UniProt UniProt http://www.uniprot.org li-2007-40 yeast Saccharomyces cerevisiae Baker's yeast anti tag coip anti tag coimmunoprecipitation anti tag coip anti tag western anti tag western blot anti tag western Li K., Ossareh-Nazari B., Liu X., Dargemont C., Marmorstein R. marmor@wistar.org Journal of molecular biology 2007 Only protein-protein interactions imex curation imex curation li-2007-37 ecoli Escherichia coli (strain K12) x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Li K., Ossareh-Nazari B., Liu X., Dargemont C., Marmorstein R. marmor@wistar.org Journal of molecular biology 2007 Only protein-protein interactions imex curation imex curation li-2007-38 in vitro In vitro pull down pull down weight by comassie molecular weight estimation by coomasie staining weight by comassie Li K., Ossareh-Nazari B., Liu X., Dargemont C., Marmorstein R. marmor@wistar.org Journal of molecular biology 2007 Only protein-protein interactions imex curation imex curation li-2007-39 in vitro In vitro itc isothermal titration calorimetry ITC ITC itc predetermined predetermined participant predetermined Li K., Ossareh-Nazari B., Liu X., Dargemont C., Marmorstein R. marmor@wistar.org Journal of molecular biology 2007 Only protein-protein interactions imex curation imex curation ubp3_yeast Ubiquitin carboxyl-terminal hydrolase 3 UBP3 Ubiquitin-specific-processing protease 3 Deubiquitinating enzyme 3 Ubiquitin thioesterase 3 YER151C protein protein yeast Saccharomyces cerevisiae Baker's yeast MNMQDANKEESYSMYPKTSSPPPPTPTNMQIPIYQAPLQMYGYTQAPYLYPTQIPAYSFNMVNQNQPIYHQSGSPHHLPPQNNINGGSTTNNNNINKKKWHSNGITNNNGSSGNQGANSSGSGMSYNKSHTYHHNYSNNHIPMMASPNSGSNAGMKKQTNSSNGNGSSATSPSYSSYNSSSQYDLYKFDVTKLKNLKENSSNLIQLPLFINTTEAEFAAASVQRYELNMKALNLNSESLENSSVEKSSAHHHTKSHSIPKHNEEVKTETHGEEEDAHDKKPHASKDAHELKKKTEVKKEDAKQDRNEKVIQEPQATVLPVVDKKEPEESVEENTSKTSSPSPSPPAAKSWSAIASDAIKSRQASNKTVSGSMVTKTPISGTTAGVSSTNMAAATIGKSSSPLLSKQPQKKDKKYVPPSTKGIEPLGSIALRMCFDPDFISYVLRNKDVENKIPVHSIIPRGIINRANICFMSSVLQVLLYCKPFIDVINVLSTRNTNSRVGTSSCKLLDACLTMYKQFDKETYEKKFLENADDAEKTTESDAKKSSKSKSFQHCATADAVKPDEFYKTLSTIPKFKDLQWGHQEDAEEFLTHLLDQLHEELISAIDGLTDNEIQNMLQSINDEQLKVFFIRNLSRYGKAEFIKNASPRLKELIEKYGVINDDSTEENGWHEVSGSSKRGKKTKTAAKRTVEIVPSPISKLFGGQFRSVLDIPNNKESQSITLDPFQTIQLDISDAGVNDLETAFKKFSEYELLPFKSSSGNDVEAKKQTFIDKLPQVLLIQFKRFSFINNVNKDNAMTNYNAYNGRIEKIRKKIKYGHELIIPEESMSSITLKNNTSGIDDRRYKLTGVIYHHGVSSDGGHYTADVYHSEHNKWYRIDDVNITELEDDDVLKGGEEASDSRTAYILMYQKRN 337FD05527C5542D bre5_yeast UBP3-associated protein BRE5 BRE5 YNR051C N3465 Brefeldin-A sensitivity protein 5 protein protein yeast Saccharomyces cerevisiae Baker's yeast MGVTVQDICFAFLQNYYERMRTDPSKLAYFYASTAELTHTNYQSKSTNEKDDVLPTVKVTGRENINKFFSRNDAKVRSLKLKLDTIDFQYTGHLHKSILIMATGEMFWTGTPVYKFCQTFILLPSSNGSTFDITNDIIRFISNSFKPYVLTDASLSQSNEENSVSAVEEDKIRHESGVEKEKEKEKSPEISKPKAKKETVKDTTAPTESSTQEKPIVDHSQPRAIPVTKESKIHTETVPSSTKGNHKQDEVSTEELGNVTKLNEKSHKAEKKAAPIKTKEGSVEAINAVNNSSLPNGKEVSDEKPVPGGVKEAETEIKPIEPQVSDAKESGNNASTPSSSPEPVANPPKMTWASKLMNENSDRISKNNTTVEYIRPETLPKKPTERKFEMGNRRDNASANSKNKKKPVFSTVNKDGFYPIYIRGTNGLREEKLRSALEKEFGKVMRITAADNFAVVDFETQKSQIDALEKKKKSIDGIEVCLERKTVKKPTSNNPPGIFTNGTRSHRKQPLKRKD ubp3-bre5-10 3321740 N/A 3321744 unspecified role unspecified role bait bait purified purified region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 N/A 3321745 unspecified role unspecified role prey prey purified purified 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 P53741:p.[Tyr17Ala;Lys82Ala] mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 physical association physical association false false false Fig. 4D bre5-ubp3-14 3321740 N/A 3321744 unspecified role unspecified role prey prey purified purified 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 false Q01477:p.Leu208_Asn211delinsAlaAlaAlaAla mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 N/A 3321745 unspecified role unspecified role bait bait purified purified region gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 physical association physical association false false false Fig. 4D bre5-ubp3-11 3321741 N/A 3321744 unspecified role unspecified role neutral component neutral component purified purified 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 3321745 unspecified role unspecified role neutral component neutral component purified purified 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 3321762 3321760 direct interaction direct interaction false false false 1.69A Rworking 0.207 Rfree 0.225 Table 1 ubp3-bre5-9 3321742 N/A 3321744 unspecified role unspecified role bait bait purified purified region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false n-terminal gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false Q01477:p.Leu208Ala mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction certain certain sequence position certain certain certain sequence position certain false Q01477:p.Phe209Ala mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction certain certain sequence position certain certain certain sequence position certain false Q01477:p.Ile210Ala mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false Q01477:p.Asn211Ala mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false Q01477:p.Thr212Ala mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction certain certain sequence position certain certain certain sequence position certain false Q01477:p.Glu216Ala mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction certain certain sequence position certain certain certain sequence position certain false Q01477:p.Phe217Ala mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction certain certain sequence position certain certain certain sequence position certain false Q01477:p.Glu214Ala mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction certain certain sequence position certain certain certain sequence position certain false Q01477:p.Leu208_Phe209delinsAlaAla mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false Q01477:p.[Ile210Ala;Phe217Ala] mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false Q01477:p.[Asn211Ala;Phe217Ala] mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false Q01477:p.Leu208_Asn211delinsAlaAlaAlaAla mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false Q01477:p.[Leu208_Asn211delinsAlaAlaAlaAla;Phe217Ala] mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false Q01477:p.Arg224Ala mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 3321745 unspecified role unspecified role prey prey purified purified region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false 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 P53741:p.Tyr17Ala mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction certain certain sequence position certain certain certain sequence position certain false P53741:p.Lys80Ala mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction certain certain sequence position certain certain certain sequence position certain false P53741:p.Lys82Ala mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction certain certain sequence position certain certain certain sequence position certain false P53741:p.Glu105Ala mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) 3321782 3321765 direct interaction direct interaction false false false The lys80ala or lys82ala mutation in BRE5 disrupted binding in combination with a ile210ala mutation of UBP3. The tyr17ala,lys82ala mutation in BRE5 disrupted binding in combination with a ile210ala mutation of UBP3 Fig. 4A, 4B bre5-ubp3-12 3321743 N/A 3321744 unspecified role unspecified role neutral component neutral component purified purified c-terminal gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst 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 Q01477:p.[Leu208_Asn211delinsAlaAlaAlaAla;Phe217Ala] mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 3321745 unspecified role unspecified role neutral component neutral component purified purified 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) 3321795 3321791 direct interaction direct interaction false false false 3321743 Fig 4C