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/ berti-2013-1 in vitro In vitro pull down pull down western blot western blot Immuno blot Immuno blot Berti M., Ray Chaudhuri A., Thangavel S., Gomathinayagam S., Kenig S., Vujanovic M., Odreman F., Glatter T., Graziano S., Mendoza-Maldonado R., Marino F., Lucic B., Biasin V., Gstaiger M., Aebersold R., Sidorova JM., Monnat RJ., Lopes M., Vindigni A. DIP original experiment: DIP-252970X Nature structural & molecular biology 2013 IMEx Human RECQ1 promotes restart of replication forks reversed by DNA topoisomerase I inhibition. Berti M., Ray Chaudhuri A., Thangavel S., Gomathinayagam S., Kenig S., Vujanovic M., Odreman F., Glatter T., Graziano S., Mendoza-Maldonado R., Marino F., Lucic B., Biasin V., Gstaiger M., Aebersold R., Sidorova JM., Monnat RJ., Lopes M., Vindigni A. Only protein-protein interactions imex curation berti-2013-2 in vitro In vitro pull down pull down autoradiography autoradiography Berti M., Ray Chaudhuri A., Thangavel S., Gomathinayagam S., Kenig S., Vujanovic M., Odreman F., Glatter T., Graziano S., Mendoza-Maldonado R., Marino F., Lucic B., Biasin V., Gstaiger M., Aebersold R., Sidorova JM., Monnat RJ., Lopes M., Vindigni A. DIP original experiment: DIP-252972X Nature structural & molecular biology 2013 IMEx Human RECQ1 promotes restart of replication forks reversed by DNA topoisomerase I inhibition. Berti M., Ray Chaudhuri A., Thangavel S., Gomathinayagam S., Kenig S., Vujanovic M., Odreman F., Glatter T., Graziano S., Mendoza-Maldonado R., Marino F., Lucic B., Biasin V., Gstaiger M., Aebersold R., Sidorova JM., Monnat RJ., Lopes M., Vindigni A. Only protein-protein interactions imex curation berti-2013-3 human Homo sapiens Human anti bait coip anti bait coimmunoprecipitation anti bait coip western blot western blot Immuno blot Immuno blot Berti M., Ray Chaudhuri A., Thangavel S., Gomathinayagam S., Kenig S., Vujanovic M., Odreman F., Glatter T., Graziano S., Mendoza-Maldonado R., Marino F., Lucic B., Biasin V., Gstaiger M., Aebersold R., Sidorova JM., Monnat RJ., Lopes M., Vindigni A. DIP original experiment: DIP-252967X Nature structural & molecular biology 2013 IMEx Human RECQ1 promotes restart of replication forks reversed by DNA topoisomerase I inhibition. Berti M., Ray Chaudhuri A., Thangavel S., Gomathinayagam S., Kenig S., Vujanovic M., Odreman F., Glatter T., Graziano S., Mendoza-Maldonado R., Marino F., Lucic B., Biasin V., Gstaiger M., Aebersold R., Sidorova JM., Monnat RJ., Lopes M., Vindigni A. Only protein-protein interactions imex curation berti-2013-4 human Homo sapiens Human tap tandem affinity purification TAP TAP tap ms participant Identification by mass spectrometry ms participant Berti M., Ray Chaudhuri A., Thangavel S., Gomathinayagam S., Kenig S., Vujanovic M., Odreman F., Glatter T., Graziano S., Mendoza-Maldonado R., Marino F., Lucic B., Biasin V., Gstaiger M., Aebersold R., Sidorova JM., Monnat RJ., Lopes M., Vindigni A. DIP original experiment: DIP-252966X Nature structural & molecular biology 2013 IMEx Human RECQ1 promotes restart of replication forks reversed by DNA topoisomerase I inhibition. Berti M., Ray Chaudhuri A., Thangavel S., Gomathinayagam S., Kenig S., Vujanovic M., Odreman F., Glatter T., Graziano S., Mendoza-Maldonado R., Marino F., Lucic B., Biasin V., Gstaiger M., Aebersold R., Sidorova JM., Monnat RJ., Lopes M., Vindigni A. Only protein-protein interactions imex curation berti-2013-5 human Homo sapiens Human anti bait coip anti bait coimmunoprecipitation anti bait coip western blot western blot Immuno blot Immuno blot Berti M., Ray Chaudhuri A., Thangavel S., Gomathinayagam S., Kenig S., Vujanovic M., Odreman F., Glatter T., Graziano S., Mendoza-Maldonado R., Marino F., Lucic B., Biasin V., Gstaiger M., Aebersold R., Sidorova JM., Monnat RJ., Lopes M., Vindigni A. DIP original experiment: DIP-252968X Nature structural & molecular biology 2013 IMEx Human RECQ1 promotes restart of replication forks reversed by DNA topoisomerase I inhibition. Berti M., Ray Chaudhuri A., Thangavel S., Gomathinayagam S., Kenig S., Vujanovic M., Odreman F., Glatter T., Graziano S., Mendoza-Maldonado R., Marino F., Lucic B., Biasin V., Gstaiger M., Aebersold R., Sidorova JM., Monnat RJ., Lopes M., Vindigni A. Only protein-protein interactions imex curation berti-2013-6 in vitro In vitro pull down pull down predetermined predetermined participant predetermined Berti M., Ray Chaudhuri A., Thangavel S., Gomathinayagam S., Kenig S., Vujanovic M., Odreman F., Glatter T., Graziano S., Mendoza-Maldonado R., Marino F., Lucic B., Biasin V., Gstaiger M., Aebersold R., Sidorova JM., Monnat RJ., Lopes M., Vindigni A. DIP original experiment: DIP-252973X Nature structural & molecular biology 2013 IMEx Human RECQ1 promotes restart of replication forks reversed by DNA topoisomerase I inhibition. Berti M., Ray Chaudhuri A., Thangavel S., Gomathinayagam S., Kenig S., Vujanovic M., Odreman F., Glatter T., Graziano S., Mendoza-Maldonado R., Marino F., Lucic B., Biasin V., Gstaiger M., Aebersold R., Sidorova JM., Monnat RJ., Lopes M., Vindigni A. Only protein-protein interactions imex curation berti-2013-7 in vitro In vitro adp ribosylase adp ribosylase assay adp ribosylase predetermined predetermined participant predetermined Berti M., Ray Chaudhuri A., Thangavel S., Gomathinayagam S., Kenig S., Vujanovic M., Odreman F., Glatter T., Graziano S., Mendoza-Maldonado R., Marino F., Lucic B., Biasin V., Gstaiger M., Aebersold R., Sidorova JM., Monnat RJ., Lopes M., Vindigni A. DIP original experiment: DIP-252971X Nature structural & molecular biology 2013 IMEx Human RECQ1 promotes restart of replication forks reversed by DNA topoisomerase I inhibition. Berti M., Ray Chaudhuri A., Thangavel S., Gomathinayagam S., Kenig S., Vujanovic M., Odreman F., Glatter T., Graziano S., Mendoza-Maldonado R., Marino F., Lucic B., Biasin V., Gstaiger M., Aebersold R., Sidorova JM., Monnat RJ., Lopes M., Vindigni A. Only protein-protein interactions imex curation berti-2013-8 in vitro In vitro far western blotting far western blotting Affinity blotting Affinity blotting predetermined predetermined participant predetermined Berti M., Ray Chaudhuri A., Thangavel S., Gomathinayagam S., Kenig S., Vujanovic M., Odreman F., Glatter T., Graziano S., Mendoza-Maldonado R., Marino F., Lucic B., Biasin V., Gstaiger M., Aebersold R., Sidorova JM., Monnat RJ., Lopes M., Vindigni A. DIP original experiment: DIP-252969X Nature structural & molecular biology 2013 IMEx Human RECQ1 promotes restart of replication forks reversed by DNA topoisomerase I inhibition. Berti M., Ray Chaudhuri A., Thangavel S., Gomathinayagam S., Kenig S., Vujanovic M., Odreman F., Glatter T., Graziano S., Mendoza-Maldonado R., Marino F., Lucic B., Biasin V., Gstaiger M., Aebersold R., Sidorova JM., Monnat RJ., Lopes M., Vindigni A. Only protein-protein interactions imex curation parp1_human Poly [ADP-ribose] polymerase 1 PARP1 ADPRT PPOL NAD(+) ADP-ribosyltransferase 1 Poly[ADP-ribose] synthase 1 ADP-ribosyltransferase diphtheria toxin-like 1 DNA ADP-ribosyltransferase PARP1 Protein poly-ADP-ribosyltransferase PARP1 protein protein human Homo sapiens Human MAESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFDGKVPHWYHFSCFWKVGHSIRHPDVEVDGFSELRWDDQQKVKKTAEAGGVTGKGQDGIGSKAEKTLGDFAAEYAKSNRSTCKGCMEKIEKGQVRLSKKMVDPEKPQLGMIDRWYHPGCFVKNREELGFRPEYSASQLKGFSLLATEDKEALKKQLPGVKSEGKRKGDEVDGVDEVAKKKSKKEKDKDSKLEKALKAQNDLIWNIKDELKKVCSTNDLKELLIFNKQQVPSGESAILDRVADGMVFGALLPCEECSGQLVFKSDAYYCTGDVTAWTKCMVKTQTPNRKEWVTPKEFREISYLKKLKVKKQDRIFPPETSASVAATPPPSTASAPAAVNSSASADKPLSNMKILTLGKLSRNKDEVKAMIEKLGGKLTGTANKASLCISTKKEVEKMNKKMEEVKEANIRVVSEDFLQDVSASTKSLQELFLAHILSPWGAEVKAEPVEVVAPRGKSGAALSKKSKGQVKEEGINKSEKRMKLTLKGGAAVDPDSGLEHSAHVLEKGGKVFSATLGLVDIVKGTNSYYKLQLLEDDKENRYWIFRSWGRVGTVIGSNKLEQMPSKEDAIEHFMKLYEEKTGNAWHSKNFTKYPKKFYPLEIDYGQDEEAVKKLTVNPGTKSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKVEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKTSLW recq1_human ATP-dependent DNA helicase Q1 RECQL RECQ1 RECQL1 DNA helicase, RecQ-like type 1 DNA-dependent ATPase Q1 RecQ protein-like 1 protein protein human Homo sapiens Human MASVSALTEELDSITSELHAVEIQIQELTERQQELIQKKKVLTKKIKQCLEDSDAGASNEYDSSPAAWNKEDFPWSGKVKDILQNVFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALCSDGFTLVICPLISLMEDQLMVLKQLGISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLEKAYEARRFTRIAVDEVHCCSQWGHDFRPDYKALGILKRQFPNASLIGLTATATNHVLTDAQKILCIEKCFTFTASFNRPNLYYEVRQKPSNTEDFIEDIVKLINGRYKGQSGIIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAGRDDMKADCILYYGFGDIFRISSMVVMENVGQQKLYEMVSYCQNISKCRRVLMAQHFDEVWNSEACNKMCDNCCKDSAFERKNITEYCRDLIKILKQAEELNEKLTPLKLIDSWMGKGAAKLRVAGVVAPTLPREDLEKIIAHFLIQQYLKEDYSFTAYATISYLKIGPKANLLNNEAHAITMQVTKSTQNSFRAESSQTCHSEQGDKKMEEKNSGNFQKKAANMLQQSGSKNTGAKKRKIDDA h2b1l_human Histone H2B type 1-L H2BC13 H2BFC HIST1H2BL Histone H2B.c protein protein human Homo sapiens Human MPELAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIASEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK h2a1a_human Histone H2A type 1-A H2AC1 H2A-clustered histone 1 H2AFR HIST1H2AA Histone H2A/r protein protein human Homo sapiens Human MSGRGKQGGKARAKSKSRSSRAGLQFPVGRIHRLLRKGNYAERIGAGAPVYLAAVLEYLTAEILELAGNASRDNKKTRIIPRHLQLAIRNDEELNKLLGGVTIAQGGVLPNIQAVLLPKKTESHHHKAQSK xrcc5_human X-ray repair cross-complementing protein 5 XRCC5 G22P2 ATP-dependent DNA helicase II 80 kDa subunit Lupus Ku autoantigen protein p86 86 kDa subunit of Ku antigen Ku86 Ku80 Thyroid-lupus autoantigen CTC box-binding factor 85 kDa subunit Nuclear factor IV DNA repair protein XRCC5 X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining) ATP-dependent DNA helicase 2 subunit 2 protein protein human Homo sapiens Human MVRSGNKAAVVLCMDVGFTMSNSIPGIESPFEQAKKVITMFVQRQVFAENKDEIALVLFGTDGTDNPLSGGDQYQNITVHRHLMLPDFDLLEDIESKIQPGSQQADFLDALIVSMDVIQHETIGKKFEKRHIEIFTDLSSRFSKSQLDIIIHSLKKCDISLQFFLPFSLGKEDGSGDRGDGPFRLGGHGPSFPLKGITEQQKEGLEIVKMVMISLEGEDGLDEIYSFSESLRKLCVFKKIERHSIHWPCRLTIGSNLSIRIAAYKSILQERVKKTWTVVDAKTLKKEDIQKETVYCLNDDDETEVLKEDIIQGFRYGSDIVPFSKVDEEQMKYKSEGKCFSVLGFCKSSQVQRRFFMGNQVLKVFAARDDEAAAVALSSLIHALDDLDMVAIVRYAYDKRANPQVGVAFPHIKHNYECLVYVQLPFMEDLRQYMFSSLKNSKKYAPTEAQLNAVDALIDSMSLAKKDEKTDTLEDLFPTTKIPNPRFQRLFQCLLHRALHPREPLPPIQQHIWNMLNPPAEVTTKSQIPLSKIKTLFPLIEAKKKDQVTAQEIFQDNHEDGPTAKKLKTEQGGAHFSVSSLAEGSVTSVGSVNPAENFRVLVKQKKASFEEASNQLINHIEQFLDTNETPYFMKSIDCIRAFREEAIKFSEEQRFNNFLKALQEKVEIKQLNHFWEIVVQDGITLITKEEASGSSVTAEEAKKFLAPKDKPSGDTAAVFEEGGDVDDLLDMI xrcc6_human X-ray repair cross-complementing protein 6 XRCC6 G22P1 ATP-dependent DNA helicase II 70 kDa subunit Lupus Ku autoantigen protein p70 70 kDa subunit of Ku antigen Thyroid-lupus autoantigen CTC box-binding factor 75 kDa subunit DNA repair protein XRCC6 X-ray repair complementing defective repair in Chinese hamster cells 6 ATP-dependent DNA helicase 2 subunit 1 5'-deoxyribose-5-phosphate lyase Ku70 protein protein human Homo sapiens Human MSGWESYYKTEGDEEAEEEQEENLEASGDYKYSGRDSLIFLVDASKAMFESQSEDELTPFDMSIQCIQSVYISKIISSDRDLLAVVFYGTEKDKNSVNFKNIYVLQELDNPGAKRILELDQFKGQQGQKRFQDMMGHGSDYSLSEVLWVCANLFSDVQFKMSHKRIMLFTNEDNPHGNDSAKASRARTKAGDLRDTGIFLDLMHLKKPGGFDISLFYRDIISIAEDEDLRVHFEESSKLEDLLRKVRAKETRKRALSRLKLKLNKDIVISVGIYNLVQKALKPPPIKLYRETNEPVKTKTRTFNTSTGGLLLPSDTKRSQIYGSRQIILEKEETEELKRFDDPGLMLMGFKPLVLLKKHHYLRPSLFVYPEESLVIGSSTLFSALLIKCLEKEVAALCRYTPRRNIPPYFVALVPQEEELDDQKIQVTPPGFQLVFLPFADDKRKMPFTEKIMATPEQVGKMKAIVEKLRFTYRSDSFENPVLQQHFRNLEALALDLMEPEQAVDLTLPKVEAMNKRLGSLVDEFKELVYPPDYNPEGKVTKRKHDNEGSGSKRPKVEYSEEELKTHISKGTLGKFTVPMLKEACRAYGLKSGLKKQELLEALTKHFQD recql-parp1-1 3250820 N/A 3250828 unspecified role unspecified role prey prey spofr Spodoptera frugiperda (Fall armyworm) Fall armyworm N/A 3250829 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 n-term range n-terminal range n-term range n-term range n-terminal range n-term range false spofr Spodoptera frugiperda (Fall armyworm) Fall armyworm direct interaction direct interaction false false false recql-parp1-2 3250821 N/A 3250828 unspecified role unspecified role prey prey 35S-label 35S-label 35s radiolabel 35s radiolabel 35S s35 radiolabelled S35 s35 radiolabelled 35S S35 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false in vitro In vitro N/A 3250829 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 n-term range n-terminal range n-term range n-term range n-terminal range n-term range false Region 391-649 Region 391-649 sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain false spofr Spodoptera frugiperda (Fall armyworm) Fall armyworm direct interaction direct interaction false false false recql-parp1-3 3250822 N/A 3250828 unspecified role unspecified role prey prey human Homo sapiens Human N/A 3250829 unspecified role unspecified role bait bait human Homo sapiens Human physical association physical association false false false recql-hist1h2aa-1 3250823 N/A 3250830 unspecified role unspecified role prey prey human Homo sapiens Human N/A 3250831 unspecified role unspecified role prey prey human Homo sapiens Human N/A 3250832 unspecified role unspecified role prey prey human Homo sapiens Human N/A 3250833 unspecified role unspecified role prey prey human Homo sapiens Human N/A 3250828 unspecified role unspecified role prey prey human Homo sapiens Human N/A 3250829 unspecified role unspecified role bait bait TAP-tag TAP-tag tandem tag tandem tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false human Homo sapiens Human association association false false false parp1-recql-1 3250824 N/A 3250828 unspecified role unspecified role bait bait human Homo sapiens Human N/A 3250829 unspecified role unspecified role prey prey human Homo sapiens Human physical association physical association false false false parp1-recql-2 3250825 N/A 3250828 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 n-term range n-terminal range n-term range n-term range n-terminal range n-term range false Region 1-371 Region 1-371 sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain false Region 384-524 Region 384-524 sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain false spofr Spodoptera frugiperda (Fall armyworm) Fall armyworm N/A 3250829 unspecified role unspecified role prey prey 35S-label 35S-label 35s radiolabel 35s radiolabel 35S s35 radiolabelled S35 s35 radiolabelled 35S S35 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false in vitro In vitro direct interaction direct interaction false false false parp1-recql-3 3250826 N/A 3250828 enzyme enzyme unspecified role unspecified role spofr Spodoptera frugiperda (Fall armyworm) Fall armyworm N/A 3250829 enzyme target enzyme target substrate substrate unspecified role unspecified role Region 474-649 Region 474-649 sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain false PAR-res PAR-res adprib1res monoadenosine diphosphoribosyl (ADP-ribosyl) modified residue ADP-rybosylation (from NAD) ADPRib1Res western blot western blot Immuno blot Immuno blot undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false GST-tag GST-tag gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false spofr Spodoptera frugiperda (Fall armyworm) Fall armyworm adp ribosylation adp ribosylation reaction adp ribosylation false false false parp1-recql-4 3250827 N/A 3250828 unspecified role unspecified role bait bait spofr Spodoptera frugiperda (Fall armyworm) Fall armyworm N/A 3250829 unspecified role unspecified role prey prey spofr Spodoptera frugiperda (Fall armyworm) Fall armyworm direct interaction direct interaction false false false