) 28 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) 47 45 physical association physical association Table 1 dbh-dna-1 2 28 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) 21 unspecified role unspecified role bait bait dna binding binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain chemical synthesis Chemical synthesis (Chemical synthesis) 3 unspecified role unspecified role bait bait dna binding binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain chemical synthesis Chemical synthesis (Chemical synthesis) 52 54 physical association physical association Table 1 dbh-dna-3 2 13 unspecified role unspecified role bait bait dna binding binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain chemical synthesis Chemical synthesis (Chemical synthesis) 14 unspecified role unspecified role bait bait dna binding binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain chemical synthesis Chemical synthesis (Chemical synthesis) 28 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) 57 59 physical association physical association Table 1 dbh-dna-4 2 11 unspecified role unspecified role bait bait dna binding binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain chemical synthesis Chemical synthesis (Chemical synthesis) 28 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) 15 unspecified role unspecified role bait bait dna binding binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain chemical synthesis Chemical synthesis (Chemical synthesis) 66 63 physical association physical association Table 1 dbh-dna-5 2 17 unspecified role unspecified role bait bait dna binding binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain chemical synthesis Chemical synthesis (Chemical synthesis) 28 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) 22 unspecified role unspecified role bait bait dna binding binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain chemical synthesis Chemical synthesis (Chemical synthesis) 72 69 physical association physical association Table 1 dbh-dna-6 2 4 unspecified role unspecified role bait bait dna binding binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain chemical synthesis Chemical synthesis (Chemical synthesis) 28 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) 16 unspecified role unspecified role bait bait dna binding binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain chemical synthesis Chemical synthesis (Chemical synthesis) 78 75 physical association physical association Fig. 3, Table 1 dbh-dna-7 2 24 unspecified role unspecified role bait bait dna binding binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain chemical synthesis Chemical synthesis (Chemical synthesis) 23 unspecified role unspecified role bait bait dna binding binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain chemical synthesis Chemical synthesis (Chemical synthesis) 28 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) 81 83 physical association physical association Table 1 dbh-dna-8 2 26 unspecified role unspecified role bait bait dna binding binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain chemical synthesis Chemical synthesis (Chemical synthesis) 5 unspecified role unspecified role bait bait dna binding binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain chemical synthesis Chemical synthesis (Chemical synthesis) 28 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) 87 89 physical association physical association Table 1 ihfa-ihfb-2 2 6 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) 10 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) 7 unspecified role unspecified role bait bait chemical synthesis Chemical synthesis (Chemical synthesis) physical association physical association Table 3 kD for nicked DNA between A23 and A24 = 0.5 nM