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/ nowicka-2015-1 in vitro In vitro pull down pull down predetermined predetermined participant predetermined Nowicka U., Zhang D., Walker O., Krutauz D., Castañeda CA., Chaturvedi A., Chen TY., Reis N., Glickman MH., Fushman D. DIP original experiment: DIP-264830X Structure (London, England : 1993) 2015 IMEx DNA-damage-inducible 1 protein (Ddi1) contains an uncharacteristic ubiquitin-like domain that binds ubiquitin. Nowicka U., Zhang D., Walker O., Krutauz D., Castañeda CA., Chaturvedi A., Chen TY., Reis N., Glickman MH., Fushman D. Only protein-protein interactions imex curation nowicka-2015-2 in vitro In vitro nmr nuclear magnetic resonance NMR NMR nmr predetermined predetermined participant predetermined Nowicka U., Zhang D., Walker O., Krutauz D., Castañeda CA., Chaturvedi A., Chen TY., Reis N., Glickman MH., Fushman D. DIP original experiment: DIP-264832X Structure (London, England : 1993) 2015 IMEx DNA-damage-inducible 1 protein (Ddi1) contains an uncharacteristic ubiquitin-like domain that binds ubiquitin. Nowicka U., Zhang D., Walker O., Krutauz D., Castañeda CA., Chaturvedi A., Chen TY., Reis N., Glickman MH., Fushman D. Only protein-protein interactions imex curation nowicka-2015-3 in vitro In vitro nmr nuclear magnetic resonance NMR NMR nmr predetermined predetermined participant predetermined Nowicka U., Zhang D., Walker O., Krutauz D., Castañeda CA., Chaturvedi A., Chen TY., Reis N., Glickman MH., Fushman D. DIP original experiment: DIP-264828X Structure (London, England : 1993) 2015 IMEx DNA-damage-inducible 1 protein (Ddi1) contains an uncharacteristic ubiquitin-like domain that binds ubiquitin. Nowicka U., Zhang D., Walker O., Krutauz D., Castañeda CA., Chaturvedi A., Chen TY., Reis N., Glickman MH., Fushman D. Only protein-protein interactions imex curation nowicka-2015-4 in vitro In vitro nmr nuclear magnetic resonance NMR NMR nmr predetermined predetermined participant predetermined Nowicka U., Zhang D., Walker O., Krutauz D., Castañeda CA., Chaturvedi A., Chen TY., Reis N., Glickman MH., Fushman D. DIP original experiment: DIP-264829X Structure (London, England : 1993) 2015 IMEx DNA-damage-inducible 1 protein (Ddi1) contains an uncharacteristic ubiquitin-like domain that binds ubiquitin. Nowicka U., Zhang D., Walker O., Krutauz D., Castañeda CA., Chaturvedi A., Chen TY., Reis N., Glickman MH., Fushman D. Only protein-protein interactions imex curation nowicka-2015-5 in vitro In vitro pull down pull down western blot western blot Immuno blot Immuno blot Nowicka U., Zhang D., Walker O., Krutauz D., Castañeda CA., Chaturvedi A., Chen TY., Reis N., Glickman MH., Fushman D. DIP original experiment: DIP-264831X Structure (London, England : 1993) 2015 IMEx DNA-damage-inducible 1 protein (Ddi1) contains an uncharacteristic ubiquitin-like domain that binds ubiquitin. Nowicka U., Zhang D., Walker O., Krutauz D., Castañeda CA., Chaturvedi A., Chen TY., Reis N., Glickman MH., Fushman D. Only protein-protein interactions imex curation nowicka-2015-6 in vitro In vitro sans small angle neutron scattering SANS SANS sans predetermined predetermined participant predetermined Nowicka U., Zhang D., Walker O., Krutauz D., Castañeda CA., Chaturvedi A., Chen TY., Reis N., Glickman MH., Fushman D. DIP original experiment: DIP-264833X Structure (London, England : 1993) 2015 IMEx DNA-damage-inducible 1 protein (Ddi1) contains an uncharacteristic ubiquitin-like domain that binds ubiquitin. Nowicka U., Zhang D., Walker O., Krutauz D., Castañeda CA., Chaturvedi A., Chen TY., Reis N., Glickman MH., Fushman D. Only protein-protein interactions imex curation ubiq_human UBIQ_HUMAN protein protein human Homo sapiens Human MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG ddi1_yeast DNA damage-inducible protein 1 DDI1 v-SNARE-master 1 VSM1 YER143W protein protein yeast Saccharomyces cerevisiae Baker's yeast MDLTISNELTGEIYGPIEVSEDMALTDLIALLQADCGFDKTKHDLYYNMDILDSNRTQSLKELGLKTDDLLLIRGKISNSIQTDAATLSDEAFIEQFRQELLNNQMLRSQLILQIPGLNDLVNDPLLFRERLGPLILQRRYGGYNTAMNPFGIPQDEYTRLMANPDDPDNKKRIAELLDQQAIDEQLRNAIEYTPEMFTQVPMLYINIEINNYPVKAFVDTGAQTTIMSTRLAKKTGLSRMIDKRFIGEARGVGTGKIIGRIHQAQVKIETQYIPCSFTVLDTDIDVLIGLDMLKRHLACVDLKENVLRIAEVETSFLSEAEIPKSFQEGLPAPTSVTTSSDKPLTPTKTSSTLPPQPGAVPALAPRTGMGPTPTGRSTAGATTATGRTFPEQTIKQLMDLGFPRDAVVKALKQTNGNAEFAASLLFQ B43425B029B7658B ufo1_yeast Ubiquitin ligase complex F-box protein UFO1 UFO1 YML088W protein protein yeast Saccharomyces cerevisiae Baker's yeast MERPGLVLQDLPPEILINIFSHLDEKDLFTLQELSTHFRNLIHDEELWKNLFKSRVHTTHFPTFSQSSKFSVEYIERTRGLHHWQHNKAIRTKYTIIPTRNWDQPSIERIVFDYPRVAAYNDGTITILQLQNHKRQKKFKKLIYIPCTTPQGCSTMDFNINAAVFGRFDGRVFGKLLSNKSYLTPVMEFTGRHSAGVTAICNSESWDTSREDWSVSGSENGEIIWWCENKLVKMWKVSNRVIWKLAFFKDWTLIMDDEKLYIIHQMQELHSIDIPKDLDEQPMRVRFFKMDFGSMTLVLADLNNVYTISVNPNGNFGNLRKLEMPEQICAVEIDEKTSQREQNWQFAGDDGCYISLLTTQNTLYIINIRDLSSSGLKVQCKISFDEQVYVSQVTNLIVVVALPNVLQILNAMTGELIKTVLKTEKFPEFLKVSQDKIIMGSGNVLNYLKFVSSDSKKHHHSTKGKNTVSNKWNETLNTELQYYDEDEDLRRKRQSEISRLIDAYGGDLELSGDTDEENDIQLRIALLESQEAQARNQAEAGEPVGDDEDEQLRRALEESQLIYETQTNSSANHGNNTNDEIDEDDEEFLRAIRQSRVEDERRRHLRNHTTGRRNGPLSDDNFATYGAAESSERTSTENTIGSSVGVDASNNVDEDLQLAIALSLSEIN 10CA467CF9417FBC yub Ubiquitin protein protein yeast Saccharomyces cerevisiae Baker's yeast MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG This sequence has been withdrawn from Uniprot. hub-ddi1-1 3275905 N/A 3275911 unspecified role unspecified role bait bait His-tag His-tag his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag 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 ecolx Escherichia coli N/A 3275912 unspecified role unspecified role prey prey Region 2-80 Region 2-80 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false His-tag His-tag his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-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 hub-ufo1-1 3275906 N/A 3275913 unspecified role unspecified role unspecified role unspecified role Region 547-668 Region 547-668 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 3275911 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli direct interaction direct interaction false false false ddi1-hub-1 3275907 N/A 3275911 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3275912 unspecified role unspecified role unspecified role unspecified role Region 389-428 Region 389-428 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli direct interaction direct interaction false false false ddi1-hub-2 3275908 N/A 3275911 unspecified role unspecified role unspecified role unspecified role lys6ala,arg42ala,arg72ala K6A/R42A/R72A mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength alanine scanning alanine scanning certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false lys6glu,arg42glu,arg72glu K6E/R42E/R72E 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 certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli N/A 3275912 unspecified role unspecified role unspecified role unspecified role Region 2-80 Region 2-80 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli direct interaction direct interaction false false false ddi1-yub-1 3275909 N/A 3275914 unspecified role unspecified role prey prey yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast N/A 3275912 unspecified role unspecified role bait bait Region 2-80 Region 2-80 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false His-tag His-tag his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecolx Escherichia coli physical association physical association false false false ddi1-hub-3 3275910 N/A 3275911 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3275912 unspecified role unspecified role unspecified role unspecified role Region 2-80 Region 2-80 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli direct interaction direct interaction false false false