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/ epshtein-2014-1 in vitro In vitro crosslink cross-linking study crosslink predetermined predetermined participant predetermined Epshtein V., Kamarthapu V., McGary K., Svetlov V., Ueberheide B., Proshkin S., Mironov A., Nudler E. DIP original experiment: DIP-259850X Nature 2014 IMEx UvrD facilitates DNA repair by pulling RNA polymerase backwards. Epshtein V., Kamarthapu V., McGary K., Svetlov V., Ueberheide B., Proshkin S., Mironov A., Nudler E. Only protein-protein interactions imex curation epshtein-2014-2 in vitro In vitro pull down pull down weight by comassie molecular weight estimation by coomasie staining weight by comassie Epshtein V., Kamarthapu V., McGary K., Svetlov V., Ueberheide B., Proshkin S., Mironov A., Nudler E. DIP original experiment: DIP-259847X Nature 2014 IMEx UvrD facilitates DNA repair by pulling RNA polymerase backwards. Epshtein V., Kamarthapu V., McGary K., Svetlov V., Ueberheide B., Proshkin S., Mironov A., Nudler E. Only protein-protein interactions imex curation epshtein-2014-3 in vitro In vitro crosslink cross-linking study crosslink predetermined predetermined participant predetermined Epshtein V., Kamarthapu V., McGary K., Svetlov V., Ueberheide B., Proshkin S., Mironov A., Nudler E. DIP original experiment: DIP-259852X Nature 2014 IMEx UvrD facilitates DNA repair by pulling RNA polymerase backwards. Epshtein V., Kamarthapu V., McGary K., Svetlov V., Ueberheide B., Proshkin S., Mironov A., Nudler E. Only protein-protein interactions imex curation epshtein-2014-4 in vitro In vitro crosslink cross-linking study crosslink predetermined predetermined participant predetermined Epshtein V., Kamarthapu V., McGary K., Svetlov V., Ueberheide B., Proshkin S., Mironov A., Nudler E. DIP original experiment: DIP-259851X Nature 2014 IMEx UvrD facilitates DNA repair by pulling RNA polymerase backwards. Epshtein V., Kamarthapu V., McGary K., Svetlov V., Ueberheide B., Proshkin S., Mironov A., Nudler E. Only protein-protein interactions imex curation epshtein-2014-5 ecolx Escherichia coli molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column weight by comassie molecular weight estimation by coomasie staining weight by comassie Epshtein V., Kamarthapu V., McGary K., Svetlov V., Ueberheide B., Proshkin S., Mironov A., Nudler E. DIP original experiment: DIP-259849X Nature 2014 IMEx UvrD facilitates DNA repair by pulling RNA polymerase backwards. Epshtein V., Kamarthapu V., McGary K., Svetlov V., Ueberheide B., Proshkin S., Mironov A., Nudler E. Only protein-protein interactions imex curation epshtein-2014-6 in vitro In vitro molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column weight by comassie molecular weight estimation by coomasie staining weight by comassie Epshtein V., Kamarthapu V., McGary K., Svetlov V., Ueberheide B., Proshkin S., Mironov A., Nudler E. DIP original experiment: DIP-259848X Nature 2014 IMEx UvrD facilitates DNA repair by pulling RNA polymerase backwards. Epshtein V., Kamarthapu V., McGary K., Svetlov V., Ueberheide B., Proshkin S., Mironov A., Nudler E. Only protein-protein interactions imex curation rpob_ecoli DNA-directed RNA polymerase subunit beta rpoB groN nitB rif ron stl stv tabD b3987 Transcriptase subunit beta RNA polymerase subunit beta JW3950 protein protein ecoli Escherichia coli (strain K12) MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQMELVPERLRGETASFDIEANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKDYIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETLRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDLSEELQILEAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE uvrd_ecoli DNA helicase II uvrD mutU pdeB rad recL b3813 JW3786 protein protein ecoli Escherichia coli (strain K12) MDVSYLLDSLNDKQREAVAAPRSNLLVLAGAGSGKTRVLVHRIAWLMSVENCSPYSIMAVTFTNKAAAEMRHRIGQLMGTSQGGMWVGTFHGLAHRLLRAHHMDANLPQDFQILDSEDQLRLLKRLIKAMNLDEKQWPPRQAMWYINSQKDEGLRPHHIQSYGNPVEQTWQKVYQAYQEACDRAGLVDFAELLLRAHELWLNKPHILQHYRERFTNILVDEFQDTNNIQYAWIRLLAGDTGKVMIVGDDDQSIYGWRGAQVENIQRFLNDFPGAETIRLEQNYRSTSNILSAANALIENNNGRLGKKLWTDGADGEPISLYCAFNELDEARFVVNRIKTWQDNGGALAECAILYRSNAQSRVLEEALLQASMPYRIYGGMRFFERQEIKDALSYLRLIANRNDDAAFERVVNTPTRGIGDRTLDVVRQTSRDRQLTLWQACRELLQEKALAGRAASALQRFMELIDALAQETADMPLHVQTDRVIKDSGLRTMYEQEKGEKGQTRIENLEELVTATRQFSYNEEDEDLMPLQAFLSHAALEAGEGQADTWQDAVQLMTLHSAKGLEFPQVFIVGMEEGMFPSQMSLDEGGRLEEERRLAYVGVTRAMQKLTLTYAETRRLYGKEVYHRPSRFIGELPEECVEEVRLRATVSRPVSHQRMGTPMVENDSGYKLGQRVRHAKFGEGTIVNMEGSGEHSRLQVAFQGQGIKWLVAAYARLESV rpoc_ecoli DNA-directed RNA polymerase subunit beta' rpoC tabB b3988 JW3951 Transcriptase subunit beta' RNA polymerase subunit beta' protein protein ecoli Escherichia coli (strain K12) MKDLLKFLKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDANGELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNKGSIKLSNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPQESGGTKDITGGLPRVADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFEGERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRRRAAGEAPAAPQVTAEDASASLAELLNAGLGGSDNE rpoa_ecoli DNA-directed RNA polymerase subunit alpha rpoA pez phs sez b3295 Transcriptase subunit alpha RNA polymerase subunit alpha JW3257 protein protein ecoli Escherichia coli (strain K12) MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQPEVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIADE rpoz_ecoli DNA-directed RNA polymerase subunit omega rpoZ b3649 Transcriptase subunit omega RNA polymerase omega subunit JW3624 protein protein ecoli Escherichia coli (strain K12) MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLINNQILDVRERQEQQEQEAAELQAVTAIAEGRR rpob-uvrd-1 3261862 N/A 3261868 unspecified role unspecified role unspecified role unspecified role K909-CL K909-CL xlnk-res-res crosslinked residues XLNK-Res-Res modified residue ms mass detection of residue modification modified residue ms certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli N/A 3261869 unspecified role unspecified role unspecified role unspecified role K124-CL K124-CL xlnk-res-res crosslinked residues XLNK-Res-Res modified residue ms mass detection of residue modification modified residue ms certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli direct interaction direct interaction false false false rpoc-rpoa-2 3261863 N/A 3261870 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 c-term range C-terminal range c-term range c-term range C-terminal range c-term range false ecolx Escherichia coli N/A 3261868 unspecified role unspecified role prey prey ecolx Escherichia coli N/A 3261871 unspecified role unspecified role prey prey ecolx Escherichia coli N/A 3261869 unspecified role unspecified role prey prey ecolx Escherichia coli association association false false false rpoc-uvrd-1 3261864 N/A 3261870 unspecified role unspecified role unspecified role unspecified role K79-CL K79-CL xlnk-res-res crosslinked residues XLNK-Res-Res modified residue ms mass detection of residue modification modified residue ms certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli N/A 3261869 unspecified role unspecified role unspecified role unspecified role K389-CL K389-CL xlnk-res-res crosslinked residues XLNK-Res-Res modified residue ms mass detection of residue modification modified residue ms certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli direct interaction direct interaction false false false rpoc-uvrd-2 3261865 N/A 3261870 unspecified role unspecified role unspecified role unspecified role K40-CL K40-CL xlnk-res-res crosslinked residues XLNK-Res-Res modified residue ms mass detection of residue modification modified residue ms certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli N/A 3261869 unspecified role unspecified role unspecified role unspecified role K448-CL K448-CL xlnk-res-res crosslinked residues XLNK-Res-Res modified residue ms mass detection of residue modification modified residue ms certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli direct interaction direct interaction false false false rpoa-rpob-10 3261866 N/A 3261872 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3261870 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3261868 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3261871 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli physical association physical association false false false rpoa-rpob-11 3261867 N/A 3261872 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3261870 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3261868 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3261871 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli N/A 3261869 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli physical association physical association false false false