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/ swinger-2007-2 Structure-based analysis of HU-DNA binding. 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 J. Mol. Biol. (0022-2836) 2007 Only protein-protein interactions imex curation swinger-2007-1 Structure-based analysis of HU-DNA binding. 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 J. Mol. Biol. (0022-2836) 2007 Only protein-protein interactions imex curation 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_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 ihfa_ecoli Integration host factor subunit alpha ihfA hid himA b1712 JW1702 protein protein ecoli Escherichia coli (strain K12) MALTKAEMSEYLFDKLGLSKRDAKELVELFFEEIRRALENGEQVKLSGFGNFDLRDKNQRPGRNPKTGEDIPITARRVVTFRPGQKLKSRVENASPKDE ihfb_ecoli Integration host factor subunit beta ihfB himD hip b0912 JW0895 protein protein ecoli Escherichia coli (strain K12) MTKSELIERLATQQSHIPAKTVEDAVKEMLEHMASTLAQGERIEIRGFGSFSLHYRAPRTGRNPKTGDKVELEGKYVPHFKPGKELRDRANIYG 7558D89EF469EA26 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_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 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 dbh_noss1 DNA-binding protein HU hup hanA asr3935 protein protein noss1 Nostoc sp. (strain PCC 7120 / UTEX 2576) MNKGELVDAVAEKASVTKKQADAVLTAALETIIEAVSSGDKVTLVGFGSFESRERKAREGRNPKTNEKMEIPATRVPAFSAGKLFREKVAPPKA 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-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-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-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_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-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_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-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-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-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_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-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-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 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_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_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 ihfa-ihfb-1 1389413 n/a 1389415 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 false chemical synthesis Chemical synthesis (Chemical synthesis) n/a 1389416 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 false chemical synthesis Chemical synthesis (Chemical synthesis) n/a 1389417 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) n/a 1389418 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) 1389445 1389443 physical association physical association false false false 1389413 Fig. 5, Table 3 ihfa-ihfb-2 1389413 n/a 1389417 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) n/a 1389418 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) n/a 1389419 unspecified role unspecified role bait bait chemical synthesis Chemical synthesis (Chemical synthesis) physical association physical association false false false 1389413 Table 3 kD for nicked DNA between A23 and A24 = 0.5 nM dbh-dna-2 1389413 n/a 1389420 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 false chemical synthesis Chemical synthesis (Chemical synthesis) n/a 1389421 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 false chemical synthesis Chemical synthesis (Chemical synthesis) n/a 1389422 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) 1389456 1389454 physical association physical association false false false 1389413 Table 1 dbh-dna-1 1389413 n/a 1389422 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) n/a 1389423 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 false chemical synthesis Chemical synthesis (Chemical synthesis) n/a 1389424 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 false chemical synthesis Chemical synthesis (Chemical synthesis) 1389463 1389461 physical association physical association false false false 1389413 Table 1 dbh-dna-3 1389413 n/a 1389425 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 false chemical synthesis Chemical synthesis (Chemical synthesis) n/a 1389426 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 false chemical synthesis Chemical synthesis (Chemical synthesis) n/a 1389422 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) 1389468 1389466 physical association physical association false false false 1389413 Table 1 dbh-dna-4 1389413 n/a 1389427 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 false chemical synthesis Chemical synthesis (Chemical synthesis) n/a 1389422 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) n/a 1389428 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 false chemical synthesis Chemical synthesis (Chemical synthesis) 1389475 1389472 physical association physical association false false false 1389413 Table 1 dbh-dna-5 1389413 n/a 1389429 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 false chemical synthesis Chemical synthesis (Chemical synthesis) n/a 1389422 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) n/a 1389430 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 false chemical synthesis Chemical synthesis (Chemical synthesis) 1389481 1389478 physical association physical association false false false 1389413 Table 1 dbh-dna-6 1389413 n/a 1389431 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 false chemical synthesis Chemical synthesis (Chemical synthesis) n/a 1389422 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) n/a 1389432 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 false chemical synthesis Chemical synthesis (Chemical synthesis) 1389487 1389484 physical association physical association false false false 1389413 Fig. 3, Table 1 dbh-dna-7 1389413 n/a 1389433 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 false chemical synthesis Chemical synthesis (Chemical synthesis) n/a 1389434 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 false chemical synthesis Chemical synthesis (Chemical synthesis) n/a 1389422 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) 1389492 1389490 physical association physical association false false false 1389413 Table 1 dbh-dna-8 1389413 n/a 1389435 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 false chemical synthesis Chemical synthesis (Chemical synthesis) n/a 1389436 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 false chemical synthesis Chemical synthesis (Chemical synthesis) n/a 1389422 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) 1389498 1389496 physical association physical association false false false 1389413 Table 1 ihfa-ihfb-1 1389414 n/a 1389437 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) n/a 1389438 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) n/a 1389439 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) n/a 1389417 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) n/a 1389418 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) n/a 1389440 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) physical association physical association false false false 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.