UniProt UniProt http://www.uniprot.org jeong-2017-4 in vitro In vitro pull down pull down weight by comassie molecular weight estimation by coomasie staining weight by comassie Jeong H., Park J., Kim HI., Lee M., Ko YJ., Lee S., Jun Y., Lee C. junys@gist.ac.kr, changwook@unist.ac.kr Proceedings of the National Academy of Sciences of the United States of America 2017 imex curation Only protein-protein interactions imex curation jeong-2017-2 in vitro In vitro molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column predetermined predetermined participant predetermined Jeong H., Park J., Kim HI., Lee M., Ko YJ., Lee S., Jun Y., Lee C. junys@gist.ac.kr, changwook@unist.ac.kr Proceedings of the National Academy of Sciences of the United States of America 2017 imex curation Only protein-protein interactions imex curation jeong-2017-3 in vitro In vitro itc isothermal titration calorimetry ITC ITC itc predetermined predetermined participant predetermined Jeong H., Park J., Kim HI., Lee M., Ko YJ., Lee S., Jun Y., Lee C. junys@gist.ac.kr, changwook@unist.ac.kr Proceedings of the National Academy of Sciences of the United States of America 2017 imex curation Only protein-protein interactions imex curation jeong-2017-6 yeast Saccharomyces cerevisiae Baker's yeast anti tag coip anti tag coimmunoprecipitation anti tag coip anti tag western anti tag western blot anti tag western Jeong H., Park J., Kim HI., Lee M., Ko YJ., Lee S., Jun Y., Lee C. junys@gist.ac.kr, changwook@unist.ac.kr Proceedings of the National Academy of Sciences of the United States of America 2017 imex curation Only protein-protein interactions imex curation jeong-2017-1 in vitro In vitro x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Jeong H., Park J., Kim HI., Lee M., Ko YJ., Lee S., Jun Y., Lee C. junys@gist.ac.kr, changwook@unist.ac.kr Proceedings of the National Academy of Sciences of the United States of America 2017 imex curation Only protein-protein interactions imex curation jeong-2017-5 in vitro In vitro density sedimentation cosedimentation through density gradient density sedimentation predetermined predetermined participant predetermined Jeong H., Park J., Kim HI., Lee M., Ko YJ., Lee S., Jun Y., Lee C. junys@gist.ac.kr, changwook@unist.ac.kr Proceedings of the National Academy of Sciences of the United States of America 2017 imex curation Only protein-protein interactions imex curation nvj1_yeast Nucleus-vacuole junction protein 1 VAB36 NVJ1 YHR195W protein protein yeast Saccharomyces cerevisiae Baker's yeast MTRPPLVRGIFSLGLSVAVLKGVEKTVRKHLERQGWIEPQKVDYELIFTIDRLKNLVDNKREALTAEQPDAGELSWRKVFNFISRQSSELDTRIYVLILLLSFLLPIAWTVLDGDRETTLEDKDNDCNVDLIENERRLKHYNDGERAVLQFGKNRSEPIILSYKDMNVLEGEHEFTSKEEHSNSHLTSKSENALNQVGSEDLLGCHLEKQLEEDKNEPNGEADGEDDNNREKDCSSSSEVESQSKCRKESTAEPDSLSRDTRTTSSLKSSTSFPISFKGSIDLKSLNQPSSLLHIQVSPTKSSNLDAQVNTEQAYSQPFRY vac8_yeast Vacuolar protein 8 VAC8 YEB3 YEL013W protein protein yeast Saccharomyces cerevisiae Baker's yeast MGSCCSCLKDSSDEASVSPIADNEREAVTLLLGYLEDKDQLDFYSGGPLKALTTLVYSDNLNLQRSAALAFAEITEKYVRQVSREVLEPILILLQSQDPQIQVAACAALGNLAVNNENKLLIVEMGGLEPLINQMMGDNVEVQCNAVGCITNLATRDDNKHKIATSGALIPLTKLAKSKHIRVQRNATGALLNMTHSEENRKELVNAGAVPVLVSLLSSTDPDVQYYCTTALSNIAVDEANRKKLAQTEPRLVSKLVSLMDSPSSRVKCQATLALRNLASDTSYQLEIVRAGGLPHLVKLIQSDSIPLVLASVACIRNISIHPLNEGLIVDAGFLKPLVRLLDYKDSEEIQCHAVSTLRNLAASSEKNRKEFFESGAVEKCKELALDSPVSVQSEISACFAILALADVSKLDLLEANILDALIPMTFSQNQEVSGNAAAALANLCSRVNNYTKIIEAWDRPNEGIRGFLIRFLKSDYATFEHIALWTILQLLESHNDKVEDLVKNDDDIINGVRKMADVTFERLQRSGIDVKNPGSNNNPSSNDNNSNNNDTGSEHQPVEDASLELYNITQQILQFLH B2E75774B47E5933 vac17_yeast vacuole-related protein 17 YCL063W YCL63W/YCL62W VAC17 Vacuole-specific MYO2 receptor VAC17 protein protein yeast Saccharomyces cerevisiae Baker's yeast MATQALEDITERLLIRSQEAILQLDLWIQRQQRSSICQTTDQESLDKLSQQYNQYMSQLNSLYVRSESVRDKLSKEQQRRLITEDNEHQRIEDLVREFQDITLRLNELATVPNEAPNDSPQSQSTRSSLGSFQPRPLKIIERQRLCMVTPSKPPKKSVGFNPINEVDCPSKTNSLPCSPKKQPARNRTLRAAKSHDTGLNKSKKPSSSDTYESFFKNRQRLSLTFFDEMDDEDFDSDQDTIILPNISTPPHVGVTAKGAEFEPLRRYNSHESILSNKPAPSKSLNLGSFSASFFRPSNPTFGTSISNVQVNCHPTVAATMAPSRNGPRISSSKALLSSFIARSDTHTVKENNTNLKHASFMDKFNSSLSTISESFQSKRGRKNKGMNEERISNHNVAQEQKNNMDISVSIEELQDALNTELLF 7F14A3A0BFE9571B atg13_yeast Autophagy-related protein 13 ATG13 APG13 YPR185W protein protein yeast Saccharomyces cerevisiae Baker's yeast MVAEEDIEKQVLQLIDSFFLKTTLLICSTESSRYQSSTENIFLFDDTWFEDHSELVSELPEIISKWSHYDGRKELPPLVVETYLDLRQLNSSHLVRLKDHEGHLWNVCKGTKKQEIVMERWLIELDNSSPTFKSYSEDETDVNELSKQLVLLFRYLLTLIQLLPTTELYQLLIKSYNGPQNEGSSNPITSTGPLVSIRTCVLDGSKPILSKGRIGLSKPIINTYSNALNESNLPAHLDQKKITPVWTKFGLLRVSVSYRRDWKFEINNTNDELFSARHASVSHNSQGPQNQPEQEGQSDQDIGKRQPQFQQQQQPQQQQQQQQQQQRQHQVQTQQQRQIPDRRSLSLSPCTRANSFEPQSWQKKVYPISRPVQPFKVGSIGSQSASRNPSNSSFFNQPPVHRPSMSSNYGPQMNIEGTSVGSTSKYSSSFGNIRRHSSVKTTENAEKVSKAVKSPLQPQESQEDLMDFVKLLEEKPDLTIKKTSGNNPPNINISDSLIRYQNLKPSNDLLSEDLSVSLSMDPNHTYHRGRSDSHSPLPSISPSMHYGSLNSRMSQGANASHLIARGGGNSSTSALNSRRNSLDKSSNKQGMSGLPPIFGGESTSYHHDNKIQKYNQLGVEEDDDDENDRLLNQMGNSATKFKSSISPRSIDSISSSFIKSRIPIRQPYHYSQPTTAPFQAQAKFHKPANKLIDNGNRSNSNNNNHNGNDAVGVMHNDEDDQDDDLVFFMSDMNLSKEG 45CD16F69B795E62 lam6_yeast Membrane-anchored lipid-binding protein LAM6 LAM6 LTC1 Lipid transfer at contact site protein 1 Lipid transfer protein anchored at membrane contact sites 1 YLR072W protein protein yeast Saccharomyces cerevisiae Baker's yeast MWGDSMRELGDAMDNELNAVKPVVEEGGMDGARKFIKGKSFQKSSTEHMLISPGRDGSVPLNGLKSSPADPHLSDVNSILDNHRGGGETALTSVNNIIMATSTNGDSDGVDGDAKRPSISNCSSRSSFFDTVLSTFSLKSNSQDTVTNEVKNIEVQFASEEANKKFRQMFKPLAPNTRLITDYFCYFHREFPYQGRIYLSNTHLCFNSTVLNWMAKLQIPLNEIKYLDKVTTNSSAISVETVTNRYTFSGFIARDEVFQLITRVWSKENLTNINDVLEVDERVSKKKGISSTPSSIFNNVSTNAYNDFISTTTTEPTSRASYMSENDMLIEEAIRSVDDYMGTPRASPSSSSSSSSSSSSLGSSTTYYCRPVYRLKPNAPFQYEGPFHVQETMDFPYKPEANNEYVLLERQFSVPPGLLFIMMFNEDNPVFELSFLKTQDSSNISHIGTFEKVNKDGQHYREFQYTKQLHFPVGPKSTNCEVAEILLHCDWERYINVLSITRTPNVPSGTSFSTRTRYMFRWDDQGQGCILKISFWVDWNASSWIKPMVESNCKNGQISATKDLVKLVEEFVEKYVELSKEKADTLKPLPSVTSFGSPRKVAAPELTMVQPESKPEAEAEISEIGSDRWRFNWVNIIILVLLVLNLLYLMKLNKKMDKLTNLMTHKDEVVAHATLLDIPAKVQWSRPRRGDVL FACE2F16326B36F6 tco89_yeast Target of rapamycin complex 1 subunit TCO89 YPL180W TCO89 89 kDa TOR complex 1 protein protein protein yeast Saccharomyces cerevisiae Baker's yeast MVHRGRTLKSDTDVTSLNASTVSHQSKPFRQFSTRSRAKSNASFKGLRRVLTHDGTLDNDYFNKHNVSQKCKSSDALFRKRTISGLNMTALTRVKSNQGKRSASFHSPVHNTLLSPKNSSHSNTGTAGFGLKPRRSKSTQSVLSLRDAQESKKSESTTDEEVECFSEDNIEDGKVNNDKVIAEHVMPEEKKNVQQLNQNELQSPDSIDEQEEDKSGTDGKENHRAVSLPLPHLSSNNYFGESSHSIEHQKDGETSPSSIETKLNATSVINEEGQSKVTKEADIDDLSSHSQNLRASLVKAGDNISEAPYDKEKKILDVGNTLAAHKSNQKPSHSDEQFDQEDHIDAPRSNSSRKSDSSFMSLRRQSSKQHKLLNEEEDLIKPDDISSAGTKDIEGHSLLENYAPNMILSQSTGVERRFENSSSIQNSLGNEIHDSGEHMASGDTFNELDDGKLRKSKKNGGRSQLGQNIPNSQSTFPTIANIGSKDNNVPQHNFSTSISSLTNNLRRAAPESFHGSRMNNIFHKKGNQNLLLRSNDLNKNSAAPASPLSNEHITSSTNSGSDANRQSNSGAKFNSFAQFLKSDGIDAESRTQRKLWLQRENSIMDLSSQNDGSDSIFMAGNIDAKREFERISHEYSNVKRFYNPLDEALLRVQPIITGNANNIRKKSHNDAQSIAHSSSDTDHKDEDDLLFTNYDKKFDDLYPHLASAKIQAVLSGIWKSESYLFNKDVNPINKNRTTSTNHSVGHTASQNARNLLRGPMGSSTTLHHQRVINSLQPTTRAVNRRMENVGYMHTQPQQR nvj1-vac8-4 3319752 N/A 3319758 unspecified role unspecified role bait bait purified purified region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false P38881:p.Ala307Arg mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false P38881:p.Phe319Glu mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain false P38881:p.[Ile295Arg;Ala307Arg;Phe319Glu] mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength 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 P38881:p.Pro299Ser mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction certain certain sequence position certain certain certain sequence position certain false P38881:p.Ser303Ala mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction certain certain sequence position certain certain certain sequence position certain false n-terminal his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false P38881:p.Ile295Arg mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false P38881:p.Lys301Glu mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 3319759 unspecified role unspecified role prey prey purified purified region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false n_terminus 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 P39968:p.[Arg276Glu;Arg317Glu;Arg359Glu] mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength 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) direct interaction direct interaction false false false Fig. 3B, 4B vac17-vac8-3 3319752 N/A 3319760 unspecified role unspecified role bait bait purified purified 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 ecoli Escherichia coli (strain K12) N/A 3319759 unspecified role unspecified role prey prey purified purified region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false n_terminus 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 P39968:p.[Arg276Glu;Arg317Glu;Arg359Glu] mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction 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) 3319784 3319782 direct interaction direct interaction false false false Fig. 4B atg13-vac8-1 3319752 N/A 3319761 unspecified role unspecified role bait bait 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 ecoli Escherichia coli (strain K12) N/A 3319759 unspecified role unspecified role prey prey purified purified region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false 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 P39968:p.[Arg276Glu;Arg317Glu;Arg359Glu] mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength 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) 3319792 3319790 direct interaction direct interaction false false false Fig. 4B lam6-vac8-1 3319752 N/A 3319762 unspecified role unspecified role bait bait purified purified n_terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false 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) N/A 3319759 unspecified role unspecified role prey prey purified purified region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false n_terminus 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 P39968:p.[Arg276Glu;Arg317Glu;Arg359Glu] mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction 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) direct interaction direct interaction false false false Supp Fig. 5B, 5C tco89-vac8-1 3319752 N/A 3319763 unspecified role unspecified role bait bait purified purified n_terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false 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) N/A 3319759 unspecified role unspecified role prey prey purified purified region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false n_terminus 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 P39968:p.[Arg276Glu;Arg317Glu;Arg359Glu] mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction 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) direct interaction direct interaction false false false Supp Fig. 5B, 5C nvj1-vac8-5 3319753 N/A 3319758 unspecified role unspecified role neutral component neutral component purified purified 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: 1.0 N/A 3319759 unspecified role unspecified role neutral component neutral component purified purified P39968:p.Leu55Arg mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain false region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false P39968:p.Ala51Arg mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 direct interaction direct interaction false false false Fig. 1B, 6E nvj1-vac8-6 3319753 N/A 3319758 unspecified role unspecified role neutral component neutral component purified purified 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 3319759 unspecified role unspecified role neutral component neutral component purified purified 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 3319822 3319820 direct interaction direct interaction false false false Fig. 6C The single VAC8 mutation ala51arg or leu55arg interfered with the dimer interface preventing the two NVJ1-VAC8 dimers from forming a tetramer as did deletion of residues 318-321 of Nvj1p. nvj1-vac8-3 3319754 N/A 3319758 unspecified role unspecified role neutral component neutral component purified purified 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: 1.0 N/A 3319759 unspecified role unspecified role neutral component neutral component purified purified 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: 1.0 3319827 3319825 direct interaction direct interaction false false false 3319754 Fig. 1C atg13-vac8-2 3319754 N/A 3319761 unspecified role unspecified role neutral component neutral component purified purified 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) N/A 3319759 unspecified role unspecified role neutral component neutral component purified purified 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) direct interaction direct interaction false false false 3319754 Fig. 4C vac8-vac8-1 3319755 N/A 3319759 unspecified role unspecified role prey prey region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 3319759 unspecified role unspecified role bait bait region egfp tag enhanced green fluorescent protein tag enhanced green fluorescent protein EGFP enhanced green fluorescent protein EGFP egfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false physical association physical association false false false Fig. 7A vac8-vac8-2 3319755 N/A 3319759 unspecified role unspecified role bait bait region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 3319759 unspecified role unspecified role prey prey region egfp tag enhanced green fluorescent protein tag enhanced green fluorescent protein EGFP enhanced green fluorescent protein EGFP egfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false physical association physical association false false false Fig. 7A nvj1-vac8-1 3319756 N/A 3319758 unspecified role unspecified role neutral component neutral component purified purified 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 3319759 unspecified role unspecified role neutral component neutral component purified purified 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 3319847 3319845 direct interaction direct interaction false false false Supp Table 1 Rworking 0.19 Rfree 0.222 2.4A nvj1-vac8-2 3319757 N/A 3319758 unspecified role unspecified role neutral component neutral component purified purified 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 3319759 unspecified role unspecified role neutral component neutral component purified purified 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 3319852 3319850 direct interaction direct interaction false false false Fig. 6D The single VAC8 mutation ala51arg or leu55arg interfered with the dimer interface preventing the two NVJ1-VAC8 dimers from forming a tetramer, as did deletion of residues 318-321 of Nvj1p.