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/ lammens-2011-1 The Mre11:Rad50 structure shows an ATP-dependent molecular clamp in DNA double-strand break repair. in vitro In vitro x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Lammens K., Bemeleit DJ., Mockel C., Clausing E., Schele A., Hartung S., Schiller CB., Lucas M., Angermuller C., Soding J., Strasser K., Hopfner KP. SPR data not captured as sequence of the nucleic acid probe was not given in the paper. hopfner@lmb.uni-muenchen.de Cell (0092-8674) 2011 Only protein-protein interactions imex curation lammens-2011-2 The Mre11:Rad50 structure shows an ATP-dependent molecular clamp in DNA double-strand break repair. in vitro In vitro saxs x ray scattering saxs predetermined predetermined participant predetermined Lammens K., Bemeleit DJ., Mockel C., Clausing E., Schele A., Hartung S., Schiller CB., Lucas M., Angermuller C., Soding J., Strasser K., Hopfner KP. SPR data not captured as sequence of the nucleic acid probe was not given in the paper. hopfner@lmb.uni-muenchen.de Cell (0092-8674) 2011 Only protein-protein interactions imex curation lammens-2011-7 The Mre11:Rad50 structure shows an ATP-dependent molecular clamp in DNA double-strand break repair. in vitro In vitro crosslink cross-linking study crosslink weight by comassie molecular weight estimation by coomasie staining weight by comassie Lammens K., Bemeleit DJ., Mockel C., Clausing E., Schele A., Hartung S., Schiller CB., Lucas M., Angermuller C., Soding J., Strasser K., Hopfner KP. BMOE SPR data not captured as sequence of the nucleic acid probe was not given in the paper. hopfner@lmb.uni-muenchen.de Cell (0092-8674) 2011 Only protein-protein interactions imex curation lammens-2011-3 The Mre11:Rad50 structure shows an ATP-dependent molecular clamp in DNA double-strand break repair. in vitro In vitro crosslink cross-linking study crosslink ms participant Identification by mass spectrometry ms participant Lammens K., Bemeleit DJ., Mockel C., Clausing E., Schele A., Hartung S., Schiller CB., Lucas M., Angermuller C., Soding J., Strasser K., Hopfner KP. 1,6-Hexane-bisvinylsulfone SPR data not captured as sequence of the nucleic acid probe was not given in the paper. hopfner@lmb.uni-muenchen.de Cell (0092-8674) 2011 Only protein-protein interactions imex curation lammens-2011-4 The Mre11:Rad50 structure shows an ATP-dependent molecular clamp in DNA double-strand break repair. in vitro In vitro molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column anti tag western anti tag western blot anti tag western Lammens K., Bemeleit DJ., Mockel C., Clausing E., Schele A., Hartung S., Schiller CB., Lucas M., Angermuller C., Soding J., Strasser K., Hopfner KP. 1,6-Hexane-bisvinylsulfone SPR data not captured as sequence of the nucleic acid probe was not given in the paper. hopfner@lmb.uni-muenchen.de Cell (0092-8674) 2011 Only protein-protein interactions imex curation lammens-2011-5 The Mre11:Rad50 structure shows an ATP-dependent molecular clamp in DNA double-strand break repair. in vitro In vitro emsa electrophoretic mobility shift assay Gel retardation assay band shift band shift Gel retardation assay emsa weight autoradiogra molecular weight estimation by autoradiography weight autoradiogra Lammens K., Bemeleit DJ., Mockel C., Clausing E., Schele A., Hartung S., Schiller CB., Lucas M., Angermuller C., Soding J., Strasser K., Hopfner KP. 1,6-Hexane-bisvinylsulfone SPR data not captured as sequence of the nucleic acid probe was not given in the paper. hopfner@lmb.uni-muenchen.de Cell (0092-8674) 2011 Only protein-protein interactions imex curation lammens-2011-6 The Mre11:Rad50 structure shows an ATP-dependent molecular clamp in DNA double-strand break repair. in vitro In vitro atpase assay atpase assay predetermined predetermined participant predetermined Lammens K., Bemeleit DJ., Mockel C., Clausing E., Schele A., Hartung S., Schiller CB., Lucas M., Angermuller C., Soding J., Strasser K., Hopfner KP. SPR data not captured as sequence of the nucleic acid probe was not given in the paper. hopfner@lmb.uni-muenchen.de Cell (0092-8674) 2011 Only protein-protein interactions imex curation rad50_thema Probable DNA double-strand break repair Rad50 ATPase rad50 TM_1636 protein protein thema Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) MRPERLTVRNFLGLKNVDIEFQSGITVVEGPNGAGKSSLFEAISFALFGNGIRYPNSYDYVNRNAVDGTARLVFQFERGGKRYEIIREINALQRKHNAKLSEILENGKKAAIAAKPTSVKQEVEKILGIEHRTFIRTVFLPQGEIDKLLISPPSEITEIISDVFQSKETLEKLEKLLKEKMKKLENEISSLQALYTAIWKYLEENDLEVLKSELKTVSEKKKELLKKREELQKEEEQLKRLLEKYRELVKKKERLRVLSLRRNELQKEVIYEQKVKKAKELEPLFREIYLRQREFERFSQELNSREKRYKELESEKEAISKEIPVHRERLSKLEEIGEKIKEELDLLEKVLKASRPLLEQRIRLKENLTRLEEEFRRLVGEKEKREKELLSIEKTENETKNELEKLLDELSILKKDHMKWLAYQIASSLNEGDTCPVCGGVFHGKVEAVEFNIDEFEKLDQKRSELENTLNVLKERKKSLSSLIEDLLMKIEEGKKNLKSIRNQIEKIEEELHRLGYSEDLEEKLDEKRKKLRKIEEERHSISQKITAADVQISQIENQLKEIKGEIEAKRETLKEQREEMDQLKSDFFDRLRKIGIGFEEFRILVKEEVKDAEKELGVVETEIRLLEESLKELESENVRDVSEDYEKVRNQLEALSQEISDLERKEGRLNHLIEETLRRERELKSLEKKLKEMSDEYNNLDLLRKYLFDKSNFSRYFTGRVLEAVLKRTKAYLDILTNGRFDIDFDDEKGGFIIKDWGIERPARGLSGGERALISISLAMSLAEVASGRLDAFFIDEGFSSLDTENKEKIASVLKELERLNKVIVFITHDREFSEAFDRKLRITGGVVVNE q9x1x0_thema Nuclease SbcCD subunit D sbcD TM_1635 protein protein thema Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) MINLKELKILHTSDWHLGVTSWTSSRPVDRREELKKALDKVVEEAEKREVDLILLTGDLLHSRNNPSVVALHDLLDYLKRMMRTAPVVVLPGNHDWKGLKLFGNFVTSISSDITFVMSFEPVDVEAKRGQKVRILPFPYPDESEALRKNEGDFRFFLESRLNKLYEEALKKEDFAIFMGHFTVEGLAGYAGIEQGREIIINRALIPSVVDYAALGHIHSFREIQKQPLTIYPGSLIRIDFGEEADEKGAVFVELKRGEPPRYERIDASPLPLKTLYYKKIDTSALKSIRDFCRNFPGYVRVVYEEDSGILPDLMGEIDNLVKIERKSRREIEEVLRESPEEFKEELDKLDYFELFKEYLKKREENHEKLLKILDELLDEVKKSEA magnesium(2+) Magnesium(2+) small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) amp-pnp AMP-PNP small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) adenosine 5'-[gamma-thio]triphosphate Adenosine 5'-[gamma-thio]triphosphate small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) mre11_pyrfu DNA double-strand break repair protein Mre11 mre11 pfMre11 PF1166 protein protein pyrfu Pyrococcus furiosus MKFAHLADIHLGYEQFHKPQREEEFAEAFKNALEIAVQENVDFILIAGDLFHSSRPSPGTLKKAIALLQIPKEHSIPVFAIEGNHDRTQRGPSVLNLLEDFGLVYVIGMRKEKVENEYLTSERLGNGEYLVKGVYKDLEIHGMKYMSSAWFEANKEILKRLFRPTDNAILMLHQGVREVSEARGEDYFEIGLGDLPEGYLYYALGHIHKRYETSYSGSPVVYPGSLERWDFGDYEVRYEWDGIKFKERYGVNKGFYIVEDFKPRFVEIKVRPFIDVKIKGSEEEIRKAIKRLIPLIPKNAYVRLNIGWRKPFDLTEIKELLNVEYLKIDTWRIKERTDEESGKIGLPSDFFTEFELKIIDILGEKDFDDFDYIIKLITEGKVEEEGPLEEAVKKVSEEKGKTVRQKIESIPKKKRGTLDSWLGGAR phix174_dsdna Enterobacteria phage phiX174 linear dsDNA ds dna double stranded deoxyribonucleic acid ds DNA ds dna bpphx Enterobacteria phage phiX174 Bacteriophage phi-X174 atp ATP Adenosine 5'-triphosphate Adenosine triphosphate ADENOSINE-5'-TRIPHOSPHATE Adephos Adetol Adynol Atipi ATP Atriphos Cardenosine Fosfobion Glucobasin H4atp Myotriphos Triadenyl Triphosphaden adenosine 5'-(tetrahydrogen triphosphate) small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) q9x1x0-rad50 1158043 n/a 1158050 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 n/a 1158051 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 direct interaction direct interaction false false false Supp. Table 1 3.4A Rworking = 25.8% Rfree = 29.5% amp_pnp-magnesium_2_ 1158043 n/a 1158052 unspecified role unspecified role neutral component neutral component Stoichiometry: 2.0 n/a 1158050 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 n/a 1158051 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 n/a 1158053 unspecified role unspecified role neutral component neutral component Stoichiometry: 2.0 direct interaction direct interaction false false false Supp. Table 2 1.9A Rworking = 15.7% Rfree = 19.1% adenosine_5__-q9x1x0 1158044 n/a 1158051 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 n/a 1158050 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 n/a 1158054 unspecified role unspecified role neutral component neutral component Stoichiometry: 2.0 direct interaction direct interaction false false false Fig. 3B atp-q9x1x0 1158044 n/a 1158050 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 n/a 1158051 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 direct interaction direct interaction false false false Fig. 3B q9x1x0 1158045 n/a 1158051 unspecified role unspecified role neutral component neutral component Q9X1X0:p.Ser110Cys mutation mutation certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 direct interaction direct interaction false false false Fig. 5C mre11-1 1158045 n/a 1158055 unspecified role unspecified role neutral component neutral component Q8U1N9:p.Phe101Cys mutation mutation certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 direct interaction direct interaction false false false Fig. 5D rad50-1 1158046 n/a 1158050 unspecified role unspecified role neutral component neutral component Q9X1X1:p.[Pro31Cys;Glu806Cys] mutation mutation certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false region his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 direct interaction direct interaction false false false Fig. 3C crosslinking efficiency substantially increases further in the presence of both ATPgammaS and DNA. q9x1x0-rad50-1 1158047 n/a 1158050 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false region his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 n/a 1158051 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 direct interaction direct interaction false false false Supp. Fig. 3A-3D Expt +/- cross-linking agents suggest there is no interactions between Mre11:Rad50 heterotetramers. phix174-q9x1x0-1 1158048 n/a 1158056 unspecified role unspecified role bait bait n/a 1158051 unspecified role unspecified role prey prey region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 n/a 1158050 unspecified role unspecified role prey prey region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false region his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag 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 Supp. Fig. 3E Expt +/- cross-linking agents suggest there is no interactions between Mre11:Rad50 heterotetramers. atp-q9x1x0-2 1158049 n/a 1158057 enzyme target enzyme target substrate substrate neutral component neutral component n/a 1158051 enzyme enzyme neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false Q9X1X0:p.Phe291Ser mutation increasing mutation increasing interaction mutation increasing mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 n/a 1158050 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false region his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false Q9X1X1:p.Ile760Cys mutation increasing mutation increasing interaction mutation increasing mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 atpase reaction atpase reaction false false false Supp. Fig. 3G