DIP Database of Interacting Proteins 611 Young Drive East; Los Angeles CA 90095; USA http://dip.doe-mbi.ucla.edu/ dip@mbi.ucla.edu TGF-beta-induced Foxp3 inhibits T(H)17 cell differentiation by antagonizing RORgammat function. TGF-beta-induced Foxp3 inhibits T(H)17 cell differentiation by antagonizing RORgammat function. Nature 2008 imex curation Zhou L., Lopes JE., Chong MM., Ivanov II., Min R., Victora GD., Shen Y., Du J., Rubtsov YP., Rudensky AY., Ziegler SF., Littman DR. IBD - Inflammatory bowel disease littman@saturn.med.nyu.edu 21-10-2015: Contacted by IntAct-Help. Only protein-protein interactions mouse-t-cell_cd4+ Mouse CD4 positive T-cell t-cell_cd4+ t cell cd4+ fluorescence imaging fluorescence microscopy fluorescence imaging immunostaining immunostaining Zhou L., Lopes JE., Chong MM., Ivanov II., Min R., Victora GD., Shen Y., Du J., Rubtsov YP., Rudensky AY., Ziegler SF., Littman DR. IBD - Inflammatory bowel disease T cells CD4+GFPint and CD4+GFP were isolated from the intestinal lamina propria of RORc(γt)+/gfp mice. littman@saturn.med.nyu.edu Accepted 2015-OCT-19 AT 10:32 BST AT 10:32 BST by MGT Nature 2008 imex curation There are Uniprot Swiss curated isoforms for human and mouse ROR. The authors are not consistent with their labeling of RORg and RORgt they used them freely, on the legend it appears as just RORg and labels on the figure appear RORgt. Looking at the references and how the mouse with RORgt deletion was made it is clear they use the RORgt isoform. They did not use a commercial Antibody, but a hybridoma sup. Agreed on colocalisation. Data of Fig1 B had been entered under incorrect Fig number. Corrected now.; As stated in the Fig 3 legend and labels on blot: Fig 3B: 293T cells were transfected with human Flag-RORgt and coip with anti-Flag. Fig 3A: 293T cells were transfected with murine Flag-foxp3 coip with anti-Flag Regarding Exon2 aa range was not saved on the Editor, I was aware that I entered an incorrect range 72-106 when I was curating and made a correction to 71-105, but was not saved then. It should appear correct now. Reference 21 defines the role of Foxp3 Exon 2 deletion to be 71-105, do I need to ad a cross reference for this publication? or is it still considered a fuzzy type?; It is clear to me that FKH mutant showns staining of the cytoplasm in all combinations. Indicating that the mutation affected its ability to be transported to the nucleous even in the presence of ROR one can see staining of the cytoplasm by this mutant, or the Foxp3-Exon2 deleted. These data is okay. However, their Exon2 conclusion is a bit strange. I do not agree with them.; It is not clear to me from the Supp Fig 1B legend on paper text if participants had a tag or feature. This is why I did not entered any features. +++++16-Oct- 2015. The cells used were from an engineered mouse which expresses the ROR_gamma_t isoform. You-Wen He et. al., Immunity Vol 9, 797-06 (1998) There was no need to treat the cells with TGFb to induce ROR_g_t expression. I think it would be accurate to use the isoform ID P51450-2 Also known as: RORgT. I hope I am getting closer to end this curation. It is taking too much time. Thank you for your reviews: TGF-beta-induced Foxp3 inhibits T(H)17 cell differentiation by antagonizing RORgammat function. TGF-beta-induced Foxp3 inhibits T(H)17 cell differentiation by antagonizing RORgammat function. Nature 2008 imex curation Zhou L., Lopes JE., Chong MM., Ivanov II., Min R., Victora GD., Shen Y., Du J., Rubtsov YP., Rudensky AY., Ziegler SF., Littman DR. IBD - Inflammatory bowel disease littman@saturn.med.nyu.edu 21-10-2015: Contacted by IntAct-Help. Only protein-protein interactions human-hela Homo sapiens epitheloid cervix carcinoma cells Human hela Human epitheloid cervix carcinoma HeLa cells derivation: cervix; epithelial; adenocarcinoma ATCC no:CCL-2 confocal microscopy confocal microscopy immunostaining immunostaining Zhou L., Lopes JE., Chong MM., Ivanov II., Min R., Victora GD., Shen Y., Du J., Rubtsov YP., Rudensky AY., Ziegler SF., Littman DR. IBD - Inflammatory bowel disease littman@saturn.med.nyu.edu Accepted 2015-OCT-19 AT 10:32 BST AT 10:32 BST by MGT Nature 2008 imex curation There are Uniprot Swiss curated isoforms for human and mouse ROR. The authors are not consistent with their labeling of RORg and RORgt they used them freely, on the legend it appears as just RORg and labels on the figure appear RORgt. Looking at the references and how the mouse with RORgt deletion was made it is clear they use the RORgt isoform. They did not use a commercial Antibody, but a hybridoma sup. Agreed on colocalisation. Data of Fig1 B had been entered under incorrect Fig number. Corrected now.; As stated in the Fig 3 legend and labels on blot: Fig 3B: 293T cells were transfected with human Flag-RORgt and coip with anti-Flag. Fig 3A: 293T cells were transfected with murine Flag-foxp3 coip with anti-Flag Regarding Exon2 aa range was not saved on the Editor, I was aware that I entered an incorrect range 72-106 when I was curating and made a correction to 71-105, but was not saved then. It should appear correct now. Reference 21 defines the role of Foxp3 Exon 2 deletion to be 71-105, do I need to ad a cross reference for this publication? or is it still considered a fuzzy type?; It is clear to me that FKH mutant showns staining of the cytoplasm in all combinations. Indicating that the mutation affected its ability to be transported to the nucleous even in the presence of ROR one can see staining of the cytoplasm by this mutant, or the Foxp3-Exon2 deleted. These data is okay. However, their Exon2 conclusion is a bit strange. I do not agree with them.; It is not clear to me from the Supp Fig 1B legend on paper text if participants had a tag or feature. This is why I did not entered any features. +++++16-Oct- 2015. The cells used were from an engineered mouse which expresses the ROR_gamma_t isoform. You-Wen He et. al., Immunity Vol 9, 797-06 (1998) There was no need to treat the cells with TGFb to induce ROR_g_t expression. I think it would be accurate to use the isoform ID P51450-2 Also known as: RORgT. I hope I am getting closer to end this curation. It is taking too much time. Thank you for your reviews: TGF-beta-induced Foxp3 inhibits T(H)17 cell differentiation by antagonizing RORgammat function. TGF-beta-induced Foxp3 inhibits T(H)17 cell differentiation by antagonizing RORgammat function. Nature 2008 imex curation Zhou L., Lopes JE., Chong MM., Ivanov II., Min R., Victora GD., Shen Y., Du J., Rubtsov YP., Rudensky AY., Ziegler SF., Littman DR. IBD - Inflammatory bowel disease littman@saturn.med.nyu.edu 21-10-2015: Contacted by IntAct-Help. Only protein-protein interactions mouse-t-cell_cd4+ Mouse CD4 positive T-cell t-cell_cd4+ t cell cd4+ fluorescence imaging fluorescence microscopy fluorescence imaging immunostaining immunostaining Zhou L., Lopes JE., Chong MM., Ivanov II., Min R., Victora GD., Shen Y., Du J., Rubtsov YP., Rudensky AY., Ziegler SF., Littman DR. IBD - Inflammatory bowel disease Naive CD4+ T cells, from spleen, were stimulated with either anti-T-cell receptor (TCR) or anti-CD3/CD28 and TGF-beta. littman@saturn.med.nyu.edu Accepted 2015-OCT-19 AT 10:32 BST AT 10:32 BST by MGT Nature 2008 imex curation TGF-beta-induced Foxp3 inhibits T(H)17 cell differentiation by antagonizing RORgammat function. TGF-beta-induced Foxp3 inhibits T(H)17 cell differentiation by antagonizing RORgammat function. Nature 2008 imex curation Zhou L., Lopes JE., Chong MM., Ivanov II., Min R., Victora GD., Shen Y., Du J., Rubtsov YP., Rudensky AY., Ziegler SF., Littman DR. IBD - Inflammatory bowel disease littman@saturn.med.nyu.edu 21-10-2015: Contacted by IntAct-Help. Only protein-protein interactions 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 Zhou L., Lopes JE., Chong MM., Ivanov II., Min R., Victora GD., Shen Y., Du J., Rubtsov YP., Rudensky AY., Ziegler SF., Littman DR. IBD - Inflammatory bowel disease littman@saturn.med.nyu.edu Accepted 2015-OCT-19 AT 10:32 BST AT 10:32 BST by MGT Nature 2008 imex curation p51450-2 Nuclear receptor ROR-gamma RORgT Rorc Nr1f3 Rorg Thor Nuclear receptor RZR-gamma Nuclear receptor subfamily 1 group F member 3 Retinoid-related orphan receptor-gamma Thymus orphan receptor RAR-related orphan receptor C protein protein mouse Mus musculus Mouse MRTQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRNRCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEVQKQLQQQQQQEQVAKTPPAGSRGADTLTYTLGLSDGQLPLGASPDLPEASACPPGLLRASGSGPPYSNTLAKTEVQGASCHLEYSPERGKAEGRDSIYSTDGQLTLGRCGLRFEETRHPELGEPEQGPDSHCIPSFCSAPEVPYASLTDIEYLVQNVCKSFRETCQLRLEDLLRQRTNLFSREEVTSYQRKSMWEMWERCAHHLTEAIQYVVEFAKRLSGFMELCQNDQIILLTAGAMEVVLVRMCRAYNANNHTVFFEGKYGGVELFRALGCSELISSIFDFSHFLSALCFSEDEIALYTALVLINANRPGLQEKRRVEHLQYNLELAFHHHLCKTHRQGLLAKLPPKGKLRSLCSQHVEKLQIFQHLHPIVVQAAFPPLYKELFSTDVESPEGLSK Produced by alternative promoter usage. A8A1C1A08921CFB6 foxp3_human Forkhead box protein P3 Scurfin FOXP3 IPEX JM2 protein protein human Homo sapiens Human MPNPRPGKPSAPSLALGPSPGASPSWRAAPKASDLLGARGPGGTFQGRDLRGGAHASSSSLNPMPPSQLQLPTLPLVMVAPSGARLGPLPHLQALLQDRPHFMHQLSTVDAHARTPVLQVHPLESPAMISLTPPTTATGVFSLKARPGLPPGINVASLEWVSREPALLCTFPNPSAPRKDSTLSAVPQSSYPLLANGVCKWPGCEKVFEEPEDFLKHCQADHLLDEKGRAQCLLQREMVQSLEQQLVLEKEKLSAMQAHLAGKMALTKASSVASSDKGSCCIVAAGSQGPVVPAWSGPREAPDSLFAVRRHLWGSHGNSTFPEFLHNMDYFKFHNMRPPFTYATLIRWAILEAPEKQRTLNEIYHWFTRMFAFFRNHPATWKNAIRHNLSLHKCFVRVESEKGAVWTVDELEFRKKRSQRPSRCSNPTPGP DIP protein Q9BZS1 original sequence version: 139 DIP protein Q9BZS1 original sequence version: 131 91737C3CEA665A15 foxp3_mouse Forkhead box protein P3 Foxp3 Scurfin protein protein mouse Mus musculus Mouse MPNPRPAKPMAPSLALGPSPGVLPSWKTAPKGSELLGTRGSGGPFQGRDLRSGAHTSSSLNPLPPSQLQLPTVPLVMVAPSGARLGPSPHLQALLQDRPHFMHQLSTVDAHAQTPVLQVRPLDNPAMISLPPPSAATGVFSLKARPGLPPGINVASLEWVSREPALLCTFPRSGTPRKDSNLLAAPQGSYPLLANGVCKWPGCEKVFEEPEEFLKHCQADHLLDEKGKAQCLLQREVVQSLEQQLELEKEKLGAMQAHLAGKMALAKAPSVASMDKSSCCIVATSTQGSVLPAWSAPREAPDGGLFAVRRHLWGSHGNSSFPEFFHNMDYFKYHNMRPPFTYATLIRWAILEAPERQRTLNEIYHWFTRMFAYFRNHPATWKNAIRHNLSLHKCFVRVESEKGAVWTVDEFEFRKKRSQRPNKCSNPCP DIP protein Q99JB6 original sequence version: 120 DIP protein Q99JB6 original sequence version: 110 DIP protein Q99JB6 original sequence version: 114 DIP protein Q99JB6 original sequence version: 102 DIP protein Q99JB6 original sequence version: 100 28D5B8E67891840C rorg_mouse Nuclear receptor ROR-gamma Rorc Nr1f3 Rorg Thor Nuclear receptor RZR-gamma Nuclear receptor subfamily 1 group F member 3 Retinoid-related orphan receptor-gamma Thymus orphan receptor RAR-related orphan receptor C protein protein mouse Mus musculus Mouse MDRAPQRHHRTSRELLAAKKTHTSQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQCNVAYSCTRQQNCPIDRTSRNRCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEVQKQLQQQQQQEQVAKTPPAGSRGADTLTYTLGLSDGQLPLGASPDLPEASACPPGLLRASGSGPPYSNTLAKTEVQGASCHLEYSPERGKAEGRDSIYSTDGQLTLGRCGLRFEETRHPELGEPEQGPDSHCIPSFCSAPEVPYASLTDIEYLVQNVCKSFRETCQLRLEDLLRQRTNLFSREEVTSYQRKSMWEMWERCAHHLTEAIQYVVEFAKRLSGFMELCQNDQIILLTAGAMEVVLVRMCRAYNANNHTVFFEGKYGGVELFRALGCSELISSIFDFSHFLSALCFSEDEIALYTALVLINANRPGLQEKRRVEHLQYNLELAFHHHLCKTHRQGLLAKLPPKGKLRSLCSQHVEKLQIFQHLHPIVVQAAFPPLYKELFSTDVESPEGLSK DIP protein P51450 original sequence version: 140 DIP protein P51450 original sequence version: 149 DIP protein P51450 original sequence version: 108 218068AF4598A93B rorg_human Nuclear receptor ROR-gamma RORC NR1F3 RORG RZRG Nuclear receptor RZR-gamma Nuclear receptor subfamily 1 group F member 3 Retinoid-related orphan receptor-gamma RAR-related orphan receptor C protein protein human Homo sapiens Human MDRAPQRQHRASRELLAAKKTHTSQIEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQRCNAAYSCTRQQNCPIDRTSRNRCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSLHAEVQKQLQQRQQQQQEPVVKTPPAGAQGADTLTYTLGLPDGQLPLGSSPDLPEASACPPGLLKASGSGPSYSNNLAKAGLNGASCHLEYSPERGKAEGRESFYSTGSQLTPDRCGLRFEEHRHPGLGELGQGPDSYGSPSFRSTPEAPYASLTEIEHLVQSVCKSYRETCQLRLEDLLRQRSNIFSREEVTGYQRKSMWEMWERCAHHLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNRTVFFEGKYGGMELFRALGCSELISSIFDFSHSLSALHFSEDEIALYTALVLINAHRPGLQEKRKVEQLQYNLELAFHHHLCKTHRQSILAKLPPKGKLRSLCSQHVERLQIFQHLHPIVVQAAFPPLYKELFSTETESPVGLSK DIP protein P51449 original sequence version: 149 7F423140BD7922BE rorc-foxp3-1 4 6 unspecified role unspecified role prey prey region foxp3hu required to bind necessary binding region required to bind range range range range 9 unspecified role unspecified role bait bait n-terminus ROR flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged n-term range n-terminal range n-term range n-term range n-terminal range n-term range physical association physical association Fig. 3B rorg-foxp3-1 2 7 unspecified role unspecified role neutral component neutral component n-terminus foxp3 flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged n-term range n-terminal range n-term range n-term range n-terminal range n-term range 5 unspecified role unspecified role neutral component neutral component colocalization colocalization Supplementary Fig. 4. FKH mutant remained in the cytoplasm even when it was co-expressed with ROR-gamma-t foxp3-rorc-2 4 5 unspecified role unspecified role prey prey 7 unspecified role unspecified role bait bait n-terminus foxp3 flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged n-term range n-terminal range n-term range n-term range n-terminal range n-term range region foxp3 required to bind necessary binding region required to bind range range range range physical association physical association Fig. 3A foxp3-rorc-1 3 5 unspecified role unspecified role neutral component neutral component 7 unspecified role unspecified role neutral component neutral component colocalization colocalization Fig. 1A, Suppementary Fig. 1A TGF-beta causes expression of the gamma-t isoform of ROR-gamma-t foxp3-rorc-3 1 7 unspecified role unspecified role neutral component neutral component 8 unspecified role unspecified role neutral component neutral component colocalization colocalization Supplementary Fig. 1B