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/ zhong-2014-1 Molecular mechanism of action of plant DRM de novo DNA methyltransferases. in vitro In vitro x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Zhong X., Du J., Hale C.J., Gallego-Bartolome J., Feng S., Vashisht A.A., Chory J., Wohlschlegel J.A., Patel D.J., Jacobsen S.E. pateld@mskcc.org, jacobsen@ucla.edu Cell (0092-8674) 2014 Only protein-protein interactions imex curation zhong-2014-2 Molecular mechanism of action of plant DRM de novo DNA methyltransferases. nicbe-leaf Nicotiana benthamiana leaf leaf leaf anti tag coip anti tag coimmunoprecipitation anti tag coip anti tag western anti tag western blot anti tag western Zhong X., Du J., Hale C.J., Gallego-Bartolome J., Feng S., Vashisht A.A., Chory J., Wohlschlegel J.A., Patel D.J., Jacobsen S.E. pateld@mskcc.org, jacobsen@ucla.edu Cell (0092-8674) 2014 Only protein-protein interactions imex curation zhong-2014-3 Molecular mechanism of action of plant DRM de novo DNA methyltransferases. arath-flower Arabidopsis thaliana flower flower Flower anti tag coip anti tag coimmunoprecipitation anti tag coip ms participant Identification by mass spectrometry ms participant Zhong X., Du J., Hale C.J., Gallego-Bartolome J., Feng S., Vashisht A.A., Chory J., Wohlschlegel J.A., Patel D.J., Jacobsen S.E. pateld@mskcc.org, jacobsen@ucla.edu Cell (0092-8674) 2014 Only protein-protein interactions imex curation zhong-2014-4 Molecular mechanism of action of plant DRM de novo DNA methyltransferases. arath-flower Arabidopsis thaliana flower flower Flower anti tag coip anti tag coimmunoprecipitation anti tag coip western blot western blot Immuno blot Immuno blot Zhong X., Du J., Hale C.J., Gallego-Bartolome J., Feng S., Vashisht A.A., Chory J., Wohlschlegel J.A., Patel D.J., Jacobsen S.E. pateld@mskcc.org, jacobsen@ucla.edu Cell (0092-8674) 2014 Only protein-protein interactions imex curation sinefungin sinefungin (2S,5S)-2,5-diamino-6-[(2R,3S,R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]hexanoic acid 6,9-Diamino-1-(6-amino-9H-purin-9-yl)-1,5,6,7,8,9-hexadeoxy-beta-D-ribo-decofuranuronic acid 6,9-Diamino-1-(6-amino-9H-purin-9-yl)-1,5,6,7,8,9-hexadeoxydecofuranuronic acid A 9145 ADENOSYL-ORNITHINE Antibiotic A 9145 sinefungin sinefungina sinefungine sinefunginum (5S)-5-amino-6-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]-L-norleucine small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) LMXOHSDXUQEUSF-YECHIGJVSA-N q76ku6_tobac NtDRM1 protein protein tobac Nicotiana tabacum (Common tobacco) Common tobacco MDNNLSGEDNDNIDWDTEDELEIQEIQDTTFSSCMDLRTTGQHTVRCDGEASSSSVPCQSKFIQQFVVMGFPEASIAKAIEQNGEDSDLVLDALLTFKALEDSPEEQPSASPQPCINSDDSSSEYNENLLDDVYEEDSWSSDSDSCRNSAKQCYVKVESSSSSEKEQTLLFLASMGYPAEEASIAMERCGPEASVAELTDFICAAQMARAEDVYLPEDVKPKLNHILNGSGGYKKRKMYNELCKRKKAKAIFEEETIRLPKPMIGFGVPTEPLPAMVRRTLPEQAVGPPFFYYENVALAPKGVWDTISRFLYDIEPEFVDSKYFCAAARKRGYIHNLPVENRFPLFPLAPRTIHEALPLSKKWWPSWDPRTKLNCLQTAIGSAQLTNRIRKAVEDFDGEPPMRVQKFVLDQCRKWNLVWVGRNKVAPLEPDEVEMLLGFPKNHTRGGGISRTDRYKSLGNSFQVDTVAYHLSVLKDLFPGGINVLSLFSGIGGGEVALYRLGIPLNTVVSVEKSEVNRDIVRSWWEQTNQRGNLIHFNDVQQLNGDRLEQLIESFGGFDLVIGGSPCNNLAGSNRVSRDGLEGKESSLFYDYVRILDLVKSIMSRHKH tpr2_arath Topless-related protein 2 TPR2 K20I9.6 At3g16830 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MSSLSRELVFLILQFLDEEKFKESVHKLEQESGFFFNIKYFEEKALAGEWDEVEKYLSGFTKVDDNRYSMKIFFEIRKQKYLEALDRNDRAKAVEILAKDLKVFATFNEELYKEITQLLTLENFRENEQLSKYGDTKSARSIMYTELKKLIEANPLFREKLAFPSFKASRLRTLINQSLNWQHQLCKNPRPNPDIKTLFLDHSCSPSNGARALTPVNLPVAAVARPSNFVPLGVHGGPFQSNPAPAPNANALAGWMANPNPSSSVPSGVVAASPFPMQPSQVNELKHPRAPSNSLGLMDYQSADHEQLMKRLRSAQTSNEVTYPAHSHPPASLDDLPRNVVSTIRQGSVVISMDFHPSHHTLLAVGCSSGEVTLWEVGSREKVVTEPFKIWNMAACSVIFQGSIVKEPSISVTRVAWSPDGNLLGVSFTKHLIHVYAYQGSDLRQHLEIDAHVGCVNDLAFAHPNKQMCVVTCGDDKLIKVWDLSGKKLFTFEGHEAPVYSICPHQKENIQFIFSTALDGKIKAWLYDNVGSRVDYDAPGQWCTTMLYSADGSRLFSCGTSKEGDSFLVEWNESEGALKRTYLGFRKKSAGVVQFDTTRNRFLAVGEDNQIKFWNMDNTNLLTVVEAEGGLPNLPRLRFNKDGNLLAVTTADNGFKILANTDGLRTLRAFEARSFEASKASIDMKVSTSAMASSISPAIGKIEHMDAGSPARPTPIPNGIEAMSRTMEKPRNLDSVDKSKPLELTEIVDPTQCRQVTMPDSKDSVSKVARLLYTNSGVGVLALGSNGVQRLWKWIRNEQNPTGKATASVTPQHWQPNSGLLMANDVPENPEGSVPCIALSKNDSYVMSACGGKVSLFNMMTFKVMTTFMPPPPASTFLAFHPQDNNIIAIGMEDSSIHIYNVRVDEVKTKLKGHQKHITGLAFSTALNILVSSGADAQLFFWTADSWEKKKSSAIQLPPGKAPVGDTRVQFHNDQIQLLVSHETQLAIYDASKMECIHKWVPQEALSSPITSASYSCNSQLVYASFADGNIAVFDAESLRLRCRIAPSAYMPQPTPNSAPIFPQVITAHPQEPNQLAVGLSDGSVKVIEPSELSRRWGVGVAAGSDKAGTENGRPSSSSAANNSSSDQIQR mint ago4_arath Protein argonaute 4 At2g27040 AGO4 OCP11 Protein OVEREXPRESSOR OF CATIONIC PEROXIDASE 11 T20P8.9 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MDSTNGNGADLESANGANGSGVTEALPPPPPVIPPNVEPVRVKTELAEKKGPVRVPMARKGFGTRGQKIPLLTNHFKVDVANLQGHFFHYSVALFYDDGRPVEQKGVGRKILDKVHQTYHSDLDGKEFAYDGEKTLFTYGALPSNKMDFSVVLEEVSATRANGNGSPNGNESPSDGDRKRLRRPNRSKNFRVEISYAAKIPLQALANAMRGQESENSQEAIRVLDIILRQHAARQGCLLVRQSFFHNDPTNCEPVGGNILGCRGFHSSFRTTQGGMSLNMDVTTTMIIKPGPVVDFLIANQNARDPYSIDWSKAKRTLKNLRVKVSPSGQEFKITGLSDKPCREQTFELKKRNPNENGEFETTEVTVADYFRDTRHIDLQYSADLPCINVGKPKRPTYIPLELCALVPLQRYTKALTTFQRSALVEKSRQKPQERMTVLSKALKVSNYDAEPLLRSCGISISSNFTQVEGRVLPAPKLKMGCGSETFPRNGRWNFNNKEFVEPTKIQRWVVVNFSARCNVRQVVDDLIKIGGSKGIEIASPFQVFEEGNQFRRAPPMIRVENMFKDIQSKLPGVPQFILCVLPDKKNSDLYGPWKKKNLTEFGIVTQCMAPTRQPNDQYLTNLLLKINAKLGGLNSMLSVERTPAFTVISKVPTIILGMDVSHGSPGQSDVPSIAAVVSSREWPLISKYRASVRTQPSKAEMIESLVKKNGTEDDGIIKELLVDFYTSSNKRKPEHIIIFRDGVSESQFNQVLNIELDQIIEACKLLDANWNPKFLLLVAQKNHHTKFFQPTSPENVPPGTIIDNKICHPKNNDFYLCAHAGMIGTTRPTHYHVLYDEIGFSADELQELVHSLSYVYQRSTSAISVVAPICYAHLAAAQLGTFMKFEDQSETSSSHGGITAPGPISVAQLPRLKDNVANSMFFC hdt3_arath Histone deacetylase HDT3 HDT3 HD2C HD-tuins protein 3 Histone deacetylase 2c F17C15_160 MED24.1 At5g03740 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MEFWGVEVKNGKPLHLDPGLDRLVHISQVALGESKNNVTEPIQLYVTVGSDKLLIGTLSHEKFPQLSTEIVLERNFALSHTWKNGSVFFSGYKVDASDPEPEDLIDDQLEAAGFKAAPKSAAKQVNFQLPNEDVKAKQDDDADGSEEDSSDDDDSENSGDEEEEKVTAESDSEEDDSSDDEEDDSSEEETPKKPEEPKKRSAEPNSSKNPASNKKAKFVTPQKTDSKKPHVHVATPHPSKQAGKNSGGGSTGETSKQQQTPKSAGAFGCKSCTRTFTSEMGLQSHTKAKHSAAA drm2_arath DNA (cytosine-5)-methyltransferase DRM2 DRM2 Protein DOMAINS REARRANGED METHYLASE 2 T15N1.110/T15N1.120 At5g14620/At5g14630 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MVIWNNDDDDFLEIDNFQSSPRSSPIHAMQCRVENLAGVAVTTSSLSSPTETTDLVQMGFSDEVFATLFDMGFPVEMISRAIKETGPNVETSVIIDTISKYSSDCEAGSSKSKAIDHFLAMGFDEEKVVKAIQEHGEDNMEAIANALLSCPEAKKLPAAVEEEDGIDWSSSDDDTNYTDMLNSDDEKDPNSNENGSKIRSLVKMGFSELEASLAVERCGENVDIAELTDFLCAAQMAREFSEFYTEHEEQKPRHNIKKRRFESKGEPRSSVDDEPIRLPNPMIGFGVPNEPGLITHRSLPELARGPPFFYYENVALTPKGVWETISRHLFEIPPEFVDSKYFCVAARKRGYIHNLPINNRFQIQPPPKYTIHDAFPLSKRWWPEWDKRTKLNCILTCTGSAQLTNRIRVALEPYNEEPEPPKHVQRYVIDQCKKWNLVWVGKNKAAPLEPDEMESILGFPKNHTRGGGMSRTERFKSLGNSFQVDTVAYHLSVLKPIFPHGINVLSLFTGIGGGEVALHRLQIKMKLVVSVEISKVNRNILKDFWEQTNQTGELIEFSDIQHLTNDTIEGLMEKYGGFDLVIGGSPCNNLAGGNRVSRVGLEGDQSSLFFEYCRILEVVRARMRGS ago9_arath Protein argonaute 9 AGO9 T10F18.180 At5g21150 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MDSDEPNGSGLPPPPPFVPANLVPEVEPVKKNILLPMARPRGSGSKGQKIPLLTNHFGVKFNKPSGYFFHYSVAINYEDGRPVEAKGIGRKILDKVQETYQSDLGAKYFAYDGEKTLFTVGALPSNKLDFSVVLEEIPSSRNHAGNDTNDADRKRSRRPNQTKKFMVEISYAAKIPMQAIASALQGKETENLQDALRVLDIILRQSAARQGCLLVRQSFFHNDVKNFVPIGGGVSGCRGFHSSFRTTQGGLSLNIDTSTTMIVQPGPVVDFLLANQNKKDPYGMDWNKARRVLKNLRVQITLSNREYKISGLSEHSCKDQLFTWRKPNDKGEFEEVEITVLNYYKERNIEVRYSGDFPCINVGKPKRPTYFPIEFCNLVSLQRYTKSLTNFQRAALVEKSRQKPPERMASLTKGLKDSNYNADPVLQDSGVSIITNFTQVEGRILPTPMLKVGKGENLSPIKGKWNFMRKTLAEPTTVTRWAVVNFSARCDTNTLIRDLIKCGREKGINVEPPFKDVINENPQFRNAPATVRVENMFEQIKSKLPKPPLFLLCILAERKNSDVYGPWKKKNLVDLGIVTQCIAPTRLNDQYLTNVLLKINAKLGGLNSLLAMERSPAMPKVTQVPTIIVGMDVSHGSPGQSDIPSIAAVVSSRQWPLISKYKACVRTQSRKMEMIDNLFKPVNGKDEGMFRELLLDFYYSSENRKPEHIIIFRDGVSESQFNQVLNIELDQMMQACKFLDDTWHPKFTVIVAQKNHHTKFFQSRGPDNVPPGTIIDSQICHPRNFDFYLCAHAGMIGTTRPTHYHVLYDEIGFATDDLQELVHSLSYVYQRSTTAISVVAPVCYAHLAAAQMGTVMKYEELSETSSSHGGITTPGAVPVPPMPQLHNNVSTSMFFC msi4_arath WD-40 repeat-containing protein MSI4 MSI4 ACG1 FVE Altered cold-responsive gene 1 protein Nucleosome remodeling factor complex component 4 Protein MULTICOPY SUPPRESSOR OF IRA1 4 F3P11.12 At2g19520 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MESDEAAAVSPQATTPSGGTGASGPKKRGRKPKTKEDSQTPSSQQQSDVKMKESGKKTQQSPSVDEKYSQWKGLVPILYDWLANHNLVWPSLSCRWGPQLEQATYKNRQRLYLSEQTDGSVPNTLVIANCEVVKPRVAAAEHISQFNEEARSPFVKKYKTIIHPGEVNRIRELPQNSKIVATHTDSPDVLIWDVETQPNRHAVLGAANSRPDLILTGHQDNAEFALAMCPTEPFVLSGGKDKSVVLWSIQDHITTIGTDSKSSGSIIKQTGEGTDKNESPTVGPRGVYHGHEDTVEDVAFSPTSAQEFCSVGDDSCLILWDARTGTNPVTKVEKAHDADLHCVDWNPHDDNLILTGSADNTVRLFDRRKLTANGVGSPIYKFEGHKAAVLCVQWSPDKSSVFGSSAEDGLLNIWDYDRVSKKSDRAAKSPAGLFFQHAGHRDKVVDFHWNASDPWTIVSVSDDCETTGGGGTLQIWRMSDLIYRPEEEVVAELEKFKSHVMTCASKP skp1a_arath SKP1-like protein 1A UFO-binding protein 1 SKP1 UIP1 At1g75950 T4O12.17 SKP1A ASK1 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MSAKKIVLKSSDGESFEVEEAVALESQTIAHMVEDDCVDNGVPLPNVTSKILAKVIEYCKRHVEAAASKAEAVEGAATSDDDLKAWDADFMKIDQATLFELILAANYLNIKNLLDLTCQTVADMIKGKTPEEIRTTFNIKNDFTPEEEEEVRRENQWAFE h2b6_arath Histone H2B.6 H2B H2BAt HTB9 F16L2.190 At3g45980 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MAPRAEKKPAEKKPAAEKPVEEKSKAEKAPAEKKPKAGKKLPKEAGAGGDKKKKMKKKSVETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLASESSKLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS ntdrm1-sinefungin 1554918 n/a 1554922 unspecified role unspecified role neutral component neutral component Stoichiometry: 2.0 n/a 1554923 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 2.8A Rworking = 0.2 Rfree = 0.22 Supp. Table 1 ntdrm1-sinefungin-1 1554918 n/a 1554923 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 Q76KU6:p.[Glu283Ser;Arg309_Phe310delinsSerSer;Tyr590_Asp591delinsSerSer] mutation mutation 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 ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 n/a 1554922 unspecified role unspecified role neutral component neutral component Stoichiometry: 2.0 direct interaction direct interaction false false false 2.5A Rworking = 0.187 Rfree = 0.23 Supp. Table 1 ntdrm1-ntdrm1 1554919 n/a 1554923 unspecified role unspecified role prey prey region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false n/a 1554923 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 Fig. 3C drm2-ago4 1554920 n/a 1554924 unspecified role unspecified role prey prey n/a 1554925 unspecified role unspecified role prey prey n/a 1554926 unspecified role unspecified role prey prey n/a 1554927 unspecified role unspecified role bait bait biotin ligase recognition peptide tag tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false n/a 1554928 unspecified role unspecified role prey prey n/a 1554929 unspecified role unspecified role prey prey n/a 1554930 unspecified role unspecified role prey prey n/a 1554931 unspecified role unspecified role prey prey association association false false false Fig. 5A drm2-ago4-1 1554921 n/a 1554927 unspecified role unspecified role bait bait biotin ligase recognition peptide tag tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false n/a 1554925 unspecified role unspecified role prey prey physical association physical association false false false Fig. 5B