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/ HIV Gag-leucine zipper chimeras form ABCE1-containing intermediates and RNase-resistant immature capsids similar to those formed by wild-type HIV-1 Gag. HIV Gag-leucine zipper chimeras form ABCE1-containing intermediates and RNase-resistant immature capsids similar to those formed by wild-type HIV-1 Gag. Journal of virology 2011 imex curation Klein KC., Reed JC., Tanaka M., Nguyen VT., Giri S., Lingappa JR. Virus - Publications including interactions involving viral proteins Interactions involving Gag-zip (or other chimeras) have not been included as these are artificial constructs whose interactions have unknown biological relevance. this was a curation request from author of pmid:16275648 - who sent an email complaining that some results had been omitted (- they had NOT) - for this publication I think the author was probably expecting results from all the chimera experiments to be included.... jais@u.washington.edu 17-Sep-2015: Contacted by IntAct-Help. by author -Lingappa Only protein-protein interactions imex curation chlae-cos_1 Chlorocebus aethiops COS-1 cells Grivet cos_1 CV-1 Simian cells (cercopithecus aethiops) transformed by SV40 anti bait coip anti bait coimmunoprecipitation anti bait coip western blot western blot Immuno blot Immuno blot Klein KC., Reed JC., Tanaka M., Nguyen VT., Giri S., Lingappa JR. Virus - Publications including interactions involving viral proteins Interactions involving Gag-zip (or other chimeras) have not been included as these are artificial constructs whose interactions have unknown biological relevance. this was a curation request from author of pmid:16275648 - who sent an email complaining that some results had been omitted (- they had NOT) - for this publication I think the author was probably expecting results from all the chimera experiments to be included.... Cell lysates underwent sucrose density sedimentation prior to immunoprecipitation. The UniProt identifier for HIV-1 Gag protein was derived by blasting the sequence given in Figure 1B; one of the top hits was from the LAI (BRU) strain, as stated to have been used in this publication - so this identifier was chosen. jais@u.washington.edu jais@u.washington.edu. Accepted 2015-AUG-17 by PPORRAS by author -Lingappa Journal of virology 2011 Only protein-protein interactions imex curation imex curation If you dont like my comment about the KR9 mutant please alter! (Lysine + histidine + arginine are normally considered as "basic" amino acids - who ever wrote this publication has other ideas... HIV Gag-leucine zipper chimeras form ABCE1-containing intermediates and RNase-resistant immature capsids similar to those formed by wild-type HIV-1 Gag. HIV Gag-leucine zipper chimeras form ABCE1-containing intermediates and RNase-resistant immature capsids similar to those formed by wild-type HIV-1 Gag. Journal of virology 2011 imex curation Klein KC., Reed JC., Tanaka M., Nguyen VT., Giri S., Lingappa JR. Virus - Publications including interactions involving viral proteins Interactions involving Gag-zip (or other chimeras) have not been included as these are artificial constructs whose interactions have unknown biological relevance. this was a curation request from author of pmid:16275648 - who sent an email complaining that some results had been omitted (- they had NOT) - for this publication I think the author was probably expecting results from all the chimera experiments to be included.... jais@u.washington.edu 17-Sep-2015: Contacted by IntAct-Help. by author -Lingappa Only protein-protein interactions imex curation chlae-cos_1 Chlorocebus aethiops COS-1 cells Grivet cos_1 CV-1 Simian cells (cercopithecus aethiops) transformed by SV40 anti bait coip anti bait coimmunoprecipitation anti bait coip western blot western blot Immuno blot Immuno blot Klein KC., Reed JC., Tanaka M., Nguyen VT., Giri S., Lingappa JR. Virus - Publications including interactions involving viral proteins Interactions involving Gag-zip (or other chimeras) have not been included as these are artificial constructs whose interactions have unknown biological relevance. this was a curation request from author of pmid:16275648 - who sent an email complaining that some results had been omitted (- they had NOT) - for this publication I think the author was probably expecting results from all the chimera experiments to be included.... The UniProt identifier for HIV-1 Gag protein was derived by blasting the sequence given in Figure 1B; one of the top hits was from the LAI (BRU) strain, as stated to have been used in this publication - so this identifier was chosen. The HIV_deltaNCp6 construct is stated in Reference 12 (pmid:17233757) to be amino acids 1-363. jais@u.washington.edu jais@u.washington.edu. Accepted 2015-AUG-17 by PPORRAS by author -Lingappa Journal of virology 2011 Only protein-protein interactions imex curation imex curation If you dont like my comment about the KR9 mutant please alter! (Lysine + histidine + arginine are normally considered as "basic" amino acids - who ever wrote this publication has other ideas... HIV Gag-leucine zipper chimeras form ABCE1-containing intermediates and RNase-resistant immature capsids similar to those formed by wild-type HIV-1 Gag. HIV Gag-leucine zipper chimeras form ABCE1-containing intermediates and RNase-resistant immature capsids similar to those formed by wild-type HIV-1 Gag. Journal of virology 2011 imex curation Klein KC., Reed JC., Tanaka M., Nguyen VT., Giri S., Lingappa JR. Virus - Publications including interactions involving viral proteins Interactions involving Gag-zip (or other chimeras) have not been included as these are artificial constructs whose interactions have unknown biological relevance. this was a curation request from author of pmid:16275648 - who sent an email complaining that some results had been omitted (- they had NOT) - for this publication I think the author was probably expecting results from all the chimera experiments to be included.... jais@u.washington.edu 17-Sep-2015: Contacted by IntAct-Help. by author -Lingappa Only protein-protein interactions imex curation chlae-cos_1 Chlorocebus aethiops COS-1 cells Grivet cos_1 CV-1 Simian cells (cercopithecus aethiops) transformed by SV40 tem transmission electron microscopy tem antibody detection identification by antibody antibody detection Klein KC., Reed JC., Tanaka M., Nguyen VT., Giri S., Lingappa JR. Virus - Publications including interactions involving viral proteins Interactions involving Gag-zip (or other chimeras) have not been included as these are artificial constructs whose interactions have unknown biological relevance. this was a curation request from author of pmid:16275648 - who sent an email complaining that some results had been omitted (- they had NOT) - for this publication I think the author was probably expecting results from all the chimera experiments to be included.... Immunogold labeling;Gag was detected by anti-mouse IgG coupled to 6-nm-diameter gold particles and ABCE1 was detected by goat anti-rabbit IgG coupled to 15-nm-diameter gold particles. The UniProt identifier for HIV-1 Gag protein was derived by blasting the sequence given in Figure 1B; one of the top hits was from the LAI (BRU) strain, as stated to have been used in this publication - so this identifier was chosen. jais@u.washington.edu jais@u.washington.edu. Accepted 2015-AUG-17 by PPORRAS by author -Lingappa Journal of virology 2011 Only protein-protein interactions imex curation imex curation If you dont like my comment about the KR9 mutant please alter! (Lysine + histidine + arginine are normally considered as "basic" amino acids - who ever wrote this publication has other ideas... gag_hv1br Gag polyprotein gag Pr55Gag protein protein hv1br Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI) HIV-1 MGARASVLSGGELDRWEKIRLRPGGKKKYKLKHIVWASRELERFAVNPGLLETSEGCRQILGQLQPSLQTGSEELRSLYNTVATLYCVHQRIEIKDTKEALDKIEEEQNKSKKKAQQAAADTGHSSQVSQNYPIVQNIQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRVHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTNNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTACQGVGGPGHKARVLAEAMSQVTNSATIMMQRGNFRNQRKIVKCFNCGKEGHIARNCRAPRKKGCWKCGKEGHQMKDCTERQANFLGKIWPSYKGRPGNFLQSRPEPTAPPFLQSRPEPTAPPEESFRSGVETTTPSQKQEPIDKELYPLTSLRSLFGNDPSSQ mint 9103D701A843466F q6ssd8_chlae protein protein chlae Chlorocebus aethiops Cercopithecus aethiops Grivet Green monkey MADKLTRIAIVNHDKCKPKKCRQECKKSCPVVRMGKLCIEVTPQSKIAWISETLCIGCGICIKKCPFGALSIVNLPSNLEKETTHRYCANAFKLHRLPIPRPGEVLGLAGTNGIGKSTALKILAGKQKPNLGKYDDPPDWQEILTYFRGSELQNYFTKILEDDLKAIIKPQYVDQIPKAAKGTVGSILDRKDETKTQAVVCQQLDLTHLKERNVEDLSGGELQRFACAVVCIQKADIFMFDEPSSYLDVKQRLKAAITIRSLINPDRYIIVVEHDLSVLDYLSDFICCLYGVPSAYGVVTMPFSVREGINIFLDGYVPTENLRFRDASLVFKVAETANEEEVKKMCMYKYPGMKKKMGEFELAIVAGEFTDSEIMVMLGENGTGKTTFIRMLAGRLKPDEGGEVPVLNVSYKPQKISPKSTGSVRQLLHEKIRDAYTHPQFVTDVMKPLQIENIIDQEVQTLSGGELQRVALALCLGKPADVYLIDEPSAYLDSEQRLMAARVVKRFILHAKKTAFVVEHDFIMATYLADRVIVFDGVPSKNTVANSPQTLLAGMNKFLSQLEITFRRDPNNYRPRINKLNSIKDVEQKKSGNYFFLDD 4F7210BB5E47FDF2 q6ssd8_chlae-gag-1 2 4 unspecified role unspecified role prey prey ma_and_ca_domains required to bind necessary binding region required to bind certain certain sequence position certain certain certain sequence position certain 5 unspecified role unspecified role bait bait physical association physical association 3A The "gag-KR9A" mutant does not bind to ABCE1. It is stated to have mutations of nine basic residues to alanine. However the exact mutations involved are not clearly stated, since figure 1B highlights 14 residues in blue. Reference 26 (Lingappa et al., 2006) only gives mutations for a "KR10A " mutant and the stated residues in both publications are not the same. q6ssd8_chlae-gag-2 1 4 unspecified role unspecified role prey prey 5 unspecified role unspecified role bait bait physical association physical association 5A Gag was coimmunoprecipitated by anti-ABCE1 from the ∼80S/150S and ∼500S regions of the gradient. q6ssd8_chlae-gag-3 3 4 unspecified role unspecified role prey prey 5 unspecified role unspecified role bait bait colocalization colocalization 6A An assembly-defective provirus HIV-1 Gag-delta-NC-delta-p6 (approximately amino acids 1-377) showed reduced colocalization.