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/ bertolaet-2001-1 yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 2 hybrid two hybrid 2H 2h Gal4 transcription regeneration two-hybrid yeast two hybrid 2-hybrid classical two hybrid classical two hybrid 2H two-hybrid 2-hybrid Gal4 transcription regeneration 2h yeast two hybrid Y2H Y-2H 2 hybrid predetermined predetermined participant predetermined Bertolaet BL., Clarke DJ., Wolff M., Watson MH., Henze M., Divita G., Reed SI. DIP original experiment: DIP-262964X Nature structural biology 2001 IMEx UBA domains of DNA damage-inducible proteins interact with ubiquitin. Bertolaet BL., Clarke DJ., Wolff M., Watson MH., Henze M., Divita G., Reed SI. Only protein-protein interactions imex curation bertolaet-2001-2 in vitro In vitro molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column predetermined predetermined participant predetermined Bertolaet BL., Clarke DJ., Wolff M., Watson MH., Henze M., Divita G., Reed SI. DIP original experiment: DIP-262969X Nature structural biology 2001 IMEx UBA domains of DNA damage-inducible proteins interact with ubiquitin. Bertolaet BL., Clarke DJ., Wolff M., Watson MH., Henze M., Divita G., Reed SI. Only protein-protein interactions imex curation bertolaet-2001-3 yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 2 hybrid two hybrid 2H 2h Gal4 transcription regeneration two-hybrid yeast two hybrid 2-hybrid classical two hybrid classical two hybrid 2H two-hybrid 2-hybrid Gal4 transcription regeneration 2h yeast two hybrid Y2H Y-2H 2 hybrid predetermined predetermined participant predetermined Bertolaet BL., Clarke DJ., Wolff M., Watson MH., Henze M., Divita G., Reed SI. DIP original experiment: DIP-262974X Nature structural biology 2001 IMEx UBA domains of DNA damage-inducible proteins interact with ubiquitin. Bertolaet BL., Clarke DJ., Wolff M., Watson MH., Henze M., Divita G., Reed SI. Only protein-protein interactions imex curation bertolaet-2001-4 yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 2 hybrid two hybrid 2H 2h Gal4 transcription regeneration two-hybrid yeast two hybrid 2-hybrid classical two hybrid classical two hybrid 2H two-hybrid 2-hybrid Gal4 transcription regeneration 2h yeast two hybrid Y2H Y-2H 2 hybrid predetermined predetermined participant predetermined Bertolaet BL., Clarke DJ., Wolff M., Watson MH., Henze M., Divita G., Reed SI. DIP original experiment: DIP-262978X Nature structural biology 2001 IMEx UBA domains of DNA damage-inducible proteins interact with ubiquitin. Bertolaet BL., Clarke DJ., Wolff M., Watson MH., Henze M., Divita G., Reed SI. Only protein-protein interactions imex curation bertolaet-2001-5 yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 2 hybrid two hybrid 2H 2h Gal4 transcription regeneration two-hybrid yeast two hybrid 2-hybrid classical two hybrid classical two hybrid 2H two-hybrid 2-hybrid Gal4 transcription regeneration 2h yeast two hybrid Y2H Y-2H 2 hybrid predetermined predetermined participant predetermined Bertolaet BL., Clarke DJ., Wolff M., Watson MH., Henze M., Divita G., Reed SI. DIP original experiment: DIP-262965X Nature structural biology 2001 IMEx UBA domains of DNA damage-inducible proteins interact with ubiquitin. Bertolaet BL., Clarke DJ., Wolff M., Watson MH., Henze M., Divita G., Reed SI. Only protein-protein interactions imex curation bertolaet-2001-6 yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 2 hybrid two hybrid 2H 2h Gal4 transcription regeneration two-hybrid yeast two hybrid 2-hybrid classical two hybrid classical two hybrid 2H two-hybrid 2-hybrid Gal4 transcription regeneration 2h yeast two hybrid Y2H Y-2H 2 hybrid predetermined predetermined participant predetermined Bertolaet BL., Clarke DJ., Wolff M., Watson MH., Henze M., Divita G., Reed SI. DIP original experiment: DIP-262975X Nature structural biology 2001 IMEx UBA domains of DNA damage-inducible proteins interact with ubiquitin. Bertolaet BL., Clarke DJ., Wolff M., Watson MH., Henze M., Divita G., Reed SI. Only protein-protein interactions imex curation bertolaet-2001-7 in vitro In vitro pull down pull down weight by staining molecular weight estimation by staining weight by staining Bertolaet BL., Clarke DJ., Wolff M., Watson MH., Henze M., Divita G., Reed SI. DIP original experiment: DIP-262970X Nature structural biology 2001 IMEx UBA domains of DNA damage-inducible proteins interact with ubiquitin. Bertolaet BL., Clarke DJ., Wolff M., Watson MH., Henze M., Divita G., Reed SI. Only protein-protein interactions imex curation bertolaet-2001-8 yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast pull down pull down predetermined predetermined participant predetermined Bertolaet BL., Clarke DJ., Wolff M., Watson MH., Henze M., Divita G., Reed SI. DIP original experiment: DIP-262966X Nature structural biology 2001 IMEx UBA domains of DNA damage-inducible proteins interact with ubiquitin. Bertolaet BL., Clarke DJ., Wolff M., Watson MH., Henze M., Divita G., Reed SI. Only protein-protein interactions imex curation bertolaet-2001-9 yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 2 hybrid two hybrid 2H 2h Gal4 transcription regeneration two-hybrid yeast two hybrid 2-hybrid classical two hybrid classical two hybrid 2H two-hybrid 2-hybrid Gal4 transcription regeneration 2h yeast two hybrid Y2H Y-2H 2 hybrid predetermined predetermined participant predetermined Bertolaet BL., Clarke DJ., Wolff M., Watson MH., Henze M., Divita G., Reed SI. DIP original experiment: DIP-262976X Nature structural biology 2001 IMEx UBA domains of DNA damage-inducible proteins interact with ubiquitin. Bertolaet BL., Clarke DJ., Wolff M., Watson MH., Henze M., Divita G., Reed SI. Only protein-protein interactions imex curation bertolaet-2001-10 in vitro In vitro pull down pull down weight by staining molecular weight estimation by staining weight by staining Bertolaet BL., Clarke DJ., Wolff M., Watson MH., Henze M., Divita G., Reed SI. DIP original experiment: DIP-262971X Nature structural biology 2001 IMEx UBA domains of DNA damage-inducible proteins interact with ubiquitin. Bertolaet BL., Clarke DJ., Wolff M., Watson MH., Henze M., Divita G., Reed SI. Only protein-protein interactions imex curation bertolaet-2001-11 in vitro In vitro fluorescence spectr classical fluorescence spectroscopy fluorescence spectr predetermined predetermined participant predetermined Bertolaet BL., Clarke DJ., Wolff M., Watson MH., Henze M., Divita G., Reed SI. DIP original experiment: DIP-262972X Nature structural biology 2001 IMEx UBA domains of DNA damage-inducible proteins interact with ubiquitin. Bertolaet BL., Clarke DJ., Wolff M., Watson MH., Henze M., Divita G., Reed SI. Only protein-protein interactions imex curation bertolaet-2001-12 yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast pull down pull down western blot western blot Immuno blot Immuno blot Bertolaet BL., Clarke DJ., Wolff M., Watson MH., Henze M., Divita G., Reed SI. DIP original experiment: DIP-262967X Nature structural biology 2001 IMEx UBA domains of DNA damage-inducible proteins interact with ubiquitin. Bertolaet BL., Clarke DJ., Wolff M., Watson MH., Henze M., Divita G., Reed SI. Only protein-protein interactions imex curation bertolaet-2001-13 yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 2 hybrid two hybrid 2H 2h Gal4 transcription regeneration two-hybrid yeast two hybrid 2-hybrid classical two hybrid classical two hybrid 2H two-hybrid 2-hybrid Gal4 transcription regeneration 2h yeast two hybrid Y2H Y-2H 2 hybrid predetermined predetermined participant predetermined Bertolaet BL., Clarke DJ., Wolff M., Watson MH., Henze M., Divita G., Reed SI. DIP original experiment: DIP-262977X Nature structural biology 2001 IMEx UBA domains of DNA damage-inducible proteins interact with ubiquitin. Bertolaet BL., Clarke DJ., Wolff M., Watson MH., Henze M., Divita G., Reed SI. Only protein-protein interactions imex curation bertolaet-2001-14 in vitro In vitro molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column predetermined predetermined participant predetermined Bertolaet BL., Clarke DJ., Wolff M., Watson MH., Henze M., Divita G., Reed SI. DIP original experiment: DIP-262968X Nature structural biology 2001 IMEx UBA domains of DNA damage-inducible proteins interact with ubiquitin. Bertolaet BL., Clarke DJ., Wolff M., Watson MH., Henze M., Divita G., Reed SI. Only protein-protein interactions imex curation bertolaet-2001-15 in vitro In vitro fluorescence spectr classical fluorescence spectroscopy fluorescence spectr predetermined predetermined participant predetermined Bertolaet BL., Clarke DJ., Wolff M., Watson MH., Henze M., Divita G., Reed SI. DIP original experiment: DIP-262973X Nature structural biology 2001 IMEx UBA domains of DNA damage-inducible proteins interact with ubiquitin. Bertolaet BL., Clarke DJ., Wolff M., Watson MH., Henze M., Divita G., Reed SI. Only protein-protein interactions imex curation ubiq_yeast Ubiquitin UBI1 RPL40A YIL148W UBI2 RPL40B YKR094C UBI3 RPS31 YLR167W L9470.14 UBI4 SCD2 YLL039C protein protein yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG obsolete protein ddi1_yeast DNA damage-inducible protein 1 DDI1 v-SNARE-master 1 VSM1 YER143W protein protein yeast Saccharomyces cerevisiae Baker's yeast MDLTISNELTGEIYGPIEVSEDMALTDLIALLQADCGFDKTKHDLYYNMDILDSNRTQSLKELGLKTDDLLLIRGKISNSIQTDAATLSDEAFIEQFRQELLNNQMLRSQLILQIPGLNDLVNDPLLFRERLGPLILQRRYGGYNTAMNPFGIPQDEYTRLMANPDDPDNKKRIAELLDQQAIDEQLRNAIEYTPEMFTQVPMLYINIEINNYPVKAFVDTGAQTTIMSTRLAKKTGLSRMIDKRFIGEARGVGTGKIIGRIHQAQVKIETQYIPCSFTVLDTDIDVLIGLDMLKRHLACVDLKENVLRIAEVETSFLSEAEIPKSFQEGLPAPTSVTTSSDKPLTPTKTSSTLPPQPGAVPALAPRTGMGPTPTGRSTAGATTATGRTFPEQTIKQLMDLGFPRDAVVKALKQTNGNAEFAASLLFQ B43425B029B7658B rad23_yeast UV excision repair protein RAD23 SYGP-ORF29 YEL037C RAD23 protein protein yeast Saccharomyces cerevisiae Baker's yeast MVSLTFKNFKKEKVPLDLEPSNTILETKTKLAQSISCEESQIKLIYSGKVLQDSKTVSECGLKDGDQVVFMVSQKKSTKTKVTEPPIAPESATTPGRENSTEASPSTDASAAPAATAPEGSQPQEEQTATTERTESASTPGFVVGTERNETIERIMEMGYQREEVERALRAAFNNPDRAVEYLLMGIPENLRQPEPQQQTAAAAEQPSTAATTAEQPAEDDLFAQAAQGGNASSGALGTTGGATDAAQGGPPGSIGLTVEDLLSLRQVVSGNPEALAPLLENISARYPQLREHIMANPEVFVSMLLEAVGDNMQDVMEGADDMVEGEDIEVTGEAAAAGLGQGEGEGSFQVDYTPEDDQAISRLCELGFERDLVIQVYFACDKNEEAAANILFSDHAD B3F0436DAB60B833 ub-ddi1-1 3135526 N/A 3135541 unspecified role unspecified role bait bait yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast N/A 3135542 unspecified role unspecified role prey prey UBA UBA Domain/necessary required to bind necessary binding region required to bind deletion analysis deletion 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 rad23-ub-1 3135527 N/A 3135543 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3135541 unspecified role unspecified role unspecified role unspecified role yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast direct interaction direct interaction false false false ub-ddi1-2 3135528 N/A 3135541 unspecified role unspecified role bait bait yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast N/A 3135542 unspecified role unspecified role prey prey UBA UBA Domain/sufficient sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion 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 ub-ddi1-3 3135529 N/A 3135541 unspecified role unspecified role bait bait yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast N/A 3135542 unspecified role unspecified role prey prey P40087:p.Lys413Ile K413I Mutation mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing substitut analysis substitution analysis substitut analysis certain certain sequence position certain certain certain sequence position certain false P40087:p.Gly417Arg G417R Mutation mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing substitut analysis substitution analysis substitut analysis certain certain sequence position certain certain certain sequence position certain false P40087:p.Gly417Val G417V Mutation mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing 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 ub-rad23-1 3135530 N/A 3135543 unspecified role unspecified role prey prey 78-354 binding region 78-354 binding region sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain false yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast N/A 3135541 unspecified role unspecified role bait bait yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast physical association physical association false false false ub-ddi1-4 3135531 N/A 3135541 unspecified role unspecified role bait bait yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast N/A 3135542 unspecified role unspecified role prey prey P40087:p.Leu426Ala L426A Mutation mutation disrupting mutation disrupting interaction mutation disrupting substitut analysis substitution analysis substitut analysis certain certain sequence position certain certain certain sequence position certain false P40087:p.Val408Leu V408L Mutation mutation disrupting mutation disrupting interaction mutation disrupting substitut analysis substitution analysis substitut analysis certain certain sequence position certain certain certain sequence position certain false P40087:p.Ala407Leu V403E Mutation mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction substitut analysis substitution analysis substitut analysis certain certain sequence position certain certain certain sequence position certain false P40087:p.Leu412Pro L412P Mutation mutation disrupting mutation disrupting interaction mutation disrupting substitut analysis substitution analysis substitut analysis certain certain sequence position certain certain certain sequence position certain false P40087:p.Leu426His L426H Mutation mutation disrupting mutation disrupting interaction mutation disrupting 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 ddi1-ub-1 3135532 N/A 3135541 unspecified role unspecified role prey prey yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast N/A 3135542 unspecified role unspecified role bait bait His Tag His Tag ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag predetermined featur predetermined feature predetermined featur undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecolx Escherichia coli physical association physical association false false false ub-ddi1-5 3135533 N/A 3135541 unspecified role unspecified role bait bait GST Tag GST Tag gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag predetermined featur predetermined feature predetermined featur n-terminal n-terminal position amino-terminus n-terminus n-term n-term amino-terminus n-terminus n-terminal n-terminal n-terminal position amino-terminus n-terminus n-term n-term amino-terminus n-terminus n-terminal false yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast N/A 3135542 unspecified role unspecified role prey prey yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast physical association physical association false false false ub-rad23-2 3135534 N/A 3135543 unspecified role unspecified role prey prey P32628:p.Leu183Ala L183A Mutation mutation disrupting mutation disrupting interaction mutation disrupting 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 N/A 3135541 unspecified role unspecified role bait bait yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast physical association physical association false false false rad23-ub-2 3135535 N/A 3135543 unspecified role unspecified role bait bait His Tag His Tag ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag predetermined featur predetermined feature predetermined featur undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecolx Escherichia coli N/A 3135541 unspecified role unspecified role prey prey yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast direct interaction direct interaction false false false ddi1-ub-2 3135536 N/A 3135541 unspecified role unspecified role unspecified role unspecified role Dansyl Label Dansyl Label dansyl label dansyl label 5-dimethylaminonaphthalene-1-sulfonyl tag dansyl tag 5-dimethylaminonaphthalene-1-sulfonyl tag predetermined featur predetermined feature predetermined featur c-terminal c-terminal position c-term carboxy-terminus c-terminus c-term c-terminus carboxy-terminus c-terminal c-terminal c-terminal position c-term carboxy-terminus c-terminus c-term c-terminus carboxy-terminus c-terminal false yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast N/A 3135542 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli direct interaction direct interaction false false false ub-rad23-3 3135537 N/A 3135543 unspecified role unspecified role prey prey yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast N/A 3135541 unspecified role unspecified role bait bait GST Tag GST Tag gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag predetermined featur predetermined feature predetermined featur n-terminal n-terminal position amino-terminus n-terminus n-term n-term amino-terminus n-terminus n-terminal n-terminal n-terminal position amino-terminus n-terminus n-term n-term amino-terminus n-terminus n-terminal false yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast physical association physical association false false false ub-rad23-4 3135538 N/A 3135543 unspecified role unspecified role prey prey P32628:p.Leu392Ala L392A Mutation mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing 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 N/A 3135541 unspecified role unspecified role bait bait yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast physical association physical association false false false ddi1-ub-3 3135539 N/A 3135541 unspecified role unspecified role unspecified role unspecified role yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast N/A 3135542 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli direct interaction direct interaction false false false rad23-ub-3 3135540 N/A 3135543 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3135541 unspecified role unspecified role unspecified role unspecified role Dansyl Label Dansyl Label dansyl label dansyl label 5-dimethylaminonaphthalene-1-sulfonyl tag dansyl tag 5-dimethylaminonaphthalene-1-sulfonyl tag predetermined featur predetermined feature predetermined featur c-terminal c-terminal position c-term carboxy-terminus c-terminus c-term c-terminus carboxy-terminus c-terminal c-terminal c-terminal position c-term carboxy-terminus c-terminus c-term c-terminus carboxy-terminus c-terminal false yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast direct interaction direct interaction false false false