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/ park-2017-3 ecoli Escherichia coli (strain K12) crosslink cross-linking study crosslink experimental particp experimental participant identification experimental particp Park YB., Hohl M., Padjasek M., Jeong E., Jin KS., Krężel A., Petrini JH., Cho Y. yunje@postech.ac.kr Nature structural & molecular biology 2017 imex curation Only protein-protein interactions imex curation park-2017-5 yeast Saccharomyces cerevisiae Baker's yeast anti bait coip anti bait coimmunoprecipitation anti bait coip experimental particp experimental participant identification experimental particp Park YB., Hohl M., Padjasek M., Jeong E., Jin KS., Krężel A., Petrini JH., Cho Y. yunje@postech.ac.kr Nature structural & molecular biology 2017 imex curation Only protein-protein interactions imex curation park-2017-1 in vitro In vitro saxs x ray scattering saxs experimental particp experimental participant identification experimental particp Park YB., Hohl M., Padjasek M., Jeong E., Jin KS., Krężel A., Petrini JH., Cho Y. yunje@postech.ac.kr Nature structural & molecular biology 2017 imex curation Only protein-protein interactions imex curation park-2017-2 in vitro In vitro x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction experimental particp experimental participant identification experimental particp Park YB., Hohl M., Padjasek M., Jeong E., Jin KS., Krężel A., Petrini JH., Cho Y. yunje@postech.ac.kr Nature structural & molecular biology 2017 imex curation Only protein-protein interactions imex curation park-2017-4 in vitro In vitro fret fluorescent resonance energy transfer FRET RET FRET analysis FRET RET FRET analysis fret experimental particp experimental participant identification experimental particp Park YB., Hohl M., Padjasek M., Jeong E., Jin KS., Krężel A., Petrini JH., Cho Y. yunje@postech.ac.kr Nature structural & molecular biology 2017 imex curation Only protein-protein interactions imex curation rad50_human DNA repair protein RAD50 RAD50 protein protein human Homo sapiens Human MSRIEKMSILGVRSFGIEDKDKQIITFFSPLTILVGPNGAGKTTIIECLKYICTGDFPPGTKGNTFVHDPKVAQETDVRAQIRLQFRDVNGELIAVQRSMVCTQKSKKTEFKTLEGVITRTKHGEKVSLSSKCAEIDREMISSLGVSKAVLNNVIFCHQEDSNWPLSEGKALKQKFDEIFSATRYIKALETLRQVRQTQGQKVKEYQMELKYLKQYKEKACEIRDQITSKEAQLTSSKEIVKSYENELDPLKNRLKEIEHNLSKIMKLDNEIKALDSRKKQMEKDNSELEEKMEKVFQGTDEQLNDLYHNHQRTVREKERKLVDCHRELEKLNKESRLLNQEKSELLVEQGRLQLQADRHQEHIRARDSLIQSLATQLELDGFERGPFSERQIKNFHKLVRERQEGEAKTANQLMNDFAEKETLKQKQIDEIRDKKTGLGRIIELKSEILSKKQNELKNVKYELQQLEGSSDRILELDQELIKAERELSKAEKNSNVETLKMEVISLQNEKADLDRTLRKLDQEMEQLNHHTTTRTQMEMLTKDKADKDEQIRKIKSRHSDELTSLLGYFPNKKQLEDWLHSKSKEINQTRDRLAKLNKELASSEQNKNHINNELKRKEEQLSSYEDKLFDVCGSQDFESDLDRLKEEIEKSSKQRAMLAGATAVYSQFITQLTDENQSCCPVCQRVFQTEAELQEVISDLQSKLRLAPDKLKSTESELKKKEKRRDEMLGLVPMRQSIIDLKEKEIPELRNKLQNVNRDIQRLKNDIEEQETLLGTIMPEEESAKVCLTDVTIMERFQMELKDVERKIAQQAAKLQGIDLDRTVQQVNQEKQEKQHKLDTVSSKIELNRKLIQDQQEQIQHLKSTTNELKSEKLQISTNLQRRQQLEEQTVELSTEVQSLYREIKDAKEQVSPLETTLEKFQQEKEELINKKNTSNKIAQDKLNDIKEKVKNIHGYMKDIENYIQDGKDDYKKQKETELNKVIAQLSECEKHKEKINEDMRLMRQDIDTQKIQERWLQDNLTLRKRNEELKEVEEERKQHLKEMGQMQVLQMKSEHQKLEENIDNIKRNHNLALGRQKGYEEEIIHFKKELREPQFRDAEEKYREMMIVMRTTELVNKDLDIYYKTLDQAIMKFHSMKMEEINKIIRDLWRSTYRGQDIEYIEIRSDADENVSASDKRRNYNYRVVMLKGDTALDMRGRCSAGQKVLASLIIRLALAETFCLNCGIIALDEPTTNLDRENIESLAHALVEIIKSRSQQRNFQLLVITHDEDFVELLGRSEYVEKFYRIKKNIDQCSEIVKCSVSSLGFNVH xrs2_yeast DNA repair protein XRS2 XRS2 D9481.13 YDR369C protein protein yeast Saccharomyces cerevisiae Baker's yeast MWVVRYQNTLEDGSISFISCCLQAFKTYSIGRSSKNPLIIKNDKSISRQHITFKWEINNSSDLKHSSLCLVNKGKLTSLNKKFMKVGETFTINASDVLKSTIIELGTTPIRIEFEWINEVWNIPPHLTQFRTMLSEYGISTEISINDIPANLMISDYPKSEDNSIRELYALVSTIPMKKSRFLMELCNTLLPTSKTNLKFDEMWNDMISNPEYNVFDFDPNILLSKFMRLNNIRVLTTIKSEPRLSSLLRTFNINLFAFDNIDSLYKYVDSLEASTEYLILTTTDKKENGKILCTIKTMLTSIIDGTLSAVINMKGASSRTLDNGKFDQISEGMSTILKTSRAPEVEASPVVSKKRKLNRRRVLPLDSLDFFAGGLSTKTLSENRSLTDAKRLNCGAESKTVISSPNIAEADEKHAPFLQNALKPTEDIGKKSGHSSPGAIIVSSPNLGTVNTSEDSLDKSLQSHKLPQPSLPEVAGIGSQTISSNSADYETAAVNSMDDAEVTKNFRVNHHQNIEQPSKNIRKLSNYSREISSPLQENCKSPVKELSIKEKSGTPHAFVEAIQETKNREVKRVKSTIVELKDEELSEEAINQLKNLAIVEPSNNLLRKSFDSEGNKTSRTTEKWENSLMEPEWHKRKNFKTFVKVRPKSKAHKEEGKNNTQSSDFIRNAAFLITRNYVPLKKYSKKDTTTKWGTEENEDMFALTEMERFGSNTFMSDNINSNTIQKRSQALNRFTNEDSSNEGEEDSFSFSRCSGTAASVQPLKNKIFITDEDDLGDIDDKSDRLNHRENNRNLFVVKEMNLRPNLSEECSKQSRHSRSATSRSRGSFGASNNGDGDDDDDDGPKFTFKRRKG 833DAD6D20F6693E mre11_yeast Double-strand break repair protein MRE11 YM9959.06C YMR224C MRE11 protein protein yeast Saccharomyces cerevisiae Baker's yeast MDYPDPDTIRILITTDNHVGYNENDPITGDDSWKTFHEVMMLAKNNNVDMVVQSGDLFHVNKPSKKSLYQVLKTLRLCCMGDKPCELELLSDPSQVFHYDEFTNVNYEDPNFNISIPVFGISGNHDDASGDSLLCPMDILHATGLINHFGKVIESDKIKVVPLLFQKGSTKLALYGLAAVRDERLFRTFKDGGVTFEVPTMREGEWFNLMCVHQNHTGHTNTAFLPEQFLPDFLDMVIWGHEHECIPNLVHNPIKNFDVLQPGSSVATSLCEAEAQPKYVFILDIKYGEAPKMTPIPLETIRTFKMKSISLQDVPHLRPHDKDATSKYLIEQVEEMIRDANEETKQKLADDGEGDMVAELPKPLIRLRVDYSAPSNTQSPIDYQVENPRRFSNRFVGRVANGNNVVQFYKKRSPVTRSKKSGINGTSISDRDVEKLFSESGGELEVQTLVNDLLNKMQLSLLPEVGLNEAVKKFVDKDEKTALKEFISHEISNEVGILSTNEEFLRTDDAEEMKALIKQVKRANSVRPTPPKENDETNFAFNGNGLDSFRSSNREVRTGSPDITQSHVDNESRITHISQAESSKPTSKPKRVRTATKKKIPAFSDSTVISDAENELGDNNDAQDDVDIDENDIIMVSTDEEDASYGLLNGRKTKTKTRPAASTKTASRRGKGRASRTPKTDILGSLLAKKRK D58433E32E852B73 rad50_yeast DNA repair protein RAD50 RAD50 YNL250W N0872 153 kDa protein protein protein yeast Saccharomyces cerevisiae Baker's yeast MSAIYKLSIQGIRSFDSNDRETIEFGKPLTLIVGMNGSGKTTIIECLKYATTGDLPPNSKGGVFIHDPKITGEKDIRAQVKLAFTSANGLNMIVTRNIQLLMKKTTTTFKTLEGQLVAINNSGDRSTLSTRSLELDAQVPLYLGVPKAILEYVIFCHQEDSLWPLSEPSNLKKKFDEIFQAMKFTKALDNLKSIKKDMSVDIKLLKQSVEHLKLDKDRSKAMKLNIHQLQTKIDQYNEEVSEIESQLNEITEKSDKLFKSNQDFQKILSKVENLKNTKLSISDQVKRLSNSIDILDLSKPDLQNLLANFSKVLMDKNNQLRDLETDISSLKDRQSSLQSLSNSLIRRQGELEAGKETYEKNRNHLSSLKEAFQHKFQGLSNIENSDMAQVNHEMSQFKAFISQDLTDTIDQFAKDIQLKETNLSDLIKSITVDSQNLEYNKKDRSKLIHDSEELAEKLKSFKSLSTQDSLNHELENLKTYKEKLQSWESENIIPKLNQKIEEKNNEMIILENQIEKFQDRIMKTNQQADLYAKLGLIKKSINTKLDELQKITEKLQNDSRIRQVFPLTQEFQRADLEMDFQKLFINMQKNIAINNKKMHELDRRYTNALYNLNTIEKDLQDNQKSKEKVIQLLSENLPEDCTIDEYNDVLEETELSYKTALENLKMHQTTLEFNRKALEIAERDSCCYLCSRKFENESFKSKLLQELKTKTDANFEKTLKDTVQNEKEYLHSLRLLEKHIITLNSINEKIDNSQKCLEKAKEETKTSKSKLDELEVDSTKLKDEKELAESEIRPLIEKFTYLEKELKDLENSSKTISEELSIYNTSEDGIQTVDELRDQQRKMNDSLRELRKTISDLQMEKDEKVRENSRMINLIKEKELTVSEIESSLTQKQNIDDSIRSKRENINDIDSRVKELEARIISLKNKKDEAQSVLDKVKNERDIQVRNKQKTVADINRLIDRFQTIYNEVVDFEAKGFDELQTTIKELELNKAQMLELKEQLDLKSNEVNEEKRKLADSNNEEKNLKQNLELIELKSQLQHIESEISRLDVQNAEAERDKYQEESLRLRTRFEKLSSENAGKLGEMKQLQNQIDSLTHQLRTDYKDIEKNYHKEWVELQTRSFVTDDIDVYSKALDSAIMKYHGLKMQDINRIIDELWKRTYSGTDIDTIKIRSDEVSSTVKGKSYNYRVVMYKQDVELDMRGRCSAGQKVLASIIIRLALSETFGANCGVIALDEPTTNLDEENIESLAKSLHNIINMRRHQKNFQLIVITHDEKFLGHMNAAAFTDHFFKVKRDDRQKSQIEWVDINRVTY 58A0AA173AC5677E rad50-7 3542578 N/A 3542583 weight by comassie molecular weight estimation by coomasie staining weight by comassie predetermined predetermined participant predetermined unspecified role unspecified role unspecified role unspecified role purified purified binding region binding region binding region binding-associated region binding region 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 ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 direct interaction direct interaction false false false Figure 4h rad50-8 3542578 N/A 3542583 weight by comassie molecular weight estimation by coomasie staining weight by comassie predetermined predetermined participant predetermined unspecified role unspecified role unspecified role unspecified role purified purified binding region binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false Q92878:p.Ser738Cys S738C mutation mutation 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 ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 N/A 3542583 weight by comassie molecular weight estimation by coomasie staining weight by comassie predetermined predetermined participant predetermined unspecified role unspecified role unspecified role unspecified role purified purified binding region binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false Q92878:p.Lys599Cys K599C mutation mutation 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 ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 3542598 3542594 direct interaction direct interaction false false false Figure 4j mre11-rad50-28 3542579 N/A 3542584 western blot western blot Immuno blot Immuno blot unspecified role unspecified role prey prey native native yeast Saccharomyces cerevisiae Baker's yeast N/A 3542585 western blot western blot Immuno blot Immuno blot unspecified role unspecified role bait bait purified purified yeast Saccharomyces cerevisiae Baker's yeast N/A 3542586 western blot western blot Immuno blot Immuno blot unspecified role unspecified role prey prey purified purified P12753:p.Glu639Pro E639P mutation mutation certain certain sequence position certain certain certain sequence position certain false P12753:p.Cys641Pro C641P mutation mutation certain certain sequence position certain certain certain sequence position certain false P12753:p.Asp644Pro D644P mutation mutation certain certain sequence position certain certain certain sequence position certain false yeast Saccharomyces cerevisiae Baker's yeast physical association physical association false false false Supplementary Figure 2e mre11-rad50-27 3542579 N/A 3542583 western blot western blot Immuno blot Immuno blot unspecified role unspecified role prey prey purified purified Q92878:p.Pro682Arg P682R mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing certain certain sequence position certain certain certain sequence position certain false binding region binding region binding region binding-associated region binding region 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 Q92878:p.Ser679Arg S679R mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing 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 yeast Saccharomyces cerevisiae Baker's yeast N/A 3542584 western blot western blot Immuno blot Immuno blot unspecified role unspecified role prey prey native native yeast Saccharomyces cerevisiae Baker's yeast N/A 3542585 western blot western blot Immuno blot Immuno blot unspecified role unspecified role bait bait native native yeast Saccharomyces cerevisiae Baker's yeast physical association physical association false false false Figure 5C rad50-4 3542580 N/A 3542583 structure determination identification by structure determination identification by structure determination structure determination unspecified role unspecified role unspecified role unspecified role purified purified binding region binding region binding region binding-associated region binding region 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 ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 direct interaction direct interaction false false false Figure 3 rad50-5 3542581 N/A 3542583 structure determination identification by structure determination identification by structure determination structure determination unspecified role unspecified role unspecified role unspecified role purified purified binding region binding region binding region binding-associated region binding region 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 ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 direct interaction direct interaction false false false Figure 1a,b, Table 1, Supplementary Fig. 1b rad50-6 3542582 N/A 3542583 predetermined predetermined participant predetermined unspecified role unspecified role fluorescence donor fluorescence donor purified purified binding region binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false fluorescent dye fluorescent dye fluorescent dye fluorescent dye label fluorescent dye undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 N/A 3542583 predetermined predetermined participant predetermined unspecified role unspecified role fluorescence accept fluorescence acceptor fluorescence accept purified purified binding region binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false fluorescent dye fluorescent dye fluorescent dye fluorescent dye label fluorescent dye undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 direct interaction direct interaction false false false Figure 4f