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/ Yeast Isw1p forms two separable complexes in vivo. Yeast Isw1p forms two separable complexes in vivo. Mol. Cell. Biol. (0270-7306) 2003 imex curation Vary JC., Gangaraju VK., Qin J., Landel CC., Kooperberg C., Bartholomew B., Tsukiyama T. Chromatin - Epigenetic interactions resulting in chromatin modulation ttsukiya@fhcrc.org 23-MAY-2007: Contacted by JYOTI. Only protein-protein interactions yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast tap tandem affinity purification TAP TAP tap weight silver stain molecular weight estimation by silver staining weight silver stain Vary JC., Gangaraju VK., Qin J., Landel CC., Kooperberg C., Bartholomew B., Tsukiyama T. Chromatin - Epigenetic interactions resulting in chromatin modulation Identity of prey proteins further confirmed by mass spectrometry but this data was not shown. ttsukiya@fhcrc.org Accepted 2007-JUN-16 by JYOTI. 23-MAY-2007: Contacted by JYOTI. Mol. Cell. Biol. (0270-7306) 2003 Only protein-protein interactions imex curation Yeast Isw1p forms two separable complexes in vivo. Yeast Isw1p forms two separable complexes in vivo. Mol. Cell. Biol. (0270-7306) 2003 imex curation Vary JC., Gangaraju VK., Qin J., Landel CC., Kooperberg C., Bartholomew B., Tsukiyama T. Chromatin - Epigenetic interactions resulting in chromatin modulation ttsukiya@fhcrc.org 23-MAY-2007: Contacted by JYOTI. Only protein-protein interactions yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast ion exchange chrom ion exchange chromatography IEC IEC ion exchange chrom ms participant Identification by mass spectrometry ms participant Vary JC., Gangaraju VK., Qin J., Landel CC., Kooperberg C., Bartholomew B., Tsukiyama T. Chromatin - Epigenetic interactions resulting in chromatin modulation ttsukiya@fhcrc.org Accepted 2007-JUN-16 by JYOTI. 23-MAY-2007: Contacted by JYOTI. Mol. Cell. Biol. (0270-7306) 2003 Only protein-protein interactions imex curation Yeast Isw1p forms two separable complexes in vivo. Yeast Isw1p forms two separable complexes in vivo. Mol. Cell. Biol. (0270-7306) 2003 imex curation Vary JC., Gangaraju VK., Qin J., Landel CC., Kooperberg C., Bartholomew B., Tsukiyama T. Chromatin - Epigenetic interactions resulting in chromatin modulation ttsukiya@fhcrc.org 23-MAY-2007: Contacted by JYOTI. Only protein-protein interactions yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast anti tag coip anti tag coimmunoprecipitation anti tag coip weight by staining molecular weight estimation by staining weight by staining Vary JC., Gangaraju VK., Qin J., Landel CC., Kooperberg C., Bartholomew B., Tsukiyama T. Chromatin - Epigenetic interactions resulting in chromatin modulation ttsukiya@fhcrc.org Accepted 2007-JUN-16 by JYOTI. 23-MAY-2007: Contacted by JYOTI. Mol. Cell. Biol. (0270-7306) 2003 Only protein-protein interactions imex curation Yeast Isw1p forms two separable complexes in vivo. Yeast Isw1p forms two separable complexes in vivo. Mol. Cell. Biol. (0270-7306) 2003 imex curation Vary JC., Gangaraju VK., Qin J., Landel CC., Kooperberg C., Bartholomew B., Tsukiyama T. Chromatin - Epigenetic interactions resulting in chromatin modulation ttsukiya@fhcrc.org 23-MAY-2007: Contacted by JYOTI. Only protein-protein interactions yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast anti tag coip anti tag coimmunoprecipitation anti tag coip anti tag western anti tag western blot anti tag western Vary JC., Gangaraju VK., Qin J., Landel CC., Kooperberg C., Bartholomew B., Tsukiyama T. Chromatin - Epigenetic interactions resulting in chromatin modulation ttsukiya@fhcrc.org Accepted 2007-JUN-16 by JYOTI. 23-MAY-2007: Contacted by JYOTI. Mol. Cell. Biol. (0270-7306) 2003 Only protein-protein interactions imex curation Yeast Isw1p forms two separable complexes in vivo. Yeast Isw1p forms two separable complexes in vivo. Mol. Cell. Biol. (0270-7306) 2003 imex curation Vary JC., Gangaraju VK., Qin J., Landel CC., Kooperberg C., Bartholomew B., Tsukiyama T. Chromatin - Epigenetic interactions resulting in chromatin modulation ttsukiya@fhcrc.org 23-MAY-2007: Contacted by JYOTI. Only protein-protein interactions in vitro In vitro enzymatic study enzymatic study predetermined predetermined participant predetermined Vary JC., Gangaraju VK., Qin J., Landel CC., Kooperberg C., Bartholomew B., Tsukiyama T. Chromatin - Epigenetic interactions resulting in chromatin modulation Revisit when ATPase added to CVs ATPase assays of purified yeast ISWI complexes were performed using radio-labelled ATP in the presence of magnesium. Reaction mixture was spotted onto thin layer chromatography plates. ATP and free phosphate were separated, localized by autoradiograph, and quantified by scintillation counting. ttsukiya@fhcrc.org Accepted 2007-JUN-16 by JYOTI. 23-MAY-2007: Contacted by JYOTI. Mol. Cell. Biol. (0270-7306) 2003 Only protein-protein interactions imex curation Yeast Isw1p forms two separable complexes in vivo. Yeast Isw1p forms two separable complexes in vivo. Mol. Cell. Biol. (0270-7306) 2003 imex curation Vary JC., Gangaraju VK., Qin J., Landel CC., Kooperberg C., Bartholomew B., Tsukiyama T. Chromatin - Epigenetic interactions resulting in chromatin modulation ttsukiya@fhcrc.org 23-MAY-2007: Contacted by JYOTI. Only protein-protein interactions yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 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 Vary JC., Gangaraju VK., Qin J., Landel CC., Kooperberg C., Bartholomew B., Tsukiyama T. Chromatin - Epigenetic interactions resulting in chromatin modulation Complexes separated on a Superose 6 10/30 column ttsukiya@fhcrc.org Accepted 2007-JUN-16 by JYOTI. 23-MAY-2007: Contacted by JYOTI. Mol. Cell. Biol. (0270-7306) 2003 Only protein-protein interactions imex curation atp ATP Adenosine 5'-triphosphate Adenosine triphosphate ADENOSINE-5'-TRIPHOSPHATE Adephos Adetol Adynol Atipi ATP Atriphos Cardenosine Fosfobion Glucobasin H4atp Myotriphos Triadenyl Triphosphaden adenosine 5'-(tetrahydrogen triphosphate) small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) ioc4_yeast ISWI one complex protein 4 YM9532.09 YMR044W IOC4 protein protein yeast Saccharomyces cerevisiae Baker's yeast MSEAIFQPTDIVLAKVKGFSAWPAMIIPNELIPDNILKTKPVSVHKGKSGSDKKANEDIDADMESEARDREQSEEEEDIEDFGESEANPEKFIIYTPVLKFRKNDTLKSTYCVKFFCDDSYIWVKPMDMKILTSEDCRKWLSGKQRKNKKLIPAYEMAMRGKNGIDIWEFVEYGSYGKPDEEEYVEEEEEENEPEKKAIRPTRSSSRQRQKRASETEKSEGGNSNKRKRVTRSTRQQAIDASEEEEEEEEEKVQEAVRKRPQRTKTKKVVVSKTKPNPKTKAKKEKPKPPKPIKYHFEDDEDWSIVGLGPQDLSIEKTMDPIAKKLSQKKNLEKHVEIKLDLEDKLAGINKLLCDVLCSAINQAVSIKDDFEIILDELQIALDTRGSRNEFITIFQSNNSLLLNFRILFNLRKRELNKWDLWDRFQDIFKHIYSYQFIPDTEDWQLEQNMEIEEMDREKPSFSEDVKEEESKVGA DFD6189E81178060 ioc2_yeast ISWI one complex protein 2 IOC2 YLR095C protein protein yeast Saccharomyces cerevisiae Baker's yeast MRTKRTRGTRNVGASMPAGAANADSEDWKEYVSEDIIAQLNKHQLPYSEILDEKIADLANHWHFQYVMAWLSNVCESYTTTTFNTDQYGGSSTKCLWKNIKFDEGVFVTDVFSKIDGKDSNYYNDEVDVDEGSQNLYDRIRLQLLHQLAGNKSGQLKDWNVIVNHHLQNSSAYSDLVTDLPFLELEIARQFDIIYSIIKLIEMKNMIFKNYLANNLHLFTFSEVILDDDNSGGEEMKSLFALPNVGVLVKKTIHRVKEGSSSQVSQTLNIPIKLQNCTIKESDPDIPDSVELIHLEYSHDIDAYLQSITIDYDVITTNWGSMLEYWSENKSSKAIDEFITNLIPVYAEHRLYSAKLLANREKERAIAELMTRRKRSSRLVAKEEENKKKDLESEWFEKLDEREQFIRHRNKLVSKEIKKIKDLLWNQLWQLYDQDYRDEKLTRRNELKDRSGSGTPFFETSLGREEDNPLNEIDIGVLDHGPNFQSSIIPVEPPIPGTVGPLQTGDVPELPSDFCITKEELDELANYGIFTPQQEPDNQDSVFQCPGEPELAPMIITEDTETDLFNNRPLICCDHCYRWQHWECQPPKIIELISSTTKSPQHTLSQRDFGVIIMGNSHGNRRSSRRPQSTLEPSTKSSRPTDKRKPLSECSTFICAWCIRDLELELRNIFVPELKIIRAKQRKQQEDRERRKKMKEEKKRLEELAKKRELTESVSPPVFNNAFANMSSSTTPSIAAYEKTNPAINPAPNVNAAHPIITYSQQTGSKTVPQAPQAPQTSQASIQPQQQQQQQQQQQPLHPKEQNFHFQFPPTN 632AD02AA8229D87 632AD02AA8229D87 isw1_yeast ISWI chromatin-remodeling complex ATPase ISW1 YBR1633 YBR245C ISW1 protein protein yeast Saccharomyces cerevisiae Baker's yeast MAYMLAIANFHFFKFYTRMRKKHENNSCNEKDKDENLFKIILAIFLQEKKKYDCISSGSIMTASEEYLENLKPFQVGLPPHDPESNKKRYLLKDANGKKFDLEGTTKRFEHLLSLSGLFKHFIESKAAKDPKFRQVLDVLEENKANGKGKGKHQDVRRRKTEHEEDAELLKEEDSDDDESIEFQFRESPAYVNGQLRPYQIQGVNWLVSLHKNKIAGILADEMGLGKTLQTISFLGYLRYIEKIPGPFLVIAPKSTLNNWLREINRWTPDVNAFILQGDKEERAELIQKKLLGCDFDVVIASYEIIIREKSPLKKINWEYIIIDEAHRIKNEESMLSQVLREFTSRNRLLITGTPLQNNLHELWALLNFLLPDIFSDAQDFDDWFSSESTEEDQDKIVKQLHTVLQPFLLRRIKSDVETSLLPKKELNLYVGMSSMQKKWYKKILEKDLDAVNGSNGSKESKTRLLNIMMQLRKCCNHPYLFDGAEPGPPYTTDEHLVYNAAKLQVLDKLLKKLKEEGSRVLIFSQMSRLLDILEDYCYFRNYEYCRIDGSTAHEDRIQAIDDYNAPDSKKFVFLLTTRAGGLGINLTSADVVVLYDSDWNPQADLQAMDRAHRIGQKKQVKVFRLVTDNSVEEKILERATQKLRLDQLVIQQNRTSLKKKENKADSKDALLSMIQHGAADVFKSGTSTGSAGTPEPGSGEKGDDIDLDELLLKSENKTKSLNAKYETLGLDDLQKFNQDSAYEWNGQDFKKKIQRDIISPLLLNPTKRERKENYSIDNYYKDVLNTGRSSTPSHPRMPKPHVFHSHQLQPPQLKVLYEKERMWTAKKTGYVPTMDDVKAAYGDISDEEEKKQKLELLKLSVNNSQPLTEEEEKMKADWESEGFTNWNKLEFRKFITVSGKYGRNSIQAIARELAPGKTLEEVRAYAKAFWSNIERIEDYEKYLKIIENEEEKIKRVKMQQEALRRKLSEYKNPFFDLKLKHPPSSNNKRTYSEEEDRFILLMLFKYGLDRDDVYELVRDEIRDCPLFELDFYFRSRTPVELARRGNTLLQCLEKEFNAGIVLDDATKDRMKKEDENGKRIREEFADQTANEKENVDGVESKKAKIEDTSNVGTEQLVAEKIPENETTH 2CF86BAF553E6695 2CF86BAF553E6695 ioc3_yeast ISWI one complex protein 3 YFR013W IOC3 protein protein yeast Saccharomyces cerevisiae Baker's yeast MDSPSNSIQNLQQEAQGSSSAQLADHDHDRVSMAMPLQTDQSVSVSQSSDNLRRSRRVPKPRTSIYDEYEEELKERANKPKRKRPAPPKKKAPSTQNSKSNDKVEKKKTTSIAKDGKPTLKTNDKKVAPKPKPAHEQVEPALIPSNWTSVIPLLTSDFKNQYSVISRLKNPNMKPVPYAGDIIKLMAFINKFSSFFHSDLQNLSFQDFEVGLDLYPGDPNGSAAGIVKGPEDTSLLLYPDFMAIKDIVYCQDKMNLLFLSLLDLTFTENFDGKSAKKKGPLTTWENLKSSSKKVFSNPLYRLRLVAREWGYPREWRQQLPSDQDISKPKTALFEQDEQTPVVDPSHPEILTPNIYTWNANEPLPLESNPLYNREMDKNGILALKPMDRVVLLRALTDWCASHSSAIHDEIYKLTHGKKDPVFGIQTQQVPRYTIEGVDNTINQFKKLCSLIQSRYEIRSKKKHFVKQLKEGKKPDLSRKLEILKEIKAELKNAVKSEKDELLFSLYDKWVPLFEGELPDQPLANPFSERLYKLRLQEFFLGRVPHIGDFYMPRLHSYGDSLEMSTFTDLRNLQALLSKFKNNEYNAFTLFENDGQSMSAQFKLFYHDTPSLAHDVARGRNTSGKVYWYELCHDSATLLEFLEFLDYKIVKPQDEKKEGNEKEKEALNNEAHILEQKSTTDNNPSINTNPLPKDAKYNTARKKLQILKEFLSDYYFILRQFEQMKVQFADMKPGKRQLRRIQRQTVNYNTEYDSEEYVDDEEDDEADIYDDNDNDSSFDDGRVKRQRT 1919A8A1F58B5340 1919A8A1F58B5340 isw1-ioc2-1 2 8 unspecified role unspecified role prey prey 11 unspecified role unspecified role prey prey 9 unspecified role unspecified role prey prey 10 unspecified role unspecified role bait bait region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined physical association physical association Identification of the proteins associated with Isw1p: Ioc2p, Ioc3p, and Ioc4p. 1 isw1-ioc2-2 3 10 unspecified role unspecified role bait bait region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 8 unspecified role unspecified role prey prey 9 unspecified role unspecified role prey prey association association To reveal interactions among Isw1 complex subunits, Isw1p was immunoprecipitated from strains from each of which the IOC2, IOC3, or IOC4 gene was deleted 1 Immunopreciptiation performed in cells not expressing IOC3 (P43596) isw1-ioc3-1 3 11 unspecified role unspecified role prey prey 10 unspecified role unspecified role bait bait region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined physical association physical association To reveal interactions among Isw1 complex subunits, Isw1p was immunoprecipitated from strains from each of which the IOC2, IOC3, or IOC4 gene was deleted 1 Coimmunoprecipitation performed in both a IOC2 and IOC4 deleted cell line. isw1-ioc2-3 6 10 unspecified role unspecified role neutral component neutral component region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 9 unspecified role unspecified role neutral component neutral component region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined physical association physical association Whole-cell extract from strain YTT642 was separated by size exclusion chromatography. Isw1p, Ioc2p, and Ioc3p were detected by Western blotting using α-FLAG, α-MYC, and α-HA antibodies, respectively. 2 isw1-ioc3-2 6 10 unspecified role unspecified role neutral component neutral component region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 11 unspecified role unspecified role neutral component neutral component region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined physical association physical association Whole-cell extract from strain YTT642 was separated by size exclusion chromatography. Isw1p, Ioc2p, and Ioc3p were detected by Western blotting using α-FLAG, α-MYC, and α-HA antibodies, respectively. 2 isw1-ioc2-4 4 9 unspecified role unspecified role prey prey region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 10 unspecified role unspecified role bait bait region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 11 unspecified role unspecified role prey prey region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined association association As shown in Fig. 2B (lanes 3 to 5), the IP of Isw1p coprecipitated Ioc2p and Ioc3p, as observed previously (Fig. 1A) (49). 2B isw1-ioc2-5 4 10 unspecified role unspecified role bait bait region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 9 unspecified role unspecified role prey prey region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined physical association physical association Anti-Myc antibodies were used to immunoprecipitate Ioc2p. As expected, Isw1p was coprecipitated; however, no detectable Ioc3p was precipitated (Fig. 2B, lanes 6 to 8). 2B isw1-ioc3-3 4 10 unspecified role unspecified role bait bait region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 11 unspecified role unspecified role prey prey region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined physical association physical association Conversely, the IP of Ioc3p with anti-HA antibodies pulled down Isw1p but not Ioc2p (Fig. 2B, lanes 9 to 11). 2B isw1-ioc2-6 1 10 unspecified role unspecified role prey prey 9 unspecified role unspecified role bait bait region tap tagged calmodulin binding peptide plus protein a tag CBP-ProtA tagged CBP-ProtA tagged tap tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 8 unspecified role unspecified role prey prey association association Ioc2p copurified two other proteins in approximately stoichiometric amounts (Fig. 2C). These proteins were subsequently identified by mass spectrometry as Isw1p and Ioc4p (data not shown). 2C isw1-ioc3-4 1 11 unspecified role unspecified role bait bait region tap tagged calmodulin binding peptide plus protein a tag CBP-ProtA tagged CBP-ProtA tagged tap tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 10 unspecified role unspecified role prey prey physical association physical association Ioc3p copurified one other protein in near-stoichiometric amounts, which was subsequently identified by mass spectrometry as Isw1p (data not shown). 2C isw1-ioc2-7 5 10 enzyme enzyme unspecified role unspecified role region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 9 unspecified role unspecified role ancillary ancillary yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 7 enzyme target enzyme target substrate substrate unspecified role unspecified role 8 unspecified role unspecified role ancillary ancillary yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast enzymatic reaction enzymatic reaction Biochemical reaction Biochemical reaction Approximately equimolar amounts of Isw1p monomer and Isw1a or Isw1b complex (as determined by normalizing the Isw1p subunit in silver-stained SDS-PAGE gels) were assayed for ATPase activity in the presence or absence of nucleosomes. 3A Nucleosomes. isw1-ioc3-5 5 7 enzyme target enzyme target substrate substrate unspecified role unspecified role 10 enzyme enzyme unspecified role unspecified role region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 11 unspecified role unspecified role ancillary ancillary region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast enzymatic reaction enzymatic reaction Biochemical reaction Biochemical reaction Approximately equimolar amounts of Isw1p monomer and Isw1a or Isw1b complex (as determined by normalizing the Isw1p subunit in silver-stained SDS-PAGE gels) were assayed for ATPase activity in the presence or absence of nucleosomes. 3A Nucleosomes