IntAct European Bioinformatics Institute IntAct intact http://www.ebi.ac.uk/ http://www.ebi.ac.uk/intact/query/${ac} EBI-[0-9]+|IA:[0-9]+ INTerAction database (IntAct) provides an open source database and toolkit for the storage, presentation and analysis of molecular interactions. http://www.ebi.ac.uk/intact European Bioinformatics Institute; Wellcome Trust Genome Campus; Hinxton, Cambridge; CB10 1SD; United Kingdom http://www.ebi.ac.uk/intact/ http://www.ebi.ac.uk/ zhang-2008c-2 Arabidopsis DDB1-CUL4 ASSOCIATED FACTOR1 forms a nuclear E3 ubiquitin ligase with DDB1 and CUL4 that is involved in multiple plant developmental processes. arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress anti tag coip anti tag coimmunoprecipitation anti tag coip western blot western blot Immuno blot Immuno blot Zhang Y., Feng S., Chen F., Chen H., Wang J., McCall C., Xiong Y., Deng XW. Transgenic Arabidopsis (ecotype Columbia) expressing FLAG tagged DCAF1 protein were used in this study. xingwang.deng@yale.edu. Plant Cell (1040-4651) 2008 Only protein-protein interactions imex curation zhang-2008c-3 Arabidopsis DDB1-CUL4 ASSOCIATED FACTOR1 forms a nuclear E3 ubiquitin ligase with DDB1 and CUL4 that is involved in multiple plant developmental processes. arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress anti bait coip anti bait coimmunoprecipitation anti bait coip anti tag western anti tag western blot anti tag western Zhang Y., Feng S., Chen F., Chen H., Wang J., McCall C., Xiong Y., Deng XW. Transgenic Arabidopsis (ecotype Columbia) expressing FLAG tagged DCAF1 protein were used in this study. xingwang.deng@yale.edu. Plant Cell (1040-4651) 2008 Only protein-protein interactions imex curation zhang-2008c-1 Arabidopsis DDB1-CUL4 ASSOCIATED FACTOR1 forms a nuclear E3 ubiquitin ligase with DDB1 and CUL4 that is involved in multiple plant developmental processes. 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 Zhang Y., Feng S., Chen F., Chen H., Wang J., McCall C., Xiong Y., Deng XW. xingwang.deng@yale.edu. Plant Cell (1040-4651) 2008 Only protein-protein interactions imex curation zhang-2008c-4 Arabidopsis DDB1-CUL4 ASSOCIATED FACTOR1 forms a nuclear E3 ubiquitin ligase with DDB1 and CUL4 that is involved in multiple plant developmental processes. arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress anti bait coip anti bait coimmunoprecipitation anti bait coip western blot western blot Immuno blot Immuno blot Zhang Y., Feng S., Chen F., Chen H., Wang J., McCall C., Xiong Y., Deng XW. Antibodies used to detect CSN5, CSN6 and CSN7 in this paper will cross-react with isoforms CSN5A or CASN5B, CSN6A or CSN6B or CSN7i or CSN7ii. Due to the lack of specificity of the antibodies used , the correct isoform of the protein could not be unambiguously identified. Therefore interactions involving these proteins were not curated. xingwang.deng@yale.edu. Plant Cell (1040-4651) 2008 Only protein-protein interactions imex curation ddb1a_arath DNA damage-binding protein 1a DDB1A C6L9.100 At4g05420 UV-damaged DNA-binding protein 1a protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MSSWNYVVTAHKPTSVTHSCVGNFTSPQELNLIVAKCTRIEIHLLTPQGLQPMLDVPIYGRIATLELFRPHGEAQDFLFIATERYKFCVLQWDPESSELITRAMGDVSDRIGRPTDNGQIGIIDPDCRLIGLHLYDGLFKVIPFDNKGQLKEAFNIRLEELQVLDIKFLFGCAKPTIAVLYQDNKDARHVKTYEVSLKDKDFVEGPWSQNSLDNGADLLIPVPPPLCGVLIIGEETIVYCSASAFKAIPIRPSITKAYGRVDVDGSRYLLGDHAGMIHLLVITHEKEKVTGLKIELLGETSIASTISYLDNAVVFVGSSYGDSQLVKLNLHPDAKGSYVEVLERYINLGPIVDFCVVDLERQGQGQVVTCSGAFKDGSLRVVRNGIGINEQASVELQGIKGMWSLKSSIDEAFDTFLVVSFISETRILAMNLEDELEETEIEGFLSQVQTLFCHDAVYNQLVQVTSNSVRLVSSTTRELRDEWHAPAGFTVNVATANASQVLLATGGGHLVYLEIGDGKLTEVQHALLEYEVSCLDINPIGDNPNYSQLAAVGMWTDISVRIFSLPELTLITKEQLGGEIIPRSVLLCAFEGISYLLCALGDGHLLNFQMDTTTGQLKDRKKVSLGTQPITLRTFSSKSATHVFAASDRPTVIYSSNKKLLYSNVNLKEVSHMCPFNSAAFPDSLAIAREGELTIGTIDDIQKLHIRTIPLGEHARRICHQEQTRTFGICSLGNQSNSEESEMHFVRLLDDQTFEFMSTYPLDSFEYGCSILSCSFTEDKNVYYCVGTAYVLPEENEPTKGRILVFIVEDGRLQLIAEKETKGAVYSLNAFNGKLLAAINQKIQLYKWMLRDDGTRELQSECGHHGHILALYVQTRGDFIVVGDLMKSISLLLYKHEEGAIEERARDYNANWMSAVEILDDDIYLGAENNFNLLTVKKNSEGATDEERGRLEVVGEYHLGEFVNRFRHGSLVMRLPDSEIGQIPTVIFGTVNGVIGVIASLPQEQYTFLEKLQSSLRKVIKGVGGLSHEQWRSFNNEKRTAEARNFLDGDLIESFLDLSRNKMEDISKSMNVQVEELCKRVEELTRLH dcaf1_arath DDB1- and CUL4-associated factor homolog 1 At4g31160 DCAF1 Protein DDB1-CUL4 ASSOCIATED FACTOR 1 F6E21_80 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MDGQEHAEVPNSMVEDDQSVVAAEAIAELANSTGEPNPEEGEEQSVEDELIAKAQKLMEDITSVANNPNPNILHALSQLLESQESLFLEENGHFSNARGSHNSGKLCILIRENDEFFELISSTFLSENSYSTAVKAASARLLMNCSLTWMYPHVFDDAVTENFKNWVMEEAVKFPGEDSAKKEASDFEMLKTYSTGLLALSLASRGQIVEDVLTSGLSAKLMHYLRVRVLKEPSTSRIHTTETKHVSLKTKEEGRSRVRKIVDTVEGDHVLETDSGREMGQTDVQPDGEFEIDGRDVFNVSGVVDCKIKPGDDNSVRDDPSRHRLNRSKSRGRGRVHEGAPDTEVLLASPRLGRLLVRDRDLSKISDGRNAEDVTVCLGKMKSGIMEIEREDNDECFQGCIIGTKNITDLVKRAVGAAETEARAAHAPDDAAKAAGDAAAELVKTAALEEFKSSGSEEAAVSAATRAAITVIDAAEVSRNPTCVTSDQTTDVSEVSLPDIESLAQLQEKYCIQCLEILGEYVEVLGPVLHEKGVDVCIVLLERTSQLDDRSTVSPLLPDVMKLICALAAHRKFAAMFVERRGILKLLAVPRVSETFYGLSSCLYTIGSLQGIMERVCALPLVVIHQVVKLAIELLDCSQDQARKNSALFFAAAFVFRAILDAFDAQDSLQKLLAILKDAASVRTGANTDRSAPEVMTSSEKQMAFHTCFALRQYFRAHLLLLVDSIRPSRISRGGVPSSMKPNIRAAYKPLDISNEAVDAIFLQLQKDRRLGPTFVKAQWPAVNNFLASSGHVTMLELCQTPPVDRYLHDLLQYAFGVLHIVTSIPDGRKAIAHATLSNNRAGIAVILDAANISNSIVDPEIIQPALNVLINLVCPPPSLSNKPPLAQNHQPVPGQATTRPSTDVAVGTQSTGNAPQTPVAPASSGLVGDRRIFLGAGTGSAGLAAKLEQVYRQAREAVRGNDGIKILLKLLQPRIYVNPPATPDCLRALACRVLLGLARDDTIAQILTKLEVGKSLSELIRDSGGQSSGTDQGRWQAELAQVALELIGIVTNSGHATTLTASDAATPTLRRIERAAIAAATPITYDSKELLLLIHEHLQASGLGDTASALLKEAQLTPLPSSASPSSIAYSTTQEMSTPLAQEQWPSGRANSGFFTSKPKVCAHDEDPNSRSNAALSAKKKHLASSTLEMPTPVAQQQWPSGRANCGFCPSIPKINARDEDPSSRGNAAPSAKKKQLTFSPSFSSQSRKQSFSHDALPQSTQRINCCSNSDPALADTSETAAELVLKNDLDADAQFKTPISFPRKRKLSELRDSSVPGKRIDLGERRNSTFADGSGLQTPASALDANQSGSSRLGQMTPASQLRLPSDPQPSNPERLSLDSLVVQYLKHQHRQCLAPITTLPPVSLLHPHVCPEPKRLLEAPLNMTGRLGTRELQSFYSGVHGNRRDRQFVFSRFKSWRSFRDETALFTCIALLGGTNHIAVGSHAGEIKIFEASSGSMLESVSGHQAPVTLVQPYVSRDTQLLLSSSSSDVQLWDASSITGGPRHSFDGCKAAKFSNSGLQFAALSCEASRKDVLLYDVQTCSPCQKLTDTVTSSRSNPYSLVHFSPCDTLILWNGVLWDRRIPEKVRRFDQFTDYGGGGFHPSRNEVIINSEIWDMRTFKLLRSVPSLDQTAITFNSRGDVIYAMLRRNIEDVMSAVHTRRVKHPLFAAFRTLDAINYSDIATIPVDRCLLDFATEPTDSFLGLITMEDQEDMFSSARMYEIGRRRPTDDDSDPDDDDETEDEDEDDEEEDDLDRILGLAGDNSDSGDDDLSSEDNEDSVSDFDEEADILIDGDFMEELIEGENEDDGNGEDEDDDDDGEMQDFMSSGEEDDYRDNIRSS cul4_arath Cullin-4 CUL4 MDE13.3 At5g46210 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MSLPTKRSTFSAASASDDSSYSSPPMKKAKNDLHHSPQHPNTADKVVGFHMEEDPTPAAANLSRKKATLPQPTKKFVIKLNKAKPTLPTNFEENTWEKLQSAIRAIFLKKKISFDLESLYQAVDNLCLHKLDGKLYDQIEKECEEHISAALQSLVGQNTDLTVFLSRVEKCWQDFCDQMLMIRSIALTLDRKYVIQNPNVRSLWEMGLQLFRKHLSLAPEVEQRTVKGLLSMIEKERLAEAVNRTLLSHLLKMFTALGIYMESFEKPFLEGTSEFYAAEGMKYMQQSDVPEYLKHVEGRLHEENERCILYIDAVTRKPLITTVERQLLERHILVVLEKGFTTLMDGRRTEDLQRMQTLFSRVNALESLRQALSSYVRKTGQKIVMDEEKDKDMVQSLLDFKASLDIIWEESFYKNESFGNTIKDSFEHLINLRQNRPAELIAKFLDEKLRAGNKGTSEEELESVLEKVLVLFRFIQGKDVFEAFYKKDLAKRLLLGKSASIDAEKSMISKLKTECGSQFTNKLEGMFKDIELSKEINESFKQSSQARTKLPSGIEMSVHVLTTGYWPTYPPMDVKLPHELNVYQDIFKEFYLSKYSGRRLMWQNSLGHCVLKADFSKGKKELAVSLFQAVVLMLFNDAMKLSFEDIKDSTSIEDKELRRTLQSLACGKVRVLQKNPKGRDVEDGDEFEFNDEFAAPLYRIKVNAIQMKETVEENTSTTERVFQDRQYQIDAAIVRIMKTRKVLSHTLLITELFQQLKFPIKPADLKKRIESLIDREYLEREKSNPQIYNYLA cop10_arath Constitutive photomorphogenesis protein 10 COP10 MRP15.21 At3g13550 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MMTPGGSGRLRPLPTAMYAGYSGTASSWVAKTSVSASGKRIQREMAELNIDPPPDCSAGPKGDNLYHWIATIIGPSGTPYEGGIFFLDIIFPSDYPFKPPKLVFKTRIYHCNVDTAGDLSVNILRDSWSPALTITKVLQAIRSIFLKPEPYSPALPVIARLYLTDREKHDEVAKEWTLRFAK det1_arath Light-mediated development protein DET1 DET1 Protein DEETIOLATED 1 T9A4.13 F28M11.100 At4g10180 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MFTSGNVTARVFERQIRTPPPGASVNRARHFYENLVPSYTLYDVESPDHCFRKFTEDGLFLISFSRNHQELIVYRPSWLTYSTTDDSTTTLPPLPRRASKFDSFFTQLYSVNLASSNELICKDFFLYHQTRRFGLFATSTAQIHDSSSPSNDAVPGVPSIDKITFVLLRLDDGVVLDERVFLHDFVNLAHNMGVFLYDDLLAILSLRYQRIHLLQIRDSGHLVDARAIGYFCREDDELFLNSSSQAMMSQDKSKQQSLSGSKEDDTGENGLRHSLSQPSGSNSFLSGVKQRLLSFIFREIWNEESDNVMRVQSLKKKFYFHFQDYVDLIIWKVQFLDRQHLLIKFGSVDGGVTRSADHHPAFFAVYNMETTDIVAFYQNSAEDLYQLFEQFSDHFTVSSSTPFMNFVTSHSNNVYALEQLKYTKNKSNSFSQFVKKMLLSLPFSCQSQSPSPYFDQSLFRFDEKLISAADRHRQSSDNPIKFISRRQPQTLKFKIKPGPECGTADGRSKKICSFLFHPHLPLAISIQQTLFMPPSVVNIHFRR cop1_arath E3 ubiquitin-protein ligase COP1 COP1 Constitutive photomorphogenesis protein 1 RING-type E3 ubiquitin transferase COP1 T21L14.11 At2g32950 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MEEISTDPVVPAVKPDPRTSSVGEGANRHENDDGGSGGSEIGAPDLDKDLLCPICMQIIKDAFLTACGHSFCYMCIITHLRNKSDCPCCSQHLTNNQLYPNFLLDKLLKKTSARHVSKTASPLDQFREALQRGCDVSIKEVDNLLTLLAERKRKMEQEEAERNMQILLDFLHCLRKQKVDELNEVQTDLQYIKEDINAVERHRIDLYRARDRYSVKLRMLGDDPSTRNAWPHEKNQIGFNSNSLSIRGGNFVGNYQNKKVEGKAQGSSHGLPKKDALSGSDSQSLNQSTVSMARKKRIHAQFNDLQECYLQKRRQLADQPNSKQENDKSVVRREGYSNGLADFQSVLTTFTRYSRLRVIAEIRHGDIFHSANIVSSIEFDRDDELFATAGVSRCIKVFDFSSVVNEPADMQCPIVEMSTRSKLSCLSWNKHEKNHIASSDYEGIVTVWDVTTRQSLMEYEEHEKRAWSVDFSRTEPSMLVSGSDDCKVKVWCTRQEASVINIDMKANICCVKYNPGSSNYIAVGSADHHIHYYDLRNISQPLHVFSGHKKAVSYVKFLSNNELASASTDSTLRLWDVKDNLPVRTFRGHTNEKNFVGLTVNSEYLACGSETNEVYVYHKEITRPVTSHRFGSPDMDDAEEEAGSYFISAVCWKSDSPTMLTANSQGTIKVLVLAA ddb1a-dcaf1-1 853512 n/a 853516 unspecified role unspecified role prey prey n/a 853517 unspecified role unspecified role bait bait region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false physical association physical association false false false Figure 2B The authors do not provide the R3 or R4 domain amino-acid coordinates and therefore these were not curated. ddb1a-dcaf1-2 853512 n/a 853516 unspecified role unspecified role bait bait region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false n/a 853517 unspecified role unspecified role prey prey physical association physical association false false false Figure 4A ddb1a-dcaf1-5 853512 n/a 853517 unspecified role unspecified role bait bait region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false n/a 853516 unspecified role unspecified role prey prey n/a 853518 unspecified role unspecified role prey prey association association false false false Figure 4D cop10-cop1-det1 853512 n/a 853519 unspecified role unspecified role bait bait region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false n/a 853520 unspecified role unspecified role prey prey n/a 853516 unspecified role unspecified role prey prey n/a 853521 unspecified role unspecified role prey prey association association false false false Figure 4G ddb1a-dcaf1-3 853513 n/a 853516 unspecified role unspecified role prey prey region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false n/a 853517 unspecified role unspecified role bait bait physical association physical association false false false Figure 4B ddb1a-dcaf1-4 853513 n/a 853517 unspecified role unspecified role bait bait n/a 853518 unspecified role unspecified role prey prey region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false physical association physical association false false false Figure 4C ddb1a-dcaf1 853514 n/a 853516 unspecified role unspecified role bait bait n/a 853517 unspecified role unspecified role prey prey Q9M086:p.[Asp1658Ala;Arg1660Ala] mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false Q9M086:p.[Asp1622Ala;Arg1624Ala;Asp1658Ala;Arg1660Ala] mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing 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 certain certain sequence position certain certain certain sequence position certain false Q9M086:p.[Asp1622Ala;Arg1624Ala] mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false physical association physical association false false false Figure 2A Figure 3B The authors do not provide the R3 or R4 domain amino-acid coordinates and therefore these were not curated. ddb1a-dcaf1-6 853515 n/a 853516 unspecified role unspecified role prey prey n/a 853517 unspecified role unspecified role bait bait physical association physical association false false false Figure 4E Figure 4F Figure 5C