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/ Deubiquitinases sharpen substrate discrimination during membrane protein degradation from the ER. Deubiquitinases sharpen substrate discrimination during membrane protein degradation from the ER. Cell (0092-8674) 2013 imex curation Zhang Z.R., Bonifacino J.S., Hegde R.S. Virus - Publications including interactions involving viral proteins Exact cell line used in this experiment was not clear however all cell lines used by the author are of human origin. Interactions involving CK2 could not be captured as there was not enough detail on the manufacturers website to map the subunits. Interactions involving BTRC could not be captured as the origin of this protein could not be traced. zairong.zhang@gmail.com, rhegde@mrc-lmb.cam.ac.uk 22-Nov-2013: Contacted by IntAct-Help. Only protein-protein interactions human Homo sapiens Human anti bait coip anti bait coimmunoprecipitation anti bait coip western blot western blot Immuno blot Immuno blot Zhang Z.R., Bonifacino J.S., Hegde R.S. Virus - Publications including interactions involving viral proteins Exact cell line used in this experiment was not clear however all cell lines used by the author are of human origin. Interactions involving CK2 could not be captured as there was not enough detail on the manufacturers website to map the subunits. Interactions involving BTRC could not be captured as the origin of this protein could not be traced. zairong.zhang@gmail.com, rhegde@mrc-lmb.cam.ac.uk Accepted 2013-NOV-15 by MGT 22-Nov-2013: Contacted by IntAct-Help. Cell (0092-8674) 2013 Only protein-protein interactions imex curation Deubiquitinases sharpen substrate discrimination during membrane protein degradation from the ER. Deubiquitinases sharpen substrate discrimination during membrane protein degradation from the ER. Cell (0092-8674) 2013 imex curation Zhang Z.R., Bonifacino J.S., Hegde R.S. Virus - Publications including interactions involving viral proteins Exact cell line used in this experiment was not clear however all cell lines used by the author are of human origin. Interactions involving CK2 could not be captured as there was not enough detail on the manufacturers website to map the subunits. Interactions involving BTRC could not be captured as the origin of this protein could not be traced. zairong.zhang@gmail.com, rhegde@mrc-lmb.cam.ac.uk 22-Nov-2013: Contacted by IntAct-Help. Only protein-protein interactions human Homo sapiens Human anti tag coip anti tag coimmunoprecipitation anti tag coip western blot western blot Immuno blot Immuno blot Zhang Z.R., Bonifacino J.S., Hegde R.S. Virus - Publications including interactions involving viral proteins Exact cell line used in this experiment was not clear however all cell lines used by the author are of human origin. Interactions involving CK2 could not be captured as there was not enough detail on the manufacturers website to map the subunits. Interactions involving BTRC could not be captured as the origin of this protein could not be traced. zairong.zhang@gmail.com, rhegde@mrc-lmb.cam.ac.uk Accepted 2013-NOV-15 by MGT 22-Nov-2013: Contacted by IntAct-Help. Cell (0092-8674) 2013 Only protein-protein interactions imex curation Deubiquitinases sharpen substrate discrimination during membrane protein degradation from the ER. Deubiquitinases sharpen substrate discrimination during membrane protein degradation from the ER. Cell (0092-8674) 2013 imex curation Zhang Z.R., Bonifacino J.S., Hegde R.S. Virus - Publications including interactions involving viral proteins Exact cell line used in this experiment was not clear however all cell lines used by the author are of human origin. Interactions involving CK2 could not be captured as there was not enough detail on the manufacturers website to map the subunits. Interactions involving BTRC could not be captured as the origin of this protein could not be traced. zairong.zhang@gmail.com, rhegde@mrc-lmb.cam.ac.uk 22-Nov-2013: Contacted by IntAct-Help. Only protein-protein interactions human-293 Homo sapiens transformed primary embryonal kidney cells Human 293 Transformed human primary embryonal kidney cells. The Cell type named 293 is synonymous with HEK-293. anti tag coip anti tag coimmunoprecipitation anti tag coip western blot western blot Immuno blot Immuno blot Zhang Z.R., Bonifacino J.S., Hegde R.S. Virus - Publications including interactions involving viral proteins Exact cell line used in this experiment was not clear however all cell lines used by the author are of human origin. Interactions involving CK2 could not be captured as there was not enough detail on the manufacturers website to map the subunits. Interactions involving BTRC could not be captured as the origin of this protein could not be traced. zairong.zhang@gmail.com, rhegde@mrc-lmb.cam.ac.uk Accepted 2013-NOV-15 by MGT 22-Nov-2013: Contacted by IntAct-Help. Cell (0092-8674) 2013 Only protein-protein interactions imex curation Deubiquitinases sharpen substrate discrimination during membrane protein degradation from the ER. Deubiquitinases sharpen substrate discrimination during membrane protein degradation from the ER. Cell (0092-8674) 2013 imex curation Zhang Z.R., Bonifacino J.S., Hegde R.S. Virus - Publications including interactions involving viral proteins Exact cell line used in this experiment was not clear however all cell lines used by the author are of human origin. Interactions involving CK2 could not be captured as there was not enough detail on the manufacturers website to map the subunits. Interactions involving BTRC could not be captured as the origin of this protein could not be traced. zairong.zhang@gmail.com, rhegde@mrc-lmb.cam.ac.uk 22-Nov-2013: Contacted by IntAct-Help. Only protein-protein interactions in vitro In vitro anti bait coip anti bait coimmunoprecipitation anti bait coip western blot western blot Immuno blot Immuno blot Zhang Z.R., Bonifacino J.S., Hegde R.S. Virus - Publications including interactions involving viral proteins Exact cell line used in this experiment was not clear however all cell lines used by the author are of human origin. Proteins are incorporated into liposomes Interactions involving CK2 could not be captured as there was not enough detail on the manufacturers website to map the subunits. Interactions involving BTRC could not be captured as the origin of this protein could not be traced. zairong.zhang@gmail.com, rhegde@mrc-lmb.cam.ac.uk Accepted 2013-NOV-15 by MGT 22-Nov-2013: Contacted by IntAct-Help. Cell (0092-8674) 2013 Only protein-protein interactions imex curation vpu_hv1h2 Protein Vpu vpu U ORF protein Viral protein U protein protein hv1h2 Human immunodeficiency virus type 1 group M subtype B (isolate HXB2) (HIV-1) HIV-1 QPIPIVAIVALVVAIIIAIVVWSIVIIEYRKILRQRKIDRLIDRLIERAEDSGNESEGEISALVEMGVEMGHHAPWDVDDL 53A951D6240556EA cul1_human Cullin-1 CUL1 protein protein human Homo sapiens Human MSSTRSQNPHGLKQIGLDQIWDDLRAGIQQVYTRQSMAKSRYMELYTHVYNYCTSVHQSNQARGAGVPPSKSKKGQTPGGAQFVGLELYKRLKEFLKNYLTNLLKDGEDLMDESVLKFYTQQWEDYRFSSKVLNGICAYLNRHWVRRECDEGRKGIYEIYSLALVTWRDCLFRPLNKQVTNAVLKLIEKERNGETINTRLISGVVQSYVELGLNEDDAFAKGPTLTVYKESFESQFLADTERFYTRESTEFLQQNPVTEYMKKAEARLLEEQRRVQVYLHESTQDELARKCEQVLIEKHLEIFHTEFQNLLDADKNEDLGRMYNLVSRIQDGLGELKKLLETHIHNQGLAAIEKCGEAALNDPKMYVQTVLDVHKKYNALVMSAFNNDAGFVAALDKACGRFINNNAVTKMAQSSSKSPELLARYCDSLLKKSSKNPEEAELEDTLNQVMVVFKYIEDKDVFQKFYAKMLAKRLVHQNSASDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLTNSEPLDLDFSIQVLSSGSWPFQQSCTFALPSELERSYQRFTAFYASRHSGRKLTWLYQLSKGELVTNCFKNRYTLQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQILLKSKLLVLEDENANVDEVELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMKMRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA DIP protein Q13616 original sequence version: 144 DIP protein Q13616 original sequence version: 133 DIP protein Q13616 original sequence version: null DIP protein Q13616 original sequence version: 135 DIP protein Q13616 original sequence version: 98 DIP protein Q13616 original sequence version: 110 DIP protein Q13616 original sequence version: 146 DIP protein Q13616 original sequence version: 148 DIP protein Q13616 original sequence version: 100 DIP protein Q13616 original sequence version: 85 DIP protein Q13616 original sequence version: 114 DIP protein Q13616 original sequence version: 119 DIP protein Q13616 original sequence version: 136 DIP protein Q13616 original sequence version: 117 DIP protein Q13616 original sequence version: 99 DIP protein Q13616 original sequence version: 108 6625A1FFA7799BBA fbw1a_human F-box/WD repeat-containing protein 1A BTRC BTRCP FBW1A FBXW1A F-box and WD repeats protein beta-TrCP E3RSIkappaB pIkappaBalpha-E3 receptor subunit Epididymis tissue protein Li 2a protein protein human Homo sapiens Human MDPAEAVLQEKALKFMCSMPRSLWLGCSSLADSMPSLRCLYNPGTGALTAFQNSSEREDCNNGEPPRKIIPEKNSLRQTYNSCARLCLNQETVCLASTAMKTENCVAKTKLANGTSSMIVPKQRKLSASYEKEKELCVKYFEQWSESDQVEFVEHLISQMCHYQHGHINSYLKPMLQRDFITALPARGLDHIAENILSYLDAKSLCAAELVCKEWYRVTSDGMLWKKLIERMVRTDSLWRGLAERRGWGQYLFKNKPPDGNAPPNSFYRALYPKIIQDIETIESNWRCGRHSLQRIHCRSETSKGVYCLQYDDQKIVSGLRDNTIKIWDKNTLECKRILTGHTGSVLCLQYDERVIITGSSDSTVRVWDVNTGEMLNTLIHHCEAVLHLRFNNGMMVTCSKDRSIAVWDMASPTDITLRRVLVGHRAAVNVVDFDDKYIVSASGDRTIKVWNTSTCEFVRTLNGHKRGIACLQYRDRLVVSGSSDNTIRLWDIECGACLRVLEGHEELVRCIRFDNKRIVSGAYDGKIKVWDLVAALDPRAPAGTLCLRTLVEHSGRVFRLQFDEFQIVSSSHDDTILIWDFLNDPAAQAEPPRSPSRTYTYISR DIP protein Q9Y297 original sequence version: 142 DIP protein Q9Y297 original sequence version: 153 DIP protein Q9Y297 original sequence version: 144 DIP protein Q9Y297 original sequence version: 145 DIP protein Q9Y297 original sequence version: 106 DIP protein Q9Y297 original sequence version: 82 DIP protein Q9Y297 original sequence version: 111 DIP protein Q9Y297 original sequence version: 125 4C67F3B7E400FD37 cd4_human T-cell surface glycoprotein CD4 CD4 T-cell surface antigen T4/Leu-3 protein protein human Homo sapiens Human MNRGVPFRHLLLVLQLALLPAATQGKKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKGPSKLNDRADSRRSLWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQNQKKVEFKIDIVVLAFQKASSIVYKKEGEQVEFSFPLAFTVEKLTGSGELWWQAERASSSKSWITFDLKNKEVSVKRVTQDPKLQMGKKLPLHLTLPQALPQYAGSGNLTLALEAKTGKLHQEVNLVVMRATQLQKNLTCEVWGPTSPKLMLSLKLENKEAKVSKREKAVWVLNPEAGMWQCLLSDSGQVLLESNIKVLPTWSTPVQPMALIVLGGVAGLLLFIGLGIFFCVRCRHRRRQAERMSQIKRLLSEKKTCQCPHRFQKTCSPI DIP protein P01730 original sequence version: 183 DIP protein P01730 original sequence version: 163 DIP protein P01730 original sequence version: 133 DIP protein P01730 original sequence version: 135 DIP protein P01730 original sequence version: 185 DIP protein P01730 original sequence version: 189 20ED893F9E56D236 cd4-vpu-1 1 5 unspecified role unspecified role prey prey c_terminus ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range P05919:p.[Ser52Asn;Ser56Asn] mutation mutation certain certain sequence position certain certain certain sequence position certain S N certain certain sequence position certain certain certain sequence position certain S N Wed May 02 14:26:29 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'ser52asn,ser56asn' Tue Jun 30 17:44:04 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.[Ser52Asn;Ser56Asn]' 8 unspecified role unspecified role bait bait nucl transfection nucleic acid transfection nucl transfection physical association physical association Supp. fig. 1F cd4-vpu-2 2 8 unspecified role unspecified role prey prey nucl transfection nucleic acid transfection nucl transfection cytoplasmic region 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 P05919:p.[Ile17Phe;Val21Phe;Val25Leu] mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain V F certain certain sequence position certain certain certain sequence position certain I F certain certain sequence position certain certain certain sequence position certain V L Fri Jul 22 11:07:49 BST 2016 This feature has been corrected as a result of our quality control procedures. The original label was 'val21phe,ile17phe,val25leu' Wed May 02 17:51:43 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'ile17phe,val21phe,val25leu' Tue Jun 30 19:05:39 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.[Ile17Phe;Val21Phe;Val25Leu]' P05919:p.[Ser52Asn;Ser56Asn] mutation mutation certain certain sequence position certain certain certain sequence position certain S N certain certain sequence position certain certain certain sequence position certain S N Wed May 02 15:22:52 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'ser52asn,ser56asn' Tue Jun 30 16:38:15 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.[Ser52Asn;Ser56Asn]' c_terminus ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range physical association physical association Fig. 1C, 1D, Supp. Fig. 1G vpu-btrc-3 3 5 unspecified role unspecified role bait bait P05919:p.[Ser52Asn;Ser56Asn] mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain S N certain certain sequence position certain certain certain sequence position certain S N Wed May 02 18:19:08 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'ser52asn,ser56asn' Tue Jun 30 16:14:54 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.[Ser52Asn;Ser56Asn]' c_terminus ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range 6 unspecified role unspecified role prey prey 7 unspecified role unspecified role prey prey association association Fig. 2A, Supp Fig. 2A vpu-cd4-2 4 8 autoradiography autoradiography western blot western blot Immuno blot Immuno blot unspecified role unspecified role prey prey nucl transfection nucleic acid transfection nucl transfection P01730:p.Pro393Met mutation mutation certain certain sequence position certain certain certain sequence position certain P M Wed May 02 15:56:56 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'pro393met' Tue Jun 30 19:28:04 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Pro393Met' region radiolabelled radiolabel radiolabeled radiolabelled undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 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 region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain c-terminal flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged c-term range C-terminal range c-term range c-term range C-terminal range c-term range in vitro In vitro 5 unspecified role unspecified role bait bait 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 c-terminal ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range in vitro In vitro physical association physical association Fig. 3C When CD4 and Vpu were coincorporated into the same liposomes, they interacted with each other, mixing separate liposomes each containing CD4 or Vpu resulted in minimal interaction