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/ Identification of CMTM6 and CMTM4 as PD-L1 protein regulators. Identification of CMTM6 and CMTM4 as PD-L1 protein regulators. Nature 2017 imex curation Mezzadra R., Sun C., Jae LT., Gomez-Eerland R., de Vries E., Wu W., Logtenberg MEW., Slagter M., Rozeman EA., Hofland I., Broeks A., Horlings HM., Wessels LFA., Blank CU., Xiao Y., Heck AJR., Borst J., Brummelkamp TR., Schumacher TNM., Mezzadra R., Sun C., Jae LT., Gomez-Eerland R., de Vries E., Wu W., Logtenberg MEW., Slagter M., Rozeman EA., Hofland I., Broeks A., Horlings HM., Wessels LFA., Blank CU., Xiao Y., Heck AJR., Borst J., Brummelkamp TR., Schumacher TNM. Cancer - Interactions investigated in the context of cancer t.brummelkamp@nki.nl, t.schumacher@nki.nl 19-Dec-2017: Contacted by IntAct-Help. Only protein-protein interactions imex curation human-a375 Human malignant melanoma a375 Human malignant melanoma ATCC catalog # CRL-1872 anti bait coip anti bait coimmunoprecipitation anti bait coip western blot western blot Immuno blot Immuno blot Mezzadra R., Sun C., Jae LT., Gomez-Eerland R., de Vries E., Wu W., Logtenberg MEW., Slagter M., Rozeman EA., Hofland I., Broeks A., Horlings HM., Wessels LFA., Blank CU., Xiao Y., Heck AJR., Borst J., Brummelkamp TR., Schumacher TNM., Mezzadra R., Sun C., Jae LT., Gomez-Eerland R., de Vries E., Wu W., Logtenberg MEW., Slagter M., Rozeman EA., Hofland I., Broeks A., Horlings HM., Wessels LFA., Blank CU., Xiao Y., Heck AJR., Borst J., Brummelkamp TR., Schumacher TNM. Cancer - Interactions investigated in the context of cancer Fig 4d: 3 interactions here owing to different 'exp-prep' and 'phys'-level combinations on the proteins. (OE and not OE) t.brummelkamp@nki.nl, t.schumacher@nki.nl Accepted 2017-NOV-21 AT 11:31 GMT AT 11:31 GMT by LIVIAP Nature 2017 imex curation no- you are right! Altered/Done Identification of CMTM6 and CMTM4 as PD-L1 protein regulators. Identification of CMTM6 and CMTM4 as PD-L1 protein regulators. Nature 2017 imex curation Mezzadra R., Sun C., Jae LT., Gomez-Eerland R., de Vries E., Wu W., Logtenberg MEW., Slagter M., Rozeman EA., Hofland I., Broeks A., Horlings HM., Wessels LFA., Blank CU., Xiao Y., Heck AJR., Borst J., Brummelkamp TR., Schumacher TNM., Mezzadra R., Sun C., Jae LT., Gomez-Eerland R., de Vries E., Wu W., Logtenberg MEW., Slagter M., Rozeman EA., Hofland I., Broeks A., Horlings HM., Wessels LFA., Blank CU., Xiao Y., Heck AJR., Borst J., Brummelkamp TR., Schumacher TNM. Cancer - Interactions investigated in the context of cancer t.brummelkamp@nki.nl, t.schumacher@nki.nl 19-Dec-2017: Contacted by IntAct-Help. Only protein-protein interactions imex curation human-rko Homo sapiens colorectal carcinoma cell line rko Human colorectal carcinoma cell line anti bait coip anti bait coimmunoprecipitation anti bait coip western blot western blot Immuno blot Immuno blot Mezzadra R., Sun C., Jae LT., Gomez-Eerland R., de Vries E., Wu W., Logtenberg MEW., Slagter M., Rozeman EA., Hofland I., Broeks A., Horlings HM., Wessels LFA., Blank CU., Xiao Y., Heck AJR., Borst J., Brummelkamp TR., Schumacher TNM., Mezzadra R., Sun C., Jae LT., Gomez-Eerland R., de Vries E., Wu W., Logtenberg MEW., Slagter M., Rozeman EA., Hofland I., Broeks A., Horlings HM., Wessels LFA., Blank CU., Xiao Y., Heck AJR., Borst J., Brummelkamp TR., Schumacher TNM. Cancer - Interactions investigated in the context of cancer t.brummelkamp@nki.nl, t.schumacher@nki.nl Accepted 2017-NOV-21 AT 11:31 GMT AT 11:31 GMT by LIVIAP Nature 2017 imex curation no- you are right! Altered/Done Identification of CMTM6 and CMTM4 as PD-L1 protein regulators. Identification of CMTM6 and CMTM4 as PD-L1 protein regulators. Nature 2017 imex curation Mezzadra R., Sun C., Jae LT., Gomez-Eerland R., de Vries E., Wu W., Logtenberg MEW., Slagter M., Rozeman EA., Hofland I., Broeks A., Horlings HM., Wessels LFA., Blank CU., Xiao Y., Heck AJR., Borst J., Brummelkamp TR., Schumacher TNM., Mezzadra R., Sun C., Jae LT., Gomez-Eerland R., de Vries E., Wu W., Logtenberg MEW., Slagter M., Rozeman EA., Hofland I., Broeks A., Horlings HM., Wessels LFA., Blank CU., Xiao Y., Heck AJR., Borst J., Brummelkamp TR., Schumacher TNM. Cancer - Interactions investigated in the context of cancer t.brummelkamp@nki.nl, t.schumacher@nki.nl 19-Dec-2017: Contacted by IntAct-Help. Only protein-protein interactions imex curation human-8505C human- 8505C undifferentiated thyroid carcinoma cell line Human 8505c 8505C-undifferentiated thyroid carcinoma cell line DSMZ: ACC 219 anti bait coip anti bait coimmunoprecipitation anti bait coip western blot western blot Immuno blot Immuno blot Mezzadra R., Sun C., Jae LT., Gomez-Eerland R., de Vries E., Wu W., Logtenberg MEW., Slagter M., Rozeman EA., Hofland I., Broeks A., Horlings HM., Wessels LFA., Blank CU., Xiao Y., Heck AJR., Borst J., Brummelkamp TR., Schumacher TNM., Mezzadra R., Sun C., Jae LT., Gomez-Eerland R., de Vries E., Wu W., Logtenberg MEW., Slagter M., Rozeman EA., Hofland I., Broeks A., Horlings HM., Wessels LFA., Blank CU., Xiao Y., Heck AJR., Borst J., Brummelkamp TR., Schumacher TNM. Cancer - Interactions investigated in the context of cancer t.brummelkamp@nki.nl, t.schumacher@nki.nl Accepted 2017-NOV-21 AT 11:31 GMT AT 11:31 GMT by LIVIAP Nature 2017 imex curation no- you are right! Altered/Done Identification of CMTM6 and CMTM4 as PD-L1 protein regulators. Identification of CMTM6 and CMTM4 as PD-L1 protein regulators. Nature 2017 imex curation Mezzadra R., Sun C., Jae LT., Gomez-Eerland R., de Vries E., Wu W., Logtenberg MEW., Slagter M., Rozeman EA., Hofland I., Broeks A., Horlings HM., Wessels LFA., Blank CU., Xiao Y., Heck AJR., Borst J., Brummelkamp TR., Schumacher TNM., Mezzadra R., Sun C., Jae LT., Gomez-Eerland R., de Vries E., Wu W., Logtenberg MEW., Slagter M., Rozeman EA., Hofland I., Broeks A., Horlings HM., Wessels LFA., Blank CU., Xiao Y., Heck AJR., Borst J., Brummelkamp TR., Schumacher TNM. Cancer - Interactions investigated in the context of cancer t.brummelkamp@nki.nl, t.schumacher@nki.nl 19-Dec-2017: Contacted by IntAct-Help. Only protein-protein interactions imex curation human-293t Homo sapiens 293 cells transformed with SV40 large T antigen 293t 293 cells expressing SV40 large T antigen. The original designation of this cell line was 293tsA1609neo. It is not in Cabri,ATCC or HyperCLDB. anti tag coip anti tag coimmunoprecipitation anti tag coip western blot western blot Immuno blot Immuno blot Mezzadra R., Sun C., Jae LT., Gomez-Eerland R., de Vries E., Wu W., Logtenberg MEW., Slagter M., Rozeman EA., Hofland I., Broeks A., Horlings HM., Wessels LFA., Blank CU., Xiao Y., Heck AJR., Borst J., Brummelkamp TR., Schumacher TNM., Mezzadra R., Sun C., Jae LT., Gomez-Eerland R., de Vries E., Wu W., Logtenberg MEW., Slagter M., Rozeman EA., Hofland I., Broeks A., Horlings HM., Wessels LFA., Blank CU., Xiao Y., Heck AJR., Borst J., Brummelkamp TR., Schumacher TNM. Cancer - Interactions investigated in the context of cancer Interactions involving chimeric molecules have not been added, as they are of dubious biological relevance. the authors volunteered the info that the PD-L1 FLAG tag is N-terminal, but my reading of text says it is C-terminal, so I have altered to a "?-?" t.brummelkamp@nki.nl, t.schumacher@nki.nl Accepted 2017-NOV-21 AT 11:31 GMT AT 11:31 GMT by LIVIAP Nature 2017 imex curation no- you are right! Altered/Done pd1l1_human Programmed cell death 1 ligand 1 CD274 B7H1 PDCD1L1 PDCD1LG1 PDL1 B7 homolog 1 protein protein human Homo sapiens Human MRIFAVFIFMTYWHLLNAFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAPYNKINQRILVVDPVTSEHELTCQAEGYPKAEVIWTSSDHQVLSGKTTTTNSKREEKLFNVTSTLRINTTTNEIFYCTFRRLDPEENHTAELVIPELPLAHPPNERTHLVILGAILLCLGVALTFIFRLRKGRMMDVKKCGIQDTNSKKQSDTHLEET FE957086E62A31A8 cklf4_human CKLF-like MARVEL transmembrane domain-containing protein 4 CMTM4 CKLFSF4 Chemokine-like factor superfamily member 4 protein protein human Homo sapiens Human MRSGEELDGFEGEASSTSMISGASSPYQPTTEPVSQRRGLAGLRCDPDYLRGALGRLKVAQVILALIAFICIETIMACSPCEGLYFFEFVSCSAFVVTGVLLIMFSLNLHMRIPQINWNLTDLVNTGLSAFLFFIASIVLAALNHRAGAEIAAVIFGFLATAAYAVNTFLAVQKWRVSVRQQSTNDYIRARTESRDVDSRPEIQRLDTFSYSTNVTVRKKSPTNLLSLNHWQLA 629B5CCEE873C895 cklf6_human CKLF-like MARVEL transmembrane domain-containing protein 6 Chemokine-like factor superfamily member 6 CMTM6 CKLFSF6 protein protein human Homo sapiens Human MENGAVYSPTTEEDPGPARGPRSGLAAYFFMGRLPLLRRVLKGLQLLLSLLAFICEEVVSQCTLCGGLYFFEFVSCSAFLLSLLILIVYCTPFYERVDTTKVKSSDFYITLGTGCVFLLASIIFVSTHDRTSAEIAAIVFGFIASFMFLLDFITMLYEKRQESQLRKPENTTRAEALTEPLNA 43DAEB652A6B50B4 pd1l2_human Programmed cell death 1 ligand 2 Butyrophilin B7-DC PDCD1LG2 B7DC CD273 PDCD1L2 PDL2 protein protein human Homo sapiens Human MIFLLLMLSLELQLHQIAALFTVTVPKELYIIEHGSNVTLECNFDTGSHVNLGAITASLQKVENDTSPHRERATLLEEQLPLGKASFHIPQVQVRDEGQYQCIIIYGVAWDYKYLTLKVKASYRKINTHILKVPETDEVELTCQATGYPLAEVSWPNVSVPANTSHSRTPEGLYQVTSVLRLKPPPGRNFSCVFWNTHVRELTLASIDLQSQMEPRTHPTWLLHIFIPFCIIAFIFIATVIALRKQLCQKLYSSKDTTKRPVTTTKREVNSAI 8B7E963C9BA26ED9 cd274-cmtm6-2 1 7 unspecified role unspecified role prey prey physiological level physiological level endogenous level endogenous endogenous endogenous level 5 unspecified role unspecified role bait bait over-expressed over expressed level over-expressed physical association physical association 4D, lanes 9+10 IFN-gamma cd274-cmtm6-1 1 7 unspecified role unspecified role prey prey physiological level physiological level endogenous level endogenous endogenous endogenous level 5 unspecified role unspecified role bait bait physiological level physiological level endogenous level endogenous endogenous endogenous level physical association physical association 4D, lanes 1+ 2 IFN-gamma cd274-cmtm6-3 1 7 unspecified role unspecified role prey prey over-expressed over expressed level over-expressed 5 unspecified role unspecified role bait bait physiological level physiological level endogenous level endogenous endogenous endogenous level physical association physical association 4D, lanes 7+8 IFN-gamma cd274-cmtm6-5 2 7 unspecified role unspecified role prey prey physiological level physiological level endogenous level endogenous endogenous endogenous level 5 unspecified role unspecified role bait bait physiological level physiological level endogenous level endogenous endogenous endogenous level physical association physical association Extended Data 7C cd274-cmtm6-6 3 7 unspecified role unspecified role bait bait physiological level physiological level endogenous level endogenous endogenous endogenous level 5 unspecified role unspecified role prey prey physiological level physiological level endogenous level endogenous endogenous endogenous level physical association physical association Extended Data 7 B IFN-gamma cd274-cmtm6-7 1 5 unspecified role unspecified role prey prey over-expressed over expressed level over-expressed 7 unspecified role unspecified role bait bait physiological level physiological level endogenous level endogenous endogenous endogenous level physical association physical association Extended data 7A, lanes 9+10 IFN-gamma cd274-cmtm6-4 3 7 unspecified role unspecified role prey prey physiological level physiological level endogenous level endogenous endogenous endogenous level 5 unspecified role unspecified role bait bait physiological level physiological level endogenous level endogenous endogenous endogenous level physical association physical association Extended Data 7B cmtm6-cd274-1 2 7 unspecified role unspecified role bait bait physiological level physiological level endogenous level endogenous endogenous endogenous level 5 unspecified role unspecified role prey prey physiological level physiological level endogenous level endogenous endogenous endogenous level 6 unspecified role unspecified role prey prey association association Extended Data 7C cd274-cmtm6-8 3 7 unspecified role unspecified role prey prey physiological level physiological level endogenous level endogenous endogenous endogenous level 6 unspecified role unspecified role prey prey physiological level physiological level endogenous level endogenous endogenous endogenous level 5 unspecified role unspecified role bait bait physiological level physiological level endogenous level endogenous endogenous endogenous level association association Extended Data 7D cd274-cmtm4-1 3 6 unspecified role unspecified role prey prey physiological level physiological level endogenous level endogenous endogenous endogenous level 5 unspecified role unspecified role bait bait physiological level physiological level endogenous level endogenous endogenous endogenous level physical association physical association Extended Data 7Di cd274-cmtm4-2 3 7 unspecified role unspecified role bait bait physiological level physiological level endogenous level endogenous endogenous endogenous level 6 unspecified role unspecified role prey prey physiological level physiological level endogenous level endogenous endogenous endogenous level 5 unspecified role unspecified role prey prey physiological level physiological level endogenous level endogenous endogenous endogenous level association association Extended Data 7Di only a weak band is seen for CMTM4 cmtm6-cd274-2 3 7 unspecified role unspecified role prey prey physiological level physiological level endogenous level endogenous endogenous endogenous level 6 unspecified role unspecified role bait bait physiological level physiological level endogenous level endogenous endogenous endogenous level 5 unspecified role unspecified role prey prey physiological level physiological level endogenous level endogenous endogenous endogenous level association association Extended Data 7Dii Only a weak band is seen for CMTM6. In the CMTM6 knockout cells there appears to be little or no interaction with PD-L1. cd274-cmtm6-9 4 7 unspecified role unspecified role prey prey over-expressed over expressed level over-expressed 5 unspecified role unspecified role bait bait over-expressed over expressed level over-expressed region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 8 unspecified role unspecified role prey prey physiological level physiological level endogenous level endogenous endogenous endogenous level association association Supp 8 F/G Only a faint band is seen for endogenous PD-L2.