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/ The yeast ski complex: crystal structure and RNA channeling to the exosome complex. The yeast ski complex: crystal structure and RNA channeling to the exosome complex. Cell (0092-8674) 2013 imex curation Halbach F., Reichelt P., Rode M., Conti E. I haven't added the exosome data (SuppFig 6) as I didn't add it when they did the referenced purification in Cell as 5 of the proteins were in the same band. conti@biochem.mpg.de 13-Jan-2014: Contacted by IntAct-Help. Only protein-protein interactions in vitro In vitro x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Halbach F., Reichelt P., Rode M., Conti E. I haven't added the exosome data (SuppFig 6) as I didn't add it when they did the referenced purification in Cell as 5 of the proteins were in the same band. conti@biochem.mpg.de Accepted 2013-DEC-23 by MGT Cell (0092-8674) 2013 Only protein-protein interactions imex curation Mock publication and experiment for abstract interactions that are not interaction evidences. Mock publication and experiment for abstract interactions that are not interaction evidences. unspecified method The yeast ski complex: crystal structure and RNA channeling to the exosome complex. The yeast ski complex: crystal structure and RNA channeling to the exosome complex. Cell (0092-8674) 2013 imex curation Halbach F., Reichelt P., Rode M., Conti E. I haven't added the exosome data (SuppFig 6) as I didn't add it when they did the referenced purification in Cell as 5 of the proteins were in the same band. conti@biochem.mpg.de 13-Jan-2014: Contacted by IntAct-Help. Only protein-protein interactions in vitro In vitro nuclease footprinting nuclease footprinting weight autoradiogra molecular weight estimation by autoradiography weight autoradiogra Halbach F., Reichelt P., Rode M., Conti E. I haven't added the exosome data (SuppFig 6) as I didn't add it when they did the referenced purification in Cell as 5 of the proteins were in the same band. conti@biochem.mpg.de Accepted 2013-DEC-23 by MGT Cell (0092-8674) 2013 Only protein-protein interactions imex curation Upf1 and Ski2 give the same pattern, and Ski2 in isolation gives no protection so I think Upf1 is a negative control, not a positive. The yeast ski complex: crystal structure and RNA channeling to the exosome complex. The yeast ski complex: crystal structure and RNA channeling to the exosome complex. Cell (0092-8674) 2013 imex curation Halbach F., Reichelt P., Rode M., Conti E. I haven't added the exosome data (SuppFig 6) as I didn't add it when they did the referenced purification in Cell as 5 of the proteins were in the same band. conti@biochem.mpg.de 13-Jan-2014: Contacted by IntAct-Help. Only protein-protein interactions in vitro In vitro pull down pull down weight by comassie molecular weight estimation by coomasie staining weight by comassie Halbach F., Reichelt P., Rode M., Conti E. I haven't added the exosome data (SuppFig 6) as I didn't add it when they did the referenced purification in Cell as 5 of the proteins were in the same band. conti@biochem.mpg.de Accepted 2013-DEC-23 by MGT Cell (0092-8674) 2013 Only protein-protein interactions imex curation The yeast ski complex: crystal structure and RNA channeling to the exosome complex. The yeast ski complex: crystal structure and RNA channeling to the exosome complex. Cell (0092-8674) 2013 imex curation Halbach F., Reichelt P., Rode M., Conti E. I haven't added the exosome data (SuppFig 6) as I didn't add it when they did the referenced purification in Cell as 5 of the proteins were in the same band. conti@biochem.mpg.de 13-Jan-2014: Contacted by IntAct-Help. Only protein-protein interactions in vitro In vitro atpase assay atpase assay predetermined predetermined participant predetermined Halbach F., Reichelt P., Rode M., Conti E. I haven't added the exosome data (SuppFig 6) as I didn't add it when they did the referenced purification in Cell as 5 of the proteins were in the same band. conti@biochem.mpg.de Accepted 2013-DEC-23 by MGT Cell (0092-8674) 2013 Only protein-protein interactions imex curation The yeast ski complex: crystal structure and RNA channeling to the exosome complex. The yeast ski complex: crystal structure and RNA channeling to the exosome complex. Cell (0092-8674) 2013 imex curation Halbach F., Reichelt P., Rode M., Conti E. I haven't added the exosome data (SuppFig 6) as I didn't add it when they did the referenced purification in Cell as 5 of the proteins were in the same band. conti@biochem.mpg.de 13-Jan-2014: Contacted by IntAct-Help. Only protein-protein interactions in vitro In vitro comigration in sds comigration in sds page comigration in sds weight by comassie molecular weight estimation by coomasie staining weight by comassie Halbach F., Reichelt P., Rode M., Conti E. I haven't added the exosome data (SuppFig 6) as I didn't add it when they did the referenced purification in Cell as 5 of the proteins were in the same band. conti@biochem.mpg.de Accepted 2013-DEC-23 by MGT Cell (0092-8674) 2013 Only protein-protein interactions imex curation ski8_yeast Antiviral protein SKI8 YGL213C SKI8 REC103 Superkiller protein 8 protein protein yeast Saccharomyces cerevisiae Baker's yeast MSKVFIATANAGKAHDADIFSVSACNSFTVSCSGDGYLKVWDNKLLDNENPKDKSYSHFVHKSGLHHVDVLQAIERDAFELCLVATTSFSGDLLFYRITREDETKKVIFEKLDLLDSDMKKHSFWALKWGASNDRLLSHRLVATDVKGTTYIWKFHPFADESNSLTLNWSPTLELQGTVESPMTPSQFATSVDISERGLIATGFNNGTVQISELSTLRPLYNFESQHSMINNSNSIRSVKFSPQGSLLAIAHDSNSFGCITLYETEFGERIGSLSVPTHSSQASLGEFAHSSWVMSLSFNDSGETLCSAGWDGKLRFWDVKTKERITTLNMHCDDIEIEEDILAVDEHGDSLAEPGVFDVKFLKKGWRSGMGADLNESLCCVCLDRSIRWFREAGGK C5E7B9D2268F9727 C5E7B9D2268F9727 ski2_yeast Antiviral helicase SKI2 SKI2 YLR398C L8084.17 Superkiller protein 2 protein protein yeast Saccharomyces cerevisiae Baker's yeast MSEGFSSSSIQELYQSLKEITNNADVELFEDRITKLDFESTDEPKHANDIIKDRFLRPSNALPWSLLDMVQDVPHTSSPEDCSGKLDYKELLKVPDPINRTSYQFKRTGLEGKISGYKEEVDLKEVANANASNSLSITRSINHNQNSVRGSTAQLPFTPGGIPMKSVKTDSEQNGSSTMANATKLLHKDGQGLFDIPEGMNRGIKPMDSPAENEDQNGQFKELKQLNEIDNELDIRIEANEAKLKEEEKSAKSISEEIMEEATEETTADNADDAEIDELLPIGIDFGRTKPVSKSVPVKKEWAHVVDLNHKIENFDELIPNPARSWPFELDTFQKEAVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAHRNMTKTIYTSPIKALSNQKFRDFKETFDDVNIGLITGDVQINPDANCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYVNDQDRGVVWEEVIIMLPQHVKFILLSATVPNTYEFANWIGRTKQKNIYVISTPKRPVPLEINIWAKKELIPVINQNSEFLEANFRKHKEILNGESAKGAPSKTDNGRGGSTARGGRGGSNTRDGRGGRGNSTRGGANRGGSRGAGAIGSNKRKFFTQDGPSKKTWPEIVNYLRKRELLPMVVFVFSKKRCEEYADWLEGINFCNNKEKSQIHMFIEKSITRLKKEDRDLPQILKTRSLLERGIAVHHGGLLPIVKELIEILFSKGFIKVLFATETFAMGLNLPTRTVIFSSIRKHDGNGLRELTPGEFTQMAGRAGRRGLDSTGTVIVMAYNSPLSIATFKEVTMGVPTRLQSQFRLTYNMILNLLRIEALRVEEMIKYSFSENAKETLQPEHEKQIKVLQEELQTIEYKSCEICDNDIEKFLELMLAYKEATVNLMQEMVKSPSILHILKEGRLVAFRDPNDCLKLGFVFKVSLKDAVCVIMTFTKPYKLPNGEPNHLIYFPKADGYRRRNFPKFQKTDFYMEEVPVTAIEVITKRKFAAPLGKVIKKDVAALNEFNAETNNILDGKTLKEAINIEKQGLKIHQILLDRTNIRDEIFKLKSIKCPNLSQHIVPKFKAHVIKKKIEELYHLMSDQNLSLLPDYEKRLAVLKDTEFIDQNHNVLLKGRVACEINSGYELVLTELILDNFLGSFEPEEIVALLSVFVYEGKTREEEPPIVTPRLAKGKQRIEEIYKKMLCVFNTHQIPLTQDEAEFLDRKRFAMMNVVYEWARGLSFKEIMEMSPEAEGTVVRVITWLDEICREVKTASIIIGNSTLHMKMSRAQELIKRDIVFAASLYL 7CCD36CFC0DF8C32 7CCD36CFC0DF8C32 atp ATP Adenosine 5'-triphosphate Adenosine triphosphate ADENOSINE-5'-TRIPHOSPHATE Adephos Adetol Adynol Atipi ATP Atriphos Cardenosine Fosfobion Glucobasin H4atp Myotriphos Triadenyl Triphosphaden adenosine 5'-(tetrahydrogen triphosphate) small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) ski3_yeast Superkiller protein 3 SKI3 P9677.7 YPR189W protein protein yeast Saccharomyces cerevisiae Baker's yeast MSDIKQLLKEAKQELTNRDYEETIEISEKVLKLDPDNYFAHIFLGKALSSLPASNNVSSNRNLERATNHYVSAAKLVPDNLLAWKGLFLLFRTTEVVPDILSYDEYFDLCGQYADALLKQEQSQVELINDIKLLKKTHPDCQKAFYQHLKPGSLMAETIGRHLSTPQDALLNLIKILSNIETTEIGKTLSQNRLKLKASDPDYQIKLNSFSWEIIKNSEIDQLYNQLVNILADDQKRSEIENQWLEYRIKVLKSMPLDVKKDFFTKVKEMVEDMVLVNHQSLLAWQKYFEWTDYEDLDNMDAPLIIKYFKKFPKDPLAMILYSWLSSKLSKYDIKSLESANKPPEGHKKTEKETDIKDVDETNEDEVKDRVEDEVKDRVEDEVKDQDEEAKEDEEEDLDDIEIGLLEEEVVTVLTENIVKCKNNILAHRILCQYYLLTKEYEAALPYIKNGISLIAYNIKDLGVHLPLTKREFSLDLATVYTYVDAPKDHNAALKLYDNILSGDFSNIQAKMGKGIIFIERKNWKDAMTLLTQVHEQSPNNLEVLSELSWSKAHMGYMDEALAGLDTVIKGIKGMDLRSIDFRALNLWRQAKVYIMKHASINDAKQENVKCAFKLLIQSIKILDTFAPGFSTLGDIYCHYYKDHLRAFKCYFKAFDLDAGDYTAAKYITETYASKPNWQAASSIASRLIKGEKAKAELRSNNWPFRVVGIAHLEKQEESDSIEWFQSALRVDPNDVESWVGLGQAYHACGRIEASIKVFDKAIQLRPSHTFAQYFKAISLCDVGEYLESLDILEKVCQEAATEESFQIGLVEVLMRCSLDLYSQGFLLKSVSIAKDTIERIKIIISELKCENQQVWIYLSQVLRLFIWIESKVDTLPVESLVSIFENSQFSGSEEIDSVDNIKIDTLLDSTTDDNVSIACKFLILASKYSVSDQKFTDIAGTVRASYWYNIGISELTAFITLKEPQYRDAAIFAFKKSIQLQSNTSETWIGLGIATMDINFRVSQHCFIKATALEPKATNTWFNLAMLGLKKKDTEFAQQVLNKLQSLAPQDSSPWLGMALILEEQGDIIGSSKLFAHSFILSNGRSKAAQFMYAKNVLENHINNGDDERDIETVEKLTTASIALEQFFKKSPDSQFALQCALLTLERLHHYENANELANRLIGILEKKFEKTQDERELFNFAIIKGQFARIHLGLGNFELSIENADLSQGIISESSDEKSMKTKISNHICLGLSYFFLNDFDQTLNQFQELLSISKDSKHLVVLIAKVLYDVGESDTKEIALQELTEYIATSGADLLVTLTIAAMSILDDKREDLSIILEELKALPLSKQIIDKHKDAPYLIEEITKRLYRNDTGKQVWQRSAYFFPNNLKVWERLDKNIQRRIASNGQNKVTAEEMSKLYCESKNLRSIQRGMFLCPWNVTAVKALNECF 18FFF78D7CA5A6E4 18FFF78D7CA5A6E4 ski7_yeast Superkiller protein 7 SKI7 YOR29-27 YOR076C protein protein yeast Saccharomyces cerevisiae Baker's yeast MSLLEQLARKRIEKSKGLLSADQSHSTSKSASLLERLHKNRETKDNNAETKRKDLKTLLAKDKVKRSDFTPNQHSVSLSLKLSALKKSNSDLEKQGKSVTLDSKENELPTKRKSPDDKLNLEESWKAIKEMNHYCFLKNDPCINQTDDFAFTNFIIKDKKNSLSTSIPLSSQNSSFLSLKKHNNELLGIFVPCNLPKTTRKVAIENFNRPSPDDIIQSAQLNAFNEKLENLNIKSVPKAEKKEPINLQTPPTESIDIHSFIATHPLNLTCLFLGDTNAGKSTLLGHLLYDLNEISMSSMRELQKKSSNLDPSSSNSFKVILDNTKTERENGFSMFKKVIQVENDLLPPSSTLTLIDTPGSIKYFNKETLNSILTFDPEVYVLVIDCNYDSWEKSLDGPNNQIYEILKVISYLNKNSACKKHLIILLNKADLISWDKHRLEMIQSELNYVLKENFQWTDAEFQFIPCSGLLGSNLNKTENITKSKYKSEFDSINYVPEWYEGPTFFSQLYLLVEHNMNKIETTLEEPFVGTILQSSVLQPIAEINYVSLKVLINSGYIQSGQTIEIHTQYEDFHYYGIVSRMKNSKQILETNTKNNISVGLNPDILEVLVKIHNTEDFTKKQFHIRKGDIIIHSRKTNTLSPNLPNTLKLLALRLIKLSIQTHALSDPVDLGSELLLYHNLTHNAVKLVKILGTNDISINPNQSLIVEVEIIEPDFALNVIDSKYITNNIVLTSIDHKVIAVGRIACQ D93B956D02050BFA D93B956D02050BFA c(uc)28 C(UC)28 rna ribonucleic acid RNA rna chemical synthesis Chemical synthesis (Chemical synthesis) CUCUCUCUCUCUCUCUCUCUCUCUCUCUCUCUCUCUCUCUCUCUCUCUCUCUCUCUC ski2-ski3-10 1 8 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 certain certain sequence position certain certain certain sequence position certain trini-high_5 Trichoplusia ni cell line from eggs high_5 Insect cell line from Trichoplusia ni egg cells Invitrogen supplies this cell line. Invitrogen supply this cell line. 10 unspecified role unspecified role neutral component neutral component trini-high_5 Trichoplusia ni cell line from eggs high_5 Insect cell line from Trichoplusia ni egg cells Invitrogen supplies this cell line. Invitrogen supply this cell line. 7 unspecified role unspecified role neutral component neutral component trini-high_5 Trichoplusia ni cell line from eggs high_5 Insect cell line from Trichoplusia ni egg cells Invitrogen supplies this cell line. Invitrogen supply this cell line. physical association physical association 3.7A Rworking = 0.23 Rfree = 0.26 Table 1 atp-ski2 5 8 enzyme enzyme neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain certain certain sequence position certain certain certain sequence position certain trini-high_5 Trichoplusia ni cell line from eggs high_5 Insect cell line from Trichoplusia ni egg cells Invitrogen supplies this cell line. Invitrogen supply this cell line. 9 enzyme target enzyme target substrate substrate unspecified role unspecified role chemical synthesis Chemical synthesis (Chemical synthesis) atpase reaction atpase reaction Fig. 1B atp-ski-1 5 9 enzyme target enzyme target substrate substrate unspecified role unspecified role chemical synthesis Chemical synthesis (Chemical synthesis) 25 enzyme enzyme unspecified role unspecified role P35207:p.Glu445Gln mutation decreasing rate mutation decreasing interaction rate mutation decreasing rate certain certain sequence position certain certain certain sequence position certain E Q 27 Tue Nov 27 16:27:18 GMT 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'P35207:p.(Glu445Gln)' Tue Jun 30 17:01:27 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Glu445Gln' trini-high_5 Trichoplusia ni cell line from eggs high_5 Insect cell line from Trichoplusia ni egg cells Invitrogen supplies this cell line. Invitrogen supply this cell line. atpase reaction atpase reaction Fig. 1B, 5B, Supp. Fig. 5B CHEBI:33697 RNA CHEBI:33697 increases activity of P35207 When in complex with Ski3 and Ski8, the ATPase rate of Ski2 decreased 5-fold, whereas the KM for ATP remained essentially unchanged. Removal of residues 1-487 of SKI2 resulted in a significant increase in the helicase and ATPase activities of the Ski complex. Removal of the insertion domain (835-1083) of Ski2 or of the N-terminal arm of Ski3 derepresses/increases the ATPase activity of Ski2 when bound in the Ski complex. c_uc_28-ski 3 12 unspecified role unspecified role neutral component neutral component region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined in vitro In vitro 25 unspecified role unspecified role neutral component neutral component P17883:p.[Gln1412_Arg1413delinsAlaAla;Phe1416Asp] mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain QR AA 33 certain certain sequence position certain certain certain sequence position certain F D 33 Tue Nov 27 17:33:54 GMT 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'P17883:p.[Gln1412_Arg1413delinsAlaAla;Phe1416Asp]' Tue Jun 30 19:25:25 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.[Gln1412_Arg1413delinsAlaAla;Phe1416Asp]' trini-high_5 Trichoplusia ni cell line from eggs high_5 Insect cell line from Trichoplusia ni egg cells Invitrogen supplies this cell line. Invitrogen supply this cell line. physical association physical association Fig. 1C, 4C ADP-beryllium fluoride was required for this interaction to occur. Mutation of SKI3 resulted in a complex containing less SKI8 than wild-type so it is assumed SKI8 plays a role in RNA binding. ski2-ski3-11 6 10 unspecified role unspecified role neutral component neutral component trini-high_5 Trichoplusia ni cell line from eggs high_5 Insect cell line from Trichoplusia ni egg cells Invitrogen supplies this cell line. Invitrogen supply this cell line. 7 unspecified role unspecified role neutral component neutral component trini-high_5 Trichoplusia ni cell line from eggs high_5 Insect cell line from Trichoplusia ni egg cells Invitrogen supplies this cell line. Invitrogen supply this cell line. 8 unspecified role unspecified role neutral component neutral component trini-high_5 Trichoplusia ni cell line from eggs high_5 Insect cell line from Trichoplusia ni egg cells Invitrogen supplies this cell line. Invitrogen supply this cell line. physical association physical association Supp. Fig. 4B Mutation of SKI3 (gln1361ala_arg1362asp_tyr1365asp) decreases binding of SKI8 ski7-ski2 4 11 unspecified role unspecified role bait bait 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 ecoli Escherichia coli (strain K12) 7 unspecified role unspecified role prey prey trini-high_5 Trichoplusia ni cell line from eggs high_5 Insect cell line from Trichoplusia ni egg cells Invitrogen supplies this cell line. Invitrogen supply this cell line. 8 unspecified role unspecified role prey prey region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain certain certain sequence position certain certain certain sequence position certain trini-high_5 Trichoplusia ni cell line from eggs high_5 Insect cell line from Trichoplusia ni egg cells Invitrogen supplies this cell line. Invitrogen supply this cell line. 10 unspecified role unspecified role prey prey trini-high_5 Trichoplusia ni cell line from eggs high_5 Insect cell line from Trichoplusia ni egg cells Invitrogen supplies this cell line. Invitrogen supply this cell line. association association Supp. Fig. 6A ski7-ski2-1 4 11 unspecified role unspecified role bait bait 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 region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain ecoli Escherichia coli (strain K12) 7 unspecified role unspecified role prey prey trini-high_5 Trichoplusia ni cell line from eggs high_5 Insect cell line from Trichoplusia ni egg cells Invitrogen supplies this cell line. Invitrogen supply this cell line. 8 unspecified role unspecified role prey prey trini-high_5 Trichoplusia ni cell line from eggs high_5 Insect cell line from Trichoplusia ni egg cells Invitrogen supplies this cell line. Invitrogen supply this cell line. association association Supp. Fig. 5C ski_yeast SKI complex SKI complex SKI2:SKI3:SKI8 Ski2p-Ski3p-Ski8p complex 8 enzyme enzyme ski3 binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain 7 unspecified role unspecified role ski3 binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain 10 unspecified role unspecified role ski2 binding region binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain ski8 binding region binding region binding-associated region binding region undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined [EBI-1371258]Certain and ragged-n-terminus positions must always be strictly superior to 0 and inferior or equal to the protein sequence length. Actual positions : 1433-1433, sequence length 1432 [EBI-1371258]1207-1433 51 54 53 55 physical association physical association yeast Saccharomyces cerevisiae Baker's yeast stable complex stable complex physical interaction evidence used in manual assertion physical interaction evidence used in manual assertion IPI inferred from physical interaction Central component of the 3'-5' cytoplasmic mRNA degradation pathway which interacts with Ski7 (Q08491) to mediate degradation by the exosome. The Ski complex appears to thread RNAs directly to the exosome, coupling the helicase and the exoribonuclease through a continuous RNA channel. Ski3 forms an array of 33 TPR motifs organized in N-terminal and C-terminal arms. The C-terminal arm of Ski3 and the two Ski8 subunits position the helicase core of Ski2 centrally within the complex, enhancing RNA binding. The Ski3 N-terminal arm and the Ski2 insertion domain allosterically modulate the ATPase and helicase activities of the complex. MW = 370-380kDa Heterotetramer created with intact-jami-dbscripts