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-2013-1 in vitro In vitro molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column predetermined predetermined participant predetermined Bhaskar V., Roudko V., Basquin J., Sharma K., Urlaub H., Séraphin B., Conti E. DIP original experiment: DIP-255671X Nature structural & molecular biology 2013 IMEx Structure and RNA-binding properties of the Not1-Not2-Not5 module of the yeast Ccr4-Not complex. Bhaskar V., Roudko V., Basquin J., Sharma K., Urlaub H., Séraphin B., Conti E. Only protein-protein interactions imex curation bhaskar-2013-2 in vitro In vitro pull down pull down weight by comassie molecular weight estimation by coomasie staining weight by comassie Bhaskar V., Roudko V., Basquin J., Sharma K., Urlaub H., Séraphin B., Conti E. DIP original experiment: DIP-255674X Nature structural & molecular biology 2013 IMEx Structure and RNA-binding properties of the Not1-Not2-Not5 module of the yeast Ccr4-Not complex. Bhaskar V., Roudko V., Basquin J., Sharma K., Urlaub H., Séraphin B., Conti E. Only protein-protein interactions imex curation bhaskar-2013-3 in vitro In vitro pull down pull down weight by comassie molecular weight estimation by coomasie staining weight by comassie Bhaskar V., Roudko V., Basquin J., Sharma K., Urlaub H., Séraphin B., Conti E. DIP original experiment: DIP-255673X Nature structural & molecular biology 2013 IMEx Structure and RNA-binding properties of the Not1-Not2-Not5 module of the yeast Ccr4-Not complex. Bhaskar V., Roudko V., Basquin J., Sharma K., Urlaub H., Séraphin B., Conti E. Only protein-protein interactions imex curation bhaskar-2013-4 yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast tap tandem affinity purification TAP TAP tap anti tag western anti tag western blot anti tag western Bhaskar V., Roudko V., Basquin J., Sharma K., Urlaub H., Séraphin B., Conti E. DIP original experiment: DIP-255676X Nature structural & molecular biology 2013 IMEx Structure and RNA-binding properties of the Not1-Not2-Not5 module of the yeast Ccr4-Not complex. Bhaskar V., Roudko V., Basquin J., Sharma K., Urlaub H., Séraphin B., Conti E. Only protein-protein interactions imex curation bhaskar-2013-5 yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast tap tandem affinity purification TAP TAP tap anti tag western anti tag western blot anti tag western Bhaskar V., Roudko V., Basquin J., Sharma K., Urlaub H., Séraphin B., Conti E. DIP original experiment: DIP-255677X Nature structural & molecular biology 2013 IMEx Structure and RNA-binding properties of the Not1-Not2-Not5 module of the yeast Ccr4-Not complex. Bhaskar V., Roudko V., Basquin J., Sharma K., Urlaub H., Séraphin B., Conti E. Only protein-protein interactions imex curation bhaskar-2013-6 yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast tap tandem affinity purification TAP TAP tap anti tag western anti tag western blot anti tag western Bhaskar V., Roudko V., Basquin J., Sharma K., Urlaub H., Séraphin B., Conti E. DIP original experiment: DIP-255679X Nature structural & molecular biology 2013 IMEx Structure and RNA-binding properties of the Not1-Not2-Not5 module of the yeast Ccr4-Not complex. Bhaskar V., Roudko V., Basquin J., Sharma K., Urlaub H., Séraphin B., Conti E. Only protein-protein interactions imex curation bhaskar-2013-7 in vitro In vitro x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Bhaskar V., Roudko V., Basquin J., Sharma K., Urlaub H., Séraphin B., Conti E. DIP original experiment: DIP-255672X Nature structural & molecular biology 2013 IMEx Structure and RNA-binding properties of the Not1-Not2-Not5 module of the yeast Ccr4-Not complex. Bhaskar V., Roudko V., Basquin J., Sharma K., Urlaub H., Séraphin B., Conti E. Only protein-protein interactions imex curation bhaskar-2013-8 yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast tap tandem affinity purification TAP TAP tap anti tag western anti tag western blot anti tag western Bhaskar V., Roudko V., Basquin J., Sharma K., Urlaub H., Séraphin B., Conti E. DIP original experiment: DIP-255675X Nature structural & molecular biology 2013 IMEx Structure and RNA-binding properties of the Not1-Not2-Not5 module of the yeast Ccr4-Not complex. Bhaskar V., Roudko V., Basquin J., Sharma K., Urlaub H., Séraphin B., Conti E. Only protein-protein interactions imex curation bhaskar-2013-9 yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast tap tandem affinity purification TAP TAP tap anti tag western anti tag western blot anti tag western Bhaskar V., Roudko V., Basquin J., Sharma K., Urlaub H., Séraphin B., Conti E. DIP original experiment: DIP-255678X Nature structural & molecular biology 2013 IMEx Structure and RNA-binding properties of the Not1-Not2-Not5 module of the yeast Ccr4-Not complex. Bhaskar V., Roudko V., Basquin J., Sharma K., Urlaub H., Séraphin B., Conti E. Only protein-protein interactions imex curation not5_yeast General negative regulator of transcription subunit 5 NOT5 YP9499.27 YPR072W protein protein yeast Saccharomyces cerevisiae Baker's yeast MSQRKLQQDIDKLLKKVKEGIEDFDDIYEKFQSTDPSNSSHREKLESDLKREIKKLQKHRDQIKTWLSKEDVKDKQSVLMTNRRLIENGMERFKSVEKLMKTKQFSKEALTNPDIIKDPKELKKRDQVLFIHDCLDELQKQLEQYEAQENEEQTERHEFHIANLENILKKLQNNEMDPEPVEEFQDDIKYYVENNDDPDFIEYDTIYEDMGCEIQPSSSNNEAPKEGNNQTSLSSIRSSKKQERSPKKKAPQRDVSISDRATTPIAPGVESASQSISSTPTPVSTDTPLHTVKDDSIKFDNSTLGTPTTHVSMKKKESENDSEQQLNFPPDRTDEIRKTIQHDVETNAAFQNPLFNDELKYWLDSKRYLMQPLQEMSPKMVSQLESSLLNCPDSLDADSPCLYTKPLSLPHPTSIFFPNEPIRFVYPYDVPLNLTNNENDTDNKFGKDSKAKSKKDDDIYSRTSLARIFMKFDLDTLFFIFYHYQGSYEQFLAARELFKNRNWLFNKVDRCWYYKEIEKLPPGMGKSEEESWRYFDYKKSWLARRCGNDFVYNEEDFEKL 073137119B3E92BC 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 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 pop2_yeast Poly(A) ribonuclease POP2 POP2 CAF1 YNR052C N3470 CCR4-associated factor 1 protein protein yeast Saccharomyces cerevisiae Baker's yeast MQSMNVQPRVLAVGGEQFFSQRQASEQHQQQNMGPQVYSPKVNRARMFPQGMPVNTINGSVNQEMNNAYLLKQKNEPLLTQQQQQQQQQQQPFNIGTPVSVASLPPGLNVLQQQQQQQQQQQQQQQGVGLNRPLASQLPKHLTNQSMPPIFLPPPNYLFVRDVWKSNLYSEFAVIRQLVSQYNHVSISTEFVGTLARPIGTFRSKVDYHYQTMRANVDFLNPIQLGLSLSDANGNKPDNGPSTWQFNFEFDPKKEIMSTESLELLRKSGINFEKHENLGIDVFEFSQLLMDSGLMMDDSVTWITYHAAYDLGFLINILMNDSMPNNKEDFEWWVHQYMPNFYDLNLVYKIIQEFKNPQLQQSSQQQQQQQYSLTTLADELGLPRFSIFTTTGGQSLLMLLSFCQLSKLSMHKFPNGTDFAKYQGVIYGIDGDQ F3CAF97106A65933 not3_yeast General negative regulator of transcription subunit 3 NOT3 YIL038C protein protein yeast Saccharomyces cerevisiae Baker's yeast MAHRKLQQEVDRVFKKINEGLEIFNSYYERHESCTNNPSQKDKLESDLKREVKKLQRLREQIKSWQSSPDIKDKDSLLDYRRSVEIAMEKYKAVEKASKEKAYSNISLKKSETLDPQERERRDISEYLSQMIDELERQYDSLQVEIDKLLLLNKKKKTSSTTNDEKKEQYKRFQARYRWHQQQMELALRLLANEELDPQDVKNVQDDINYFVESNQDPDFVEDETIYDGLNLQSNEAIAHEVAQYFASQNAEDNNTSDANESLQDISKLSKKEQRKLEREAKKAAKLAAKNATGAAIPVAGPSSTPSPVIPVADASKETERSPSSSPIHNATKPEEAVKTSIKSPRSSADNLLPSLQKSPSSATPETPTNVHTHIHQTPNGITGATTLKPATLPAKPAGELKWAVAASQAVEKDRKVTSASSTISNTSTKTPTTAAATTTSSNANSRIGSALNTPKLSTSSLSLQPDNTGASSSAATAAAVLAAGAAAVHQNNQAFYRNMSSSHHPLVSLATNPKSEHEVATTVNQNGPENTTKKVMEQKEEESPEERNKLQVPTFGVFDDDFESDRDSETEPEEEEQPSTPKYLSLEQREAKTNEIKKEFVSDFETLLLPSGVQEFIMSSELYNSQIESKITYKRSRDMCEISRLVEVPQGVNPPSPLDAFRSTQQWDVMRCSLRDIIIGSERLKEDSSSIYAKILENFRTLEMFSLFYNYYFAITPLEREIAYKILNERDWKVSKDGTMWFLRQGEVKFFNEICEVGDYKIFKLDDWTVIDKINFRLDYSFLQPPVDTASEVRDVSVDNNNVNDQSNVTLEQQKQEISHGKQLLKQLKQGKISV 69B76694FCC6846F not1-not2-1 3259321 N/A 3259330 unspecified role unspecified role unspecified role unspecified role Region 298-560 Region 298-560 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli N/A 3259331 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3259332 unspecified role unspecified role unspecified role unspecified role Region 1541-2093 Region 1541-2093 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli physical association physical association false false false not2-not5-1 3259322 N/A 3259330 unspecified role unspecified role prey prey Region 405-560 Region 405-560 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli N/A 3259331 unspecified role unspecified role bait bait Region 76-191 Region 76-191 sufficient to bind sufficient binding region sufficient to bind 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 ecolx Escherichia coli direct interaction direct interaction false false false not1-not2-2 3259323 N/A 3259330 unspecified role unspecified role prey prey Region 298-560 Region 298-560 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli N/A 3259331 unspecified role unspecified role prey prey ecolx Escherichia coli N/A 3259332 unspecified role unspecified role bait bait Region 1541-2093 Region 1541-2093 sufficient to bind sufficient binding region sufficient to bind 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 ecolx Escherichia coli association association false false false not1-not2-3 3259324 N/A 3259333 unspecified role unspecified role prey prey VSV-tag VSV-tag vsv tag vsv tag vesicular stomatitis virus tag vesicular stomatitis virus tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast N/A 3259331 unspecified role unspecified role prey prey HA-tag HA-tag ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast N/A 3259332 unspecified role unspecified role bait bait TAP-tag TAP-tag tandem tag tandem tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast association association false false false not1-pop2-1 3259325 N/A 3259333 unspecified role unspecified role prey prey VSV-tag VSV-tag vsv tag vsv tag vesicular stomatitis virus tag vesicular stomatitis virus tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast N/A 3259332 unspecified role unspecified role bait bait TAP-tag TAP-tag tandem tag tandem tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast physical association physical association false false false not3-not2-1 3259326 N/A 3259331 unspecified role unspecified role prey prey HA-tag HA-tag ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast N/A 3259334 unspecified role unspecified role bait bait TAP-tag TAP-tag tandem tag tandem tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast physical association physical association false false false not1-not2-4 3259327 N/A 3259330 unspecified role unspecified role unspecified role unspecified role Region 298-560 Region 298-560 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli N/A 3259331 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3259332 unspecified role unspecified role unspecified role unspecified role Region 1541-2093 Region 1541-2093 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli physical association physical association false false false not1-not2-5 3259328 N/A 3259331 unspecified role unspecified role prey prey HA-tag HA-tag ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast N/A 3259334 unspecified role unspecified role prey prey VSV-tag VSV-tag vsv tag vsv tag vesicular stomatitis virus tag vesicular stomatitis virus tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast N/A 3259332 unspecified role unspecified role bait bait P25655:p.[Arg1811Glu;Leu1814Glu] R1811E/L1814E mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength substitut analysis substitution analysis substitut analysis certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false P25655:p.Phe1751Glu F1751E mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength substitut analysis substitution analysis substitut analysis certain certain sequence position certain certain certain sequence position certain false TAP-tag TAP-tag tandem tag tandem tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast association association false false false not1-not2-6 3259329 N/A 3259331 unspecified role unspecified role prey prey HA-tag HA-tag ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast N/A 3259332 unspecified role unspecified role bait bait TAP-tag TAP-tag tandem tag tandem tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false P25655:p.[Arg1811Glu;Leu1814Glu] R1811E/L1814E mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength substitut analysis substitution analysis substitut analysis certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false P25655:p.Phe1751Glu F1751E mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength substitut analysis substitution analysis substitut analysis certain certain sequence position certain certain certain sequence position certain false yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast physical association physical association false false false