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/ joachimiak-2014-3 The structural basis of substrate recognition by the eukaryotic chaperonin TRiC/CCT. in vitro In vitro crosslink cross-linking study crosslink sequence tag sequence tag identification sequence tag Joachimiak L.A., Walzthoeni T., Liu C.W., Aebersold R., Frydman J. Crosslinking agent was Disuccinimidyl suberate. After Cross linking proteolysis was carried out, and samples were fractionated prior to MS/MS analysis. Crosslinks to actin and tubulin were not added as the composition of these complexes was unknown. lajoachi@gmail.com, jfrydman@stanford.edu Cell (0092-8674) 2014 imex curation Only protein-protein interactions joachimiak-2014-1 The structural basis of substrate recognition by the eukaryotic chaperonin TRiC/CCT. in vitro In vitro spr surface plasmon resonance Optical biosensor BIAcore(r) BIAcore(r) Optical biosensor spr predetermined predetermined participant predetermined Joachimiak L.A., Walzthoeni T., Liu C.W., Aebersold R., Frydman J. Source of CCT1 taken from PMID: 17018290 as referenced in the text, CCT3 from work of contributing scientist and mutant mapping. lajoachi@gmail.com, jfrydman@stanford.edu Cell (0092-8674) 2014 imex curation Only protein-protein interactions joachimiak-2014-2 The structural basis of substrate recognition by the eukaryotic chaperonin TRiC/CCT. in vitro In vitro nmr nuclear magnetic resonance NMR NMR nmr predetermined predetermined participant predetermined Joachimiak L.A., Walzthoeni T., Liu C.W., Aebersold R., Frydman J. lajoachi@gmail.com, jfrydman@stanford.edu Cell (0092-8674) 2014 imex curation Only protein-protein interactions gag_hv1h2 Gag polyprotein gag Pr55Gag protein protein hv1h2 Human immunodeficiency virus type 1 group M subtype B (isolate HXB2) (HIV-1) HIV-1 MGARASVLSGGELDRWEKIRLRPGGKKKYKLKHIVWASRELERFAVNPGLLETSEGCRQILGQLQPSLQTGSEELRSLYNTVATLYCVHQRIEIKDTKEALDKIEEEQNKSKKKAQQAAADTGHSNQVSQNYPIVQNIQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRVHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTNNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTACQGVGGPGHKARVLAEAMSQVTNSATIMMQRGNFRNQRKIVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQANFLGKIWPSYKGRPGNFLQSRPEPTAPPEESFRSGVETTTPPQKQEPIDKELYPLTSLRSLFGNDPSSQ tcpb_bovin T-complex protein 1 subunit beta CCT2 CCT-beta protein protein bovin Bos taurus (Bovine) Bovine MASLSLAPVNIFKAGADEERAETARLSSFIGAIAIGDLVKSTLGPKGMDKILLSSGRDASLMVTNDGATILKNIGVDNPAAKVLVDMSRVQDDEVGDGTTSVTVLAAELLREAESLIAKKIHPQTIIAGWREATKAARQALLNSAVDHGSDEVKFRQDLMNIAGTTLSSKLLTHHKDHFTKLAVEAVLRLKGSGNLEAIHVIKKLGGSLADSYLDEGFLLDKKIGVNQPKRIENAKILIANTGMDTDKIKIFGSRVRVDSTAKVAEIEHAEKEKMKEKVERILKHGINCFINRQLIYNYPEQLFGAAGVMAIEHADFVGVERLALVTGGEIASTFDHPELVKLGSCKLIEEVMIGEDKLIHFSGVALGEACTIVLRGATQQILDEAERSLHDALCVLAQTVKDSRTVYGGGCSEMLMAHAVTQLASRTPGKEAVAMESYAKALRMLPTIIADNAGYDSADLVAQLRAAHSEGKTTAGLDMKEGTIGDMSVLGITESFQVKRQVLLSAAEAAEVILRVDNIIKAAPRKRVPDHHPC tcpz_bovin T-complex protein 1 subunit zeta CCT6A CCT-zeta CCT-zeta-1 protein protein bovin Bos taurus (Bovine) Bovine MAAVKTLNPKAEVARAQAALAVNISAARGLQDVLRTNLGPKGTMKMLVSGAGDIKLTKDGNVLLHEMQIQHPTASLIAKVATAQDDITGDGTTSNVLIIGELLKQADLYISEGLHPRIITEGFEAAKEKALQFLEQVKVSKEMDRETLIDVARTSLRTKVHAELADVLTEAVVDSILAIKKQDEPIDLFMVEIMEMKHKSETDTSLIRGLVLDHGARHPDMKKRVEDAYILTCNVSLEYEKTEVNSGFFYKSAEEREKLVKAERKFIEDRVKKIIELKKKVCGDSDKGFVVINQKGIDPFSLDALAKEGIIALRRAKRRNMERLTLACGGIALNSLDDLNPDCLGHAGLVYEYTLGEEKFTFIEKCNNPRSVTLLIKGPNKHTLTQIKDAIRDGLRAVKNAIDDGCVVPGAGAVEVAMAEALVKYKPSVKGRAQLGVQAFADALLIIPKVLAQNSGFDLQETLVKVQAEHSESGQLVGVDLNTGEPMVAAEAGIWDNYCVKKQLLHSCTVIATNILLVDEIMRAGMSSLKG tcph_bovin T-complex protein 1 subunit eta CCT7 CCT-eta protein protein bovin Bos taurus (Bovine) Bovine MMPTPVILLKEGTDSSQGIPQLVSNISACQVIAEAVRTTLGPRGMDKLIVDGRGKATISNDGATILKLLDVVHPAAKTLVDIAKSQDAEVGDGTTSVTLLAAEFLKQVKPYVEEGLHPQIIIRAFRTATQLAVNKIKEIAVTVKKEDKVEQRKLLEKCAMTALSSKLISQQKAFFAKMVVDAVMMLDDLLQLKMIGIKKVQGGALEESQLVAGVAFKKTFSYAGFEMQPKKYHNPMIALLNVELELKAEKDNAEIRVHTVEDYQAIVDAEWNILYDKLEKIHHSGAKVVLSKLPIGDVATQYFADRDMFCAGRVPEEDLKRTMMACGGSIQTSVNALSSDVLGRCQVFEETQIGGERYNFFTGCPKAKTCTIILRGGAEQFMEETERSLHDAIMIVRRAIKNDSVVAGGGAIEMELSKYLRDYSRTIPGKQQLLIGAYAKALEIIPRQLCDNAGFDATNILNKLRARHAQGGMWYGVDINTEDIADNFEAFVWEPAMVRINALTAASEAACLIVSVDETIKNPRSTVDASPAAGRGRGRGRLH tcpg_mouse T-complex protein 1 subunit gamma CCT-gamma Matricin mTRiC-P5 Cct3 Cctg protein protein mouse Mus musculus Mouse MMGHRPVLVLSQNTKRESGRKVQSGNINAAKTIADIIRTCLGPKSMMKMLLDPMGGIVMTNDGNAILREIQVQHPAAKSMIEISRTQDEEVGDGTTSVIILAGEMLSVAEHFLEQQMHPTVVISAYRMALDDMISTLKKISTPVDVNNREMMLSIINSSITTKVISRWSSLACNIALDAVKTVQFEENGRKEIDIKKYARVEKIPGGIIEDSCVLRGVMINKDVTHPRMRRYIKNPRIVLLDSSLEYKKGESQTDIEITREEDFTRILQMEEEYIHQLCEDIIQLKPDVVITEKGISDLAQHYLMRANVTAIRRVRKTDNNRIARACGARIVSRPEELREDDVGTGAGLLEIKKIGDEYFTFITDCKDPKACTILLRGASKEILSEVERNLQDAMQVCRNVLLDPQLVPGGGASEMAVAHALTEKSKAMTGVEQWPYRAVAQALEVIPRTLIQNCGASTIRLLTSLRAKHTQESCETWGVNGETGTLVDMKELGIWEPLAVKLQTYKTAVETAVLLLRIDDIVSGHKKKGDDQNRQTGAPDAGQE p04591-pro_0000038598 p6-gag gag Pr55Gag protein protein hv1h2 Human immunodeficiency virus type 1 group M subtype B (isolate HXB2) (HIV-1) HIV-1 LQSRPEPTAPPEESFRSGVETTTPPQKQEPIDKELYPLTSLRSLFGNDPSSQ 449 500 9117D426B88A73CB vhl_human von Hippel-Lindau disease tumor suppressor VHL pVHL Protein G7 protein protein human Homo sapiens Human MPRRAENWDEAEVGAEEAGVEEYGPEEDGGEESGAEESGPEESGPEELGAEEEMEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD tcpa_yeast T-complex protein 1 subunit alpha TCP1 CCT1 YDR212W YD8142.13 YD8142B.04 CCT-alpha protein protein yeast Saccharomyces cerevisiae Baker's yeast MSQLFNNSRSDTLFLGGEKISGDDIRNQNVLATMAVANVVKSSLGPVGLDKMLVDDIGDFTVTNDGATILSLLDVQHPAGKILVELAQQQDREIGDGTTSVVIIASELLKRANELVKNKIHPTTIITGFRVALREAIRFINEVLSTSVDTLGKETLINIAKTSMSSKIIGADSDFFSNMVVDALLAVKTQNSKGEIKYPVKAVNVLKAHGKSATESLLVPGYALNCTVASQAMPKRIAGGNVKIACLDLNLQKARMAMGVQINIDDPEQLEQIRKREAGIVLERVKKIIDAGAQVVLTTKGIDDLCLKEFVEAKIMGVRRCKKEDLRRIARATGATLVSSMSNLEGEETFESSYLGLCDEVVQAKFSDDECILIKGTSKHSSSSIILRGANDYSLDEMERSLHDSLSVVKRTLESGNVVPGGGCVEAALNIYLDNFATTVGSREQLAIAEFAAALLIIPKTLAVNAAKDSSELVAKLRSYHAASQMAKPEDVKRRSYRNYGLDLIRGKIVDEIHAGVLEPTISKVKSLKSALEACVAILRIDTMITVDPEPPKEDPHDH 02C625D329359E61 cct2-gag 1779476 n/a 1779479 unspecified role unspecified role neutral component neutral component lys-397 cross linker cross linker crosslinker crosslinker certain certain sequence position certain certain certain sequence position certain false n/a 1779480 unspecified role unspecified role neutral component neutral component lys-284 cross linker cross linker crosslinker crosslinker certain certain sequence position certain certain certain sequence position certain false bovin Bos taurus (Bovine) Bovine 1779491 1779489 physical association physical association false false false 1779476 Fig 6B cct6a-gag 1779476 n/a 1779479 unspecified role unspecified role neutral component neutral component lys-110 cross linker cross linker crosslinker crosslinker certain certain sequence position certain certain certain sequence position certain false n/a 1779481 unspecified role unspecified role neutral component neutral component lys-258 cross linker cross linker crosslinker crosslinker certain certain sequence position certain certain certain sequence position certain false bovin Bos taurus (Bovine) Bovine 1779496 1779494 physical association physical association false false false 1779476 Fig 6B cct7-gag 1779476 n/a 1779479 unspecified role unspecified role neutral component neutral component lys-424 cross linker cross linker crosslinker crosslinker certain certain sequence position certain certain certain sequence position certain false n/a 1779482 unspecified role unspecified role neutral component neutral component lys-287 cross linker cross linker crosslinker crosslinker certain certain sequence position certain certain certain sequence position certain false bovin Bos taurus (Bovine) Bovine 1779501 1779499 physical association physical association false false false 1779476 Fig 6B gag-cct3-2 1779477 n/a 1779483 unspecified role unspecified role prey prey apical_domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false P80318:p.Arg228Ala mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength alanine scanning alanine scanning certain certain sequence position certain certain certain sequence position certain false P80318:p.Arg230Ala mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength alanine scanning alanine scanning certain certain sequence position certain certain certain sequence position certain false P80318:p.Arg231Ala mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength alanine scanning alanine scanning certain certain sequence position certain certain certain sequence position certain false P80318:p.Leu299Ala mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength alanine scanning alanine scanning certain certain sequence position certain certain certain sequence position certain false P80318:p.Gln301Ala mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength alanine scanning alanine scanning certain certain sequence position certain certain certain sequence position certain false P80318:p.His302Ala mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength alanine scanning alanine scanning certain certain sequence position certain certain certain sequence position certain false P80318:p.Tyr303Ala mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false c-terminal 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 ecoli Escherichia coli (strain K12) n/a 1779484 unspecified role unspecified role bait bait P04591-PRO_0000038598:p.Ser3Cys mutation mutation certain certain sequence position certain certain certain sequence position certain false region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false chemical synthesis Chemical synthesis (Chemical synthesis) 1779515 1779504 direct interaction direct interaction false false false 1779477 Fig 1E, 1F, 3, Supp Fig 1A, 3, Supp. Table 1 Mutations which increase the Kd to >1uM have been taken as mutants which decrease the strength of the interaction. tcp1-vhl-1 1779477 n/a 1779485 unspecified role unspecified role unspecified role unspecified role box1 region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false P40337:p.Ser111Cys mutation mutation certain certain sequence position certain certain certain sequence position certain false n/a 1779486 unspecified role unspecified role unspecified role unspecified role apical_domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false P12612:p.Arg319Ala mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false P12612:p.Leu326Ala mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false P12612:p.Val311Ala mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false P12612:p.Leu305Ala mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false 1779521 1779518 direct interaction direct interaction false false false 1779477 Fig. 1E, 1F, Supp. Fig. 1C, 5C gag-cct3-1 1779478 n/a 1779484 unspecified role unspecified role bait bait region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false P04591-PRO_0000038598:p.Ser3Cys mutation mutation certain certain sequence position certain certain certain sequence position certain false region required to bind necessary binding region required to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) n/a 1779483 unspecified role unspecified role prey prey apical_region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false region 15n label 15n label 15N N15 15N N15 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecoli Escherichia coli (strain K12) 1779532 1779528 direct interaction direct interaction false false false Fig 2 and Supp. Fig. 2 gag-cct3-3 1779478 N/A 1779484 unspecified role unspecified role bait bait region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false P04591-PRO_0000038598:p.Ser3Cys mutation mutation certain certain sequence position certain certain certain sequence position certain false P04591-PRO_0000038598:p.Ser43_Asn47delinsAlaAlaAlaAlaAla mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain false N/A 15n label 15n label 15N N15 15N N15 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecoli Escherichia coli (strain K12) N/A 1779483 unspecified role unspecified role prey prey apical_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) 1779541 1779536 direct interaction direct interaction false false false Fig 4 B/D