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/ aker-2007-3 In vivo hexamerization and characterization of the Arabidopsis AAA ATPase CDC48A complex using forster resonance energy transfer-fluorescence lifetime imaging microscopy and fluorescence correlation spectroscopy. arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress fret fluorescent resonance energy transfer FRET RET FRET analysis FRET RET FRET analysis fret predetermined predetermined participant predetermined Aker J., Hesselink R., Engel R., Karlova R., Borst JW., Visser AJ., de Vries SC. sacco.devries@wur.nl Plant Physiol. (0032-0889) 2007 Only protein-protein interactions imex curation aker-2007-4 In vivo hexamerization and characterization of the Arabidopsis AAA ATPase CDC48A complex using forster resonance energy transfer-fluorescence lifetime imaging microscopy and fluorescence correlation spectroscopy. in vitro In vitro protein kinase assay protein kinase assay weight autoradiogra molecular weight estimation by autoradiography weight autoradiogra Aker J., Hesselink R., Engel R., Karlova R., Borst JW., Visser AJ., de Vries SC. sacco.devries@wur.nl Plant Physiol. (0032-0889) 2007 Only protein-protein interactions imex curation aker-2007-1 In vivo hexamerization and characterization of the Arabidopsis AAA ATPase CDC48A complex using forster resonance energy transfer-fluorescence lifetime imaging microscopy and fluorescence correlation spectroscopy. arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress comigration in gel comigration in gel electrophoresis comigration in gel anti tag western anti tag western blot anti tag western Aker J., Hesselink R., Engel R., Karlova R., Borst JW., Visser AJ., de Vries SC. sacco.devries@wur.nl Plant Physiol. (0032-0889) 2007 Only protein-protein interactions imex curation aker-2007-2 In vivo hexamerization and characterization of the Arabidopsis AAA ATPase CDC48A complex using forster resonance energy transfer-fluorescence lifetime imaging microscopy and fluorescence correlation spectroscopy. arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress fluorescence imaging fluorescence microscopy fluorescence imaging tag fluorescence tag visualisation by fluorescence tag fluorescence Aker J., Hesselink R., Engel R., Karlova R., Borst JW., Visser AJ., de Vries SC. sacco.devries@wur.nl Plant Physiol. (0032-0889) 2007 Only protein-protein interactions imex curation aker-2007-5 In vivo hexamerization and characterization of the Arabidopsis AAA ATPase CDC48A complex using forster resonance energy transfer-fluorescence lifetime imaging microscopy and fluorescence correlation spectroscopy. in vitro In vitro in gel kinase assay in-gel kinase assay in gel kinase assay fingerprinting peptide massfingerprinting fingerprinting Aker J., Hesselink R., Engel R., Karlova R., Borst JW., Visser AJ., de Vries SC. An in-vitro kinase assay was carried out using unlabelled ATP and the proteins isolated from a gel and analysed by liquid chromatography (LC)-tandem mass spectrometry. sacco.devries@wur.nl Plant Physiol. (0032-0889) 2007 Only protein-protein interactions imex curation serk1_arath Somatic embryogenesis receptor kinase 1 SERK1 Somatic embryogenesis receptor-like kinase 1 F14O23.21 F14O23_24 At1g71830 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MESSYVVFILLSLILLPNHSLWLASANLEGDALHTLRVTLVDPNNVLQSWDPTLVNPCTWFHVTCNNENSVIRVDLGNAELSGHLVPELGVLKNLQYLELYSNNITGPIPSNLGNLTNLVSLDLYLNSFSGPIPESLGKLSKLRFLRLNNNSLTGSIPMSLTNITTLQVLDLSNNRLSGSVPDNGSFSLFTPISFANNLDLCGPVTSHPCPGSPPFSPPPPFIQPPPVSTPSGYGITGAIAGGVAAGAALLFAAPAIAFAWWRRRKPLDIFFDVPAEEDPEVHLGQLKRFSLRELQVASDGFSNKNILGRGGFGKVYKGRLADGTLVAVKRLKEERTPGGELQFQTEVEMISMAVHRNLLRLRGFCMTPTERLLVYPYMANGSVASCLRERPPSQPPLDWPTRKRIALGSARGLSYLHDHCDPKIIHRDVKAANILLDEEFEAVVGDFGLAKLMDYKDTHVTTAVRGTIGHIAPEYLSTGKSSEKTDVFGYGIMLLELITGQRAFDLARLANDDDVMLLDWVKGLLKEKKLEMLVDPDLQTNYEERELEQVIQVALLCTQGSPMERPKMSEVVRMLEGDGLAEKWDEWQKVEILREEIDLSPNPNSDWILDSTYNLHAVELSGPR cd48a_arath Cell division control protein 48 homolog A CDC48A CDC48 F8A24.11 At3g09840 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MSTPAESSDSKSKKDFSTAILERKKSPNRLVVDEAINDDNSVVSLHPATMEKLQLFRGDTILIKGKKRKDTVCIALADETCEEPKIRMNKVVRSNLRVRLGDVISVHQCPDVKYGKRVHILPVDDTVEGVTGNLFDAYLKPYFLEAYRPVRKGDLFLVRGGMRSVEFKVIETDPAEYCVVAPDTEIFCEGEPVKREDEERLDDVGYDDVGGVRKQMAQIRELVELPLRHPQLFKSIGVKPPKGILLYGPPGSGKTLIARAVANETGAFFFCINGPEIMSKLAGESESNLRKAFEEAEKNAPSIIFIDEIDSIAPKREKTNGEVERRIVSQLLTLMDGLKSRAHVIVMGATNRPNSIDPALRRFGRFDREIDIGVPDEIGRLEVLRIHTKNMKLAEDVDLERISKDTHGYVGADLAALCTEAALQCIREKMDVIDLEDDSIDAEILNSMAVTNEHFHTALGNSNPSALRETVVEVPNVSWNDIGGLENVKRELQETVQYPVEHPEKFEKFGMSPSKGVLFYGPPGCGKTLLAKAIANECQANFISVKGPELLTMWFGESEANVREIFDKARQSAPCVLFFDELDSIATQRGGGSGGDGGGAADRVLNQLLTEMDGMNAKKTVFIIGATNRPDIIDSALLRPGRLDQLIYIPLPDEDSRLNIFKAALRKSPIAKDVDIGALAKYTQGFSGADITEICQRACKYAIRENIEKDIEKEKRRSENPEAMEEDGVDEVSEIKAAHFEESMKYARRSVSDADIRKYQAFAQTLQQSRGFGSEFRFENSAGSGATTGVADPFATSAAAAGDDDDLYN cd48c_arath Cell division control protein 48 homolog C EMB1354 Protein EMBRYO DEFECTIVE 1354 CDC48C F4P13.15 At3g01610 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MGRRGRGGGGGMGGGINRRYLSQVMDTCGKDLSTAEDIVDDLRSRYGNFARLTRQVLLLNVRQVLNVRNNKRVKDEDEDDNIGDEEGSASQRKKQRRVDEKEEKLQRAEQSHLRKRNMERSVSSSPSSSSSSEDSGDVSTSEDAVYGEKLSPPRFDLINDSLRDNYAKLNSSSKKPIGSPAEKNVEVETVSNKGRSKLATMGARKEAKVSLSLSGATGNGDLEVEGTKGPTFKDFGGIKKILDELEMNVLFPILNPEPFKKIGVKPPSGILFHGPPGCGKTKLANAIANEAGVPFYKISATEVISGVSGASEENIRELFSKAYRTAPSIVFIDEIDAIGSKRENQQREMEKRIVTQLLTCMDGPGNKGDKNAPDSSAGFVLVIGATNRPDALDPALRRSGRFETEIALTAPDEDARAEILSVVAQKLRLEGPFDKKRIARLTPGFVGADLESVAYLAGRKAIKRILDSRKSEQSGDGEDDKSWLRMPWPEEELEKLFVKMSDFEEAVNLVQASLTREGFSIVPDVKWDDVGGLDHLRLQFNRYIVRPIKKPDIYKAFGVDLETGFLLYGPPGCGKTLIAKAAANEAGANFMHIKGAELLNKYVGESELAIRTLFQRARTCAPCVIFFDEVDALTTSRGKEGAWVVERLLNQFLVELDGGERRNVYVIGATNRPDVVDPAFLRPGRFGNLLYVPLPNADERASILKAIARKKPIDPSVDLDGIAKNNCEGFSGADLAHLVQKATFQAVEEMIGSSESSEDDVTDITQCTIKTRHFEQALSLVSPSVNKQQRRHYDALSTKLQESVGRNTEQVTIGPSFTLE cdc48a-serk1 Interaction of CDC48A and SERK1 682396 N/A 682401 unspecified role unspecified role fluorescence accept fluorescence acceptor fluorescence accept region yfp tag yellow fluorescent protein tag YFP yellow fluorescent protein yellow fluorescent protein YFP yfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 682402 unspecified role unspecified role fluorescence donor fluorescence donor region cfp tag cyan fluorescent protein tag CFP cyan fluorescent protein cyan fluorescent protein CFP cfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false Stoichiometry: 6.0 direct interaction direct interaction false false false 4 Table 1 The proteins colocalised to the plasma membrane The authors contest that "in those membrane areas where interaction between SERK1 and CDC48A occurs, a substantial amount of CDC48A is in oligomeric form". cdc48c Oligomerisation of CDC48C 682396 N/A 682403 unspecified role unspecified role fluorescence donor fluorescence donor n terminal cfp tag cyan fluorescent protein tag CFP cyan fluorescent protein cyan fluorescent protein CFP cfp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false N/A 682403 unspecified role unspecified role fluorescence accept fluorescence acceptor fluorescence accept n terminal yfp tag yellow fluorescent protein tag YFP yellow fluorescent protein yellow fluorescent protein YFP yfp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false direct interaction direct interaction false false false 4, 5, Table 1 cdc48a-5 Oligomerisation of CDC48A 682396 N/A 682402 unspecified role unspecified role fluorescence donor fluorescence donor region cfp tag cyan fluorescent protein tag CFP cyan fluorescent protein cyan fluorescent protein CFP cfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 682402 unspecified role unspecified role fluorescence accept fluorescence acceptor fluorescence accept region rfp tag red fluorescent protein tag red fluorescent protein RFP red fluorescent protein RFP rfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false direct interaction direct interaction false false false 4 Table 1 cdc48a-serk1-1 Phosphorylation of CDC48A by SERK1 682397 N/A 682401 enzyme enzyme neutral component neutral component region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false region binding region binding-associated region binding region range range range range false ecoli Escherichia coli (strain K12) N/A 682402 enzyme target enzyme target substrate substrate neutral component neutral component region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecoli Escherichia coli (strain K12) Stoichiometry: 6.0 phosphorylation phosphorylation reaction phosphorylation false false false 6 phosphorylation of CDC48A The coordinates of the SERK1 kinase domain did not appear in the paper and the coordinates of this domain are taken from the UniProt record of this protein. serk1-5 Autophosphorylation of SERK1 682397 N/A 682401 putative self putative self putative self putative self region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false region binding region binding-associated region binding region range range range range false ecoli Escherichia coli (strain K12) phosphorylation phosphorylation reaction phosphorylation false true false 6 Autophosphorylation of Q94AG2 The coordinates of the SERK1 kinase domain did not appear in the paper and the coordinates of this domain are taken from the UniProt record of this protein. cdc48a Oligomerisation of CDC48A 682398 N/A 682402 unspecified role unspecified role neutral component neutral component c-terminal yfp tag yellow fluorescent protein tag YFP yellow fluorescent protein yellow fluorescent protein YFP yfp tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false n terminal required to bind necessary binding region required to bind certain certain sequence position certain certain certain sequence position certain false c-terminal required to bind necessary binding region required to bind certain certain sequence position certain certain certain sequence position certain false Stoichiometry: 6.0 physical association physical association false false false 1 The complex of CDC48A proteins was identified as a hexamer on the basis of its calculated molecular weight. cdc48a-1 Colocalisation of CDC48A and CDC48C 682399 N/A 682403 unspecified role unspecified role neutral component neutral component region cfp tag cyan fluorescent protein tag CFP cyan fluorescent protein cyan fluorescent protein CFP cfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 682402 unspecified role unspecified role neutral component neutral component c-terminal yfp tag yellow fluorescent protein tag YFP yellow fluorescent protein yellow fluorescent protein YFP yfp tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false region required to bind necessary binding region required to bind certain certain sequence position certain certain certain sequence position certain false Stoichiometry: 6.0 colocalization colocalization false false false 2 The proteins colocalised to the nucleus. cdc48a-serk1-2 Phosphorylation of CDC48A by SERK1 682400 N/A 682402 enzyme target enzyme target substrate substrate neutral component neutral component region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecoli Escherichia coli (strain K12) Stoichiometry: 6.0 N/A 682401 enzyme enzyme neutral component neutral component region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false region binding region binding-associated region binding region range range range range false ecoli Escherichia coli (strain K12) phosphorylation phosphorylation reaction phosphorylation false false false 6 phosphorylation of CDC48A at Serine 41 The coordinates of the SERK1 kinase domain did not appear in the paper and the coordinates of this domain are taken from the UniProt record of this protein. The authors point out that they did " not have any peptide coverage in the C-terminal tail (from amino acid 775 onward; Fig. 6B), where three Sers, three Thrs, and one Tyr are present, so there may be additional targets for SERK1 phosphorylation".