DIP Database of Interacting Proteins 611 Young Drive East; Los Angeles CA 90095; USA http://dip.doe-mbi.ucla.edu/ dip@mbi.ucla.edu 611 Young Drive East; Los Angeles CA 90095; USA http://dip.doe-mbi.ucla.edu/ bhaskar-2015-2 in vitro In vitro pull down pull down experimental particp experimental participant identification experimental particp Bhaskar V., Basquin J., Conti E., Bhaskar V., Basquin J., Conti E. Coordinates of NOT5C taken from PMID:24121231 conti@biochem.mpg.de Structure (London, England : 1993) 2015 imex curation Only protein-protein interactions imex curation bhaskar-2015-1 ecoli Escherichia coli (strain K12) x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction experimental particp experimental participant identification experimental particp Bhaskar V., Basquin J., Conti E., Bhaskar V., Basquin J., Conti E. conti@biochem.mpg.de Structure (London, England : 1993) 2015 imex curation Only protein-protein interactions imex curation bhaskar-2015-3 in vitro In vitro molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column experimental particp experimental participant identification experimental particp Bhaskar V., Basquin J., Conti E., Bhaskar V., Basquin J., Conti E. conti@biochem.mpg.de Structure (London, England : 1993) 2015 imex curation Only protein-protein interactions imex curation not4_yeast General negative regulator of transcription subunit 4 MOT2 CCL1 NOT4 SIG1 SSF1 Modulator of transcription 2 YER068W protein protein yeast Saccharomyces cerevisiae Baker's yeast MMNPHVQENLQAIHNALSNFDTSFLSEDEEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNPELNGRCPACRRKYDDENVRYVTLSPEELKMERAKLARKEKERKHREKERKENEYTNRKHLSGTRVIQKNLVYVVGINPPVPYEEVAPTLKSEKYFGQYGKINKIVVNRKTPHSNNTTSEHYHHHSPGYGVYITFGSKDDAARCIAQVDGTYMDGRLIKAAYGTTKYCSSYLRGLPCPNPNCMFLHEPGEEADSFNKRELHNKQQAQQQSGGTAFTRSGIHNNISTSTAGSNTNLLSENFTGTPSPAAMRAQLHHDSHTNAGTPVLTPAPVPAGSNPWGVTQSATPVTSINLSKNSSSINLPTLNDSLGHHTTPTTENTITSTTTTTNTNATSHSHGSKKKQSLAAEEYKDPYDALGNAVDFLDARLHSLSNYQKRPISIKSNIIDEETYKKYPSLFSWDKIEASKKSDNTLANKLVEILAIKPIDYTASVVQFLQSVNVGVNDNITITDNTKTPTQPIRLQTVSQQIQPPLNVSTPPPGIFGPQHKVPIQQQQMGDTSSRNSSDLLNQLINGRKIIAGN 8847084BD9BF48B7 not1_yeast General negative regulator of transcription subunit 1 CDC39 NOT1 ROS1 YCR093W YCR93W YCR1151 Cell division cycle protein 39 protein protein yeast Saccharomyces cerevisiae Baker's yeast MLSATYRDLNTASNLETSKEKQAAQIVIAQISLLFTTLNNDNFESVEREIRHILDRSSVDIYIKVWERLLTLSSRDILQAGKFLLQENLLHRLLLEFAKDLPKKSTDLIELLKERTFNNQEFQKQTGITLSLFIDLFDKSANKDIIESLDRSSQINDFKTIKMNHTNYLRNFFLQTTPETLESNLRDLLHSLEGESLNDLLALLLSEILSPGSQNLQNDPTRSWLTPPMVLDATNRGNVIARSISSLQANQINWNRVFNLMSTKYFLSAPLMPTTASLSCLFAALHDGPVIDEFFSCDWKVIFKLDLAIQLHKWSVQNGCFDLLNAEGTRKVSETIPNTKQSLLYLLSIASLNLELFLQREELSDGPMLAYFQECFFEDFNYAPEYLILALVKEMKRFVLLIENRTVIDEILITLLIQVHNKSPSSFKDVISTITDDSKIVDAAKIIINSDDAPIANFLKSLLDTGRLDTVINKLPFNEAFKILPCARQIGWEGFDTFLKTKVSPSNVDVVLESLEVQTKMTDTNTPFRSLKTFDLFAFHSLIEVLNKCPLDVLQLQRFESLEFSLLIAFPRLINFGFGHDEAILANGDIAGINNDIEKEMQNYLQKMYSGELAIKDVIELLRRLRDSDLPRDQEVFTCITHAVIAESTFFQDYPLDALATTSVLFGSMILFQLLRGFVLDVAFRIIMRFAKEPPESKMFKFAVQAIYAFRIRLAEYPQYCKDLLRDVPALKSQAQVYQSIVEAATLANAPKERSRPVQEMIPLKFFAVDEVSCQINQEGAPKDVVEKVLFVLNNVTLANLNNKVDELKKSLTPNYFSWFSTYLVTQRAKTEPNYHDLYSKVIVAMGSGLLHQFMVNVTLRQLFVLLSTKDEQAIDKKHLKNLASWLGCITLALNKPIKHKNIAFREMLIEAYKENRLEIVVPFVTKILQRASESKIFKPPNPWTVGILKLLIELNEKANWKLSLTFEVEVLLKSFNLTTKSLKPSNFINTPEVIETLSGALGSITLEQQQTEQQRQIILMQQHQQQMLIYQQRQQQQQQRQQQQQHHISANTIADQQAAFGGEGSISHDNPFNNLLGSTIFVTHPDLKRVFQMALAKSVREILLEVVEKSSGIAVVTTTKIILKDFATEVDESKLKTAAIIMVRHLAQSLARATSIEPLKEGIRSTMQSLAPNLMSLSSSPAEELDTAINENIGIALVLIEKASMDKSTQDLADQLMQAIAIRRYHKERRADQPFITQNTNPYSLSLPEPLGLKNTGVTPQQFRVYEEFGKNIPNLDVIPFAGLPAHAPPMTQNVGLTQPQQQQAQMPTQILTSEQIRAQQQQQQLQKSRLNQPSQSAQPPGVNVPNPQGGIAAVQSDLEQNQRVLVHLMDILVSQIKENATKNNLAELGDQNQIKTIIFQILTFIAKSAQKDQLALKVSQAVVNSLFATSESPLCREVLSLLLEKLCSLSLVARKDVVWWLVYALDSRKFNVPVIRSLLEVNLIDATELDNVLVTAMKNKMENSTEFAMKLIQNTVLSDDPILMRMDFIKTLEHLASSEDENVKKFIKEFEDTKIMPVRKGTKTTRTEKLYLVFTEWVKLLQRVENNDVITTVFIKQLVEKGVISDTDNLLTFVKSSLELSVSSFKESDPTDEVFIAIDALGSLIIKLLILQGFKDDTRRDYINAIFSVIVLVFAKDHSQEGTTFNERPYFRLFSNILYEWATIRTHNFVRISDSSTRQELIEFDSVFYNTFSGYLHALQPFAFPGFSFAWVTLLSHRMLLPIMLRLPNKIGWEKLMLLIIDLFKFLDQYTSKHAVSDAVSVVYKGTLRVILGISNDMPSFLIENHYELMNNLPPTYFQLKNVILSAIPKNMTVPNPYDVDLNMEDIPACKELPEVFFDPVIDLHSLKKPVDNYLRIPSNSLLRTILSAIYKDTYDIKKGVGYDFLSVDSKLIRAIVLHVGIEAGIEYKRTSSNAVFNTKSSYYTLLFNLIQNGSIEMKYQIILSIVEQLRYPNIHTYWFSFVLMNMFKSDEWNDQKLEVQEIILRNFLKRIIVNKPHTWGVSVFFTQLINNNDINLLDLPFVQSVPEIKLILQQLVKYSKKYTTSEQDDQSATINRRQTPLQSNA 5B2AE15BCF95E009 not2_yeast General negative regulator of transcription subunit 2 CDC36 DNA19 NOT2 YDL165W cell division cycle protein 36 protein protein yeast Saccharomyces cerevisiae Baker's yeast MEKFGLKALVPLLKLEDKELSSTYDHSMTLGADLSSMLYSLGIPRDSQDHRVLDTFQSPWAETSRSEVEPRFFTPESFTNIPGVLQSTVTPPCFNSIQNDQQRVALFQDETLFFLFYKHPGTVIQELTYLELRKRNWRYHKTLKAWLTKDPMMEPIVSADGLSERGSYVFFDPQRWEKCQRDFLLFYNAIM 7D0B69657F791371 not5_yeast General negative regulator of transcription subunit 5 NOT5 YP9499.27 YPR072W protein protein yeast Saccharomyces cerevisiae Baker's yeast MSQRKLQQDIDKLLKKVKEGIEDFDDIYEKFQSTDPSNSSHREKLESDLKREIKKLQKHRDQIKTWLSKEDVKDKQSVLMTNRRLIENGMERFKSVEKLMKTKQFSKEALTNPDIIKDPKELKKRDQVLFIHDCLDELQKQLEQYEAQENEEQTERHEFHIANLENILKKLQNNEMDPEPVEEFQDDIKYYVENNDDPDFIEYDTIYEDMGCEIQPSSSNNEAPKEGNNQTSLSSIRSSKKQERSPKKKAPQRDVSISDRATTPIAPGVESASQSISSTPTPVSTDTPLHTVKDDSIKFDNSTLGTPTTHVSMKKKESENDSEQQLNFPPDRTDEIRKTIQHDVETNAAFQNPLFNDELKYWLDSKRYLMQPLQEMSPKMVSQLESSLLNCPDSLDADSPCLYTKPLSLPHPTSIFFPNEPIRFVYPYDVPLNLTNNENDTDNKFGKDSKAKSKKDDDIYSRTSLARIFMKFDLDTLFFIFYHYQGSYEQFLAARELFKNRNWLFNKVDRCWYYKEIEKLPPGMGKSEEESWRYFDYKKSWLARRCGNDFVYNEEDFEKL 073137119B3E92BC ubc4_yeast Ubiquitin-conjugating enzyme E2 4 UBC4 YBR082C YBR0745 Ubiquitin-protein ligase 4 Ubiquitin carrier protein 4 E2 ubiquitin-conjugating enzyme 4 protein protein yeast Saccharomyces cerevisiae Baker's yeast MSSSKRIAKELSDLERDPPTSCSAGPVGDDLYHWQASIMGPADSPYAGGVFFLSIHFPTDYPFKPPKISFTTKIYHPNINANGNICLDILKDQWSPALTLSKVLLSICSLLTDANPDDPLVPEIAHIYKTDRPKYEATAREWTKKYAV 8E96137D3EB20F80 mot2-cdc39-2 3590580 N/A 3590583 weight by comassie molecular weight estimation by coomasie staining weight by comassie unspecified role unspecified role bait bait over-expressed over expressed level over-expressed purified purified Not4C-N Not4C-N sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain false GST tag GST tag 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 binding region binding region required to bind necessary binding region required to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 3590584 weight by comassie molecular weight estimation by coomasie staining weight by comassie unspecified role unspecified role prey prey over-expressed over expressed level over-expressed purified purified region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Figure 2B, 3D, 3E, 4B mot2-cdc36-1 3590580 N/A 3590585 predetermined predetermined participant predetermined unspecified role unspecified role prey prey over-expressed over expressed level over-expressed purified purified ecoli Escherichia coli (strain K12) N/A 3590583 predetermined predetermined participant predetermined unspecified role unspecified role bait bait over-expressed over expressed level over-expressed purified purified Binding region Binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false GST tag GST tag 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 ecoli Escherichia coli (strain K12) N/A 3590584 predetermined predetermined participant predetermined unspecified role unspecified role prey prey over-expressed over expressed level over-expressed purified purified Binding region Binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 3590586 predetermined predetermined participant predetermined unspecified role unspecified role prey prey over-expressed over expressed level over-expressed purified purified region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) association association false false false Figure 4B not5-cdc36-1 3590580 N/A 3590585 weight by comassie molecular weight estimation by coomasie staining weight by comassie unspecified role unspecified role prey prey over-expressed over expressed level over-expressed purified purified ecoli Escherichia coli (strain K12) N/A 3590586 weight by comassie molecular weight estimation by coomasie staining weight by comassie unspecified role unspecified role bait bait over-expressed over expressed level over-expressed purified purified GST Tag GST Tag 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 region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 3590584 weight by comassie molecular weight estimation by coomasie staining weight by comassie unspecified role unspecified role prey prey over-expressed over expressed level over-expressed purified purified Binding region Binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) association association false false false Fig 2B mot2-cdc39-1 3590580 N/A 3590583 weight by comassie molecular weight estimation by coomasie staining weight by comassie unspecified role unspecified role bait bait over-expressed over expressed level over-expressed purified purified GST tag GST tag 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 Not4 binding region Not4 binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false P34909:p.Leu463_Phe464delinsGluGlu L463E F464E mutation disrupting mutation disrupting interaction mutation disrupting mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false P34909:p.[Phe464Glu;Trp466Glu] F464E;W466E mutation disrupting mutation disrupting interaction mutation disrupting mutation analysis mutation analysis 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 3590584 weight by comassie molecular weight estimation by coomasie staining weight by comassie unspecified role unspecified role prey prey over-expressed over expressed level over-expressed purified purified region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Figure 3E x-ray diffraction-8 3590581 N/A 3590587 structure determination identification by structure determination identification by structure determination structure determination unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed purified purified ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 N/A 3590583 structure determination identification by structure determination identification by structure determination structure determination unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed purified purified Binding Region Binding Region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 direct interaction direct interaction false false false Figure 1 B&C. Table 1 x-ray diffraction-9 3590581 N/A 3590583 predetermined predetermined participant predetermined structure determination identification by structure determination identification by structure determination structure determination unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed purified purified Binding region Binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 N/A 3590584 predetermined predetermined participant predetermined structure determination identification by structure determination identification by structure determination structure determination unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed purified purified Binding region Binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 direct interaction direct interaction false false false Fig 2C Table 1 cdc39-mot2-1 3590582 N/A 3590583 ms participant Identification by mass spectrometry ms participant partial id prot seq partial identification of protein sequence partial id prot seq unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed purified purified Binding region Binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 N/A 3590584 ms participant Identification by mass spectrometry ms participant partial id prot seq partial identification of protein sequence partial id prot seq unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed purified purified Binding region Binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 direct interaction direct interaction false false false Fig S2