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/ http://www.ebi.ac.uk/ johansson-2010-4 Phosphorylated nucleolin interacts with translationally controlled tumor protein during mitosis and with Oct4 during interphase in ES cells. mouse-embryonic_stem cell Mus musculus embryonic stem cell es cells embryonic stem cells pla proximity ligation assay pELISA pELISA PLA antibody detection identification by antibody antibody detection Johansson H., Svensson F., Runnberg R., Simonsson T., Simonsson S. Affinomics - Interactions curated for the Affinomics consortium. Mitotic cells arrested in metaphase with demecolcine stina.simonsson@gu.se PLoS ONE 2010 Only protein-protein interactions imex curation johansson-2010-2 Phosphorylated nucleolin interacts with translationally controlled tumor protein during mitosis and with Oct4 during interphase in ES cells. mouse-embryonic_stem cell Mus musculus embryonic stem cell es cells embryonic stem cells confocal microscopy confocal microscopy immunocytochemistry immunocytochemistry Johansson H., Svensson F., Runnberg R., Simonsson T., Simonsson S. Affinomics - Interactions curated for the Affinomics consortium. stina.simonsson@gu.se PLoS ONE 2010 Only protein-protein interactions imex curation johansson-2010-5 Phosphorylated nucleolin interacts with translationally controlled tumor protein during mitosis and with Oct4 during interphase in ES cells. human-embryonic_stem_ cells Human-embryonic_stem_ cells (es cells) embryonic_stem_cell Embryonic stem cell (es cells) pla proximity ligation assay pELISA pELISA PLA antibody detection identification by antibody antibody detection Johansson H., Svensson F., Runnberg R., Simonsson T., Simonsson S. Affinomics - Interactions curated for the Affinomics consortium. stina.simonsson@gu.se PLoS ONE 2010 Only protein-protein interactions imex curation johansson-2010-1 Phosphorylated nucleolin interacts with translationally controlled tumor protein during mitosis and with Oct4 during interphase in ES cells. in vitro In vitro pull down pull down ms participant Identification by mass spectrometry ms participant Johansson H., Svensson F., Runnberg R., Simonsson T., Simonsson S. Affinomics - Interactions curated for the Affinomics consortium. Several proteins other than those entered here were found on the gel, but the only identifications given are ambiguous; notably:- Myosin heavy polypeptide 9. Actin - cytoplasmic type 8, gamma-actin, Ribosomal protein L10, Tropomyosin. stina.simonsson@gu.se PLoS ONE 2010 Only protein-protein interactions imex curation johansson-2010-3 Phosphorylated nucleolin interacts with translationally controlled tumor protein during mitosis and with Oct4 during interphase in ES cells. mouse-embryonic_stem cell Mus musculus embryonic stem cell es cells embryonic stem cells anti bait coip anti bait coimmunoprecipitation anti bait coip western blot western blot Immuno blot Immuno blot Johansson H., Svensson F., Runnberg R., Simonsson T., Simonsson S. Affinomics - Interactions curated for the Affinomics consortium. Mitotic extracts were prepared by arresting ES cells in metaphase by adding Demecolcine. stina.simonsson@gu.se PLoS ONE 2010 Only protein-protein interactions imex curation nucl_mouse Nucleolin Protein C23 Ncl Nuc protein protein mouse Mus musculus Mouse MVKLAKAGKTHGEAKKMAPPPKEVEEDSEDEEMSEDEDDSSGEEEVVIPQKKGKKATTTPAKKVVVSQTKKAAVPTPAKKAAVTPGKKAVATPAKKNITPAKVIPTPGKKGAAQAKALVPTPGKKGAATPAKGAKNGKNAKKEDSDEDEDEEDEDDSDEDEDDEEEDEFEPPIVKGVKPAKAAPAAPASEDEEDDEDEDDEEDDDEEEEDDSEEEVMEITTAKGKKTPAKVVPMKAKSVAEEEDDEEEDEDDEDEDDEEEDDEDDDEEEEEEEPVKAAPGKRKKEMTKQKEAPEAKKQKVEGSEPTTPFNLFIGNLNPNKSVNELKFAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDAMEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGQRQERTGKTSTWSGESKTLVLSNLSYSATKETLEEVFEKATFIKVPQNPHGKPKGYAFIEFASFEDAKEALNSCNKMEIEGRTIRLELQGSNSRSQPSKTLFVKGLSEDTTEETLKESFEGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEGGFGGRGGGRGGFGGRGGGRGGRGGFGGRGRGGFGGRGGFRGGRGGGGDFKPQGKKTKFE tctp_mouse Translationally-controlled tumor protein Tpt1 Trt p23 21 kDa polypeptide p21 protein protein mouse Mus musculus Mouse MIIYRDLISHDELFSDIYKIREIADGLCLEVEGKMVSRTEGAIDDSLIGGNASAEGPEGEGTESTVVTGVDIVMNHHLQETSFTKEAYKKYIKDYMKSLKGKLEEQKPERVKPFMTGAAEQIKHILANFNNYQFFIGENMNPDGMVALLDYREDGVTPFMIFFKDGLEMEKC po5f1_mouse POU domain, class 5, transcription factor 1 Pou5f1 Oct-3 Oct-4 Otf-3 Otf3 Octamer-binding transcription factor 3 NF-A3 Octamer-binding protein 3 Octamer-binding protein 4 protein protein mouse Mus musculus Mouse MAGHLASDFAFSPPPGGGDGSAGLEPGWVDPRTWLSFQGPPGGPGIGPGSEVLGISPCPPAYEFCGGMAYCGPQVGLGLVPQVGVETLQPEGQAGARVESNSEGTSSEPCADRPNAVKLEKVEPTPEESQDMKALQKELEQFAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTICRFEALQLSLKNMCKLRPLLEKWVEEADNNENLQEICKSETLVQARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKRSSIEYSQREEYEATGTPFPGGAVSFPLPPGPHFGTPGYGSPHFTTLYSVPFPEGEAFPSVPVTALGSPMHSN npm_mouse Nucleophosmin Nucleolar phosphoprotein B23 Numatrin Nucleolar protein NO38 Npm1 protein protein mouse Mus musculus Mouse MEDSMDMDMSPLRPQNYLFGCELKADKDYHFKVDNDENEHQLSLRTVSLGAGAKDELHIVEAEAMNYEGSPIKVTLATLKMSVQPTVSLGGFEITPPVVLRLKCGSGPVHISGQHLVAVEEDAESEDEDEEDVKLLGMSGKRSAPGGGNKVPQKKVKLDEDDEDDDEDDEDDEDDDDDDFDEEETEEKVPVKKSVRDTPAKNAQKSNQNGKDLKPSTPRSKGQESFKKQEKTPKTPKGPSSVEDIKAKMQASIEKGGSLPKVEAKFINYVKNCFRMTDQEAIQDLWQWRKSL po5f1_human POU domain, class 5, transcription factor 1 Octamer-binding transcription factor 3 Octamer-binding protein 3 POU5F1 OCT3 OCT4 OTF3 Octamer-binding protein 4 protein protein human Homo sapiens Human MAGHLASDFAFSPPPGGGGDGPGGPEPGWVDPRTWLSFQGPPGGPGIGPGVGPGSEVWGIPPCPPPYEFCGGMAYCGPQVGVGLVPQGGLETSQPEGEAGVGVESNSDGASPEPCTVTPGAVKLEKEKLEQNPEESQDIKALQKELEQFAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTICRFEALQLSFKNMCKLRPLLQKWVEEADNNENLQEICKAETLVQARKRKRTSIENRVRGNLENLFLQCPKPTLQQISHIAQQLGLEKDVVRVWFCNRRQKGKRSSSDYAQREDFEAAGSPFSGGPVSFPLAPGPHFGTPGYGSPHFTALYSSVPFPEGEAFPPVSVTTLGSPMHSN nucl_human Nucleolin NCL Protein C23 protein protein human Homo sapiens Human MVKLAKAGKNQGDPKKMAPPPKEVEEDSEDEEMSEDEEDDSSGEEVVIPQKKGKKAAATSAKKVVVSPTKKVAVATPAKKAAVTPGKKAAATPAKKTVTPAKAVTTPGKKGATPGKALVATPGKKGAAIPAKGAKNGKNAKKEDSDEEEDDDSEEDEEDDEDEDEDEDEIEPAAMKAAAAAPASEDEDDEDDEDDEDDDDDEEDDSEEEAMETTPAKGKKAAKVVPVKAKNVAEDEDEEEDDEDEDDDDDEDDEDDDDEDDEEEEEEEEEEPVKEAPGKRKKEMAKQKAAPEAKKQKVEGTEPTTAFNLFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRIGMTRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGKDSKKERDARTLLAKNLPYKVTQDELKEVFEDAAEIRLVSKDGKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRSISLYYTGEKGQNQDYRGGKNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPRGSPNARSQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEGGFGGRGGGRGGFGGRGGGRGGRGGFGGRGRGGFGGRGGFRGGRGGGGDHKPQGKKTKFE npm_human Nucleophosmin NPM1 NPM Nucleolar phosphoprotein B23 Numatrin Nucleolar protein NO38 protein protein human Homo sapiens Human MEDSMDMDMSPLRPQNYLFGCELKADKDYHFKVDNDENEHQLSLRTVSLGAGAKDELHIVEAEAMNYEGSPIKVTLATLKMSVQPTVSLGGFEITPPVVLRLKCGSGPVHISGQHLVAVEEDAESEDEEEEDVKLLSISGKRSAPGGGSKVPQKKVKLAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVKKSIRDTPAKNAQKSNQNGKDSKPSSTPRSKGQESFKKQEKTPKTPKGPSSVEDIKAKMQASIEKGGSLPKVEAKFINYVKNCFRMTDQEAIQDLWQWRKSL h11_mouse Histone H1.1 H1-1 H1 VAR.3 H1a H1f1 Hist1h1a Histone H1a protein protein mouse Mus musculus Mouse MSETAPVAQAASTATEKPAAAKKTKKPAKAAAPRKKPAGPSVSELIVQAVSSSKERSGVSLAALKKSLAAAGYDVEKNNSRIKLGLKSLVNKGTLVQTKGTGAAGSFKLNKKAESKAITTKVSVKAKASGAAKKPKKTAGAAAKKTVKTPKKPKKPAVSKKTSKSPKKPKVVKAKKVAKSPAKAKAVKPKASKAKVTKPKTPAKPKKAAPKKK Histones H1 are necessary for the condensation of nucleosome chains into higher order structures mint actb_mouse Actin, cytoplasmic 1 Actb Beta-actin protein protein mouse Mus musculus Mouse MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSIVHRKCF rl8_mouse 60S ribosomal protein L8 Rpl8 protein protein mouse Mus musculus Mouse MGRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAKVVFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKPGDRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPILKAGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAARRTGRLRGTKTVQEKEN h15_mouse Histone H1.5 H1-5 H1 VAR.5 H1b H1f5 Hist1h1b protein protein mouse Mus musculus Mouse MSETAPAETAAPAPVEKSPAKKKTTKKAGAAKRKATGPPVSELITKAVSASKERGGVSLPALKKALAAGGYDVEKNNSRIKLGLKSLVSKGTLVQTKGTGASGSFKLNKKAASGEAKPKAKKTGAAKAKKPAGATPKKPKKTAGAKKTVKKTPKKAKKPAAAGVKKVAKSPKKAKAAAKPKKAAKSPAKPKAVKSKASKPKVTKPKTAKPKAAKAKKAVSKKK h14_mouse Histone H1.4 H1-4 H1 VAR.2 H1e H1f4 Hist1h1e protein protein mouse Mus musculus Mouse MSETAPAAPAAPAPAEKTPVKKKARKAAGGAKRKTSGPPVSELITKAVAASKERSGVSLAALKKALAAAGYDVEKNNSRIKLGLKSLVSKGTLVQTKGTGASGSFKLNKKAASGEAKPKAKRAGAAKAKKPAGAAKKPKKAAGTATAKKSTKKTPKKAKKPAAAAGAKKAKSPKKAKATKAKKAPKSPAKAKTVKPKAAKPKTSKPKAAKPKKTAAKKK h13_mouse Histone H1.3 H1-3 H1 VAR.4 H1d H1f3 Hist1h1d protein protein mouse Mus musculus Mouse MSETAPAAPAAPAPVEKTPVKKKAKKTGAAAGKRKASGPPVSELITKAVAASKERSGVSLAALKKALAAAGYDVEKNNSRIKLGLKSLVSKGTLVQTKGTGASGSFKLNKKAASGEAKPKAKKAGAAKAKKPAGAAKKPKKATGAATPKKTAKKTPKKAKKPAAAAGAKKVSKSPKKVKAAKPKKAAKSPAKAKAPKAKASKPKASKPKATKAKKAAPRKK ncl-tpt1-2 1531592 n/a 1531597 unspecified role unspecified role neutral component neutral component possible_phosphores phosres phosphorylated residue PhosRes Phospho Phosphorylation Phosphorylation (O of Serine, Threonine, Tyrosine and Aspartate, N epsilon of Lysine) undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false n/a 1531598 unspecified role unspecified role neutral component neutral component proximity proximity close-contact colocalization neighbourhood interaction false false false 2 E/F ncl-pou5f1 1531592 n/a 1531597 unspecified role unspecified role neutral component neutral component possible_phosphores phosres phosphorylated residue PhosRes Phospho Phosphorylation Phosphorylation (O of Serine, Threonine, Tyrosine and Aspartate, N epsilon of Lysine) undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false n/a 1531599 unspecified role unspecified role neutral component neutral component proximity proximity close-contact colocalization neighbourhood interaction false false false 3 B/C ncl-npm1 1531592 n/a 1531600 unspecified role unspecified role neutral component neutral component n/a 1531597 unspecified role unspecified role neutral component neutral component proximity proximity close-contact colocalization neighbourhood interaction false false false Supp 2A Positive control ncl-tpt1 1531593 n/a 1531598 unspecified role unspecified role neutral component neutral component n/a 1531597 unspecified role unspecified role neutral component neutral component required_phosphores phosres phosphorylated residue PhosRes Phospho Phosphorylation Phosphorylation (O of Serine, Threonine, Tyrosine and Aspartate, N epsilon of Lysine) undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false colocalization colocalization false false false 2 B/C Demecolcine (colcemid) It depolymerises microtubules and inactivates spindle fibre formation, thus arresting cells in metaphase. Substantially more colocalization is visualized with phosphorylated Nucleolin and Tpt1 (Figure 2B–C) as compared to non- phosphorylated Nucleolin and Tpt1.(Fig 2A) ncl-tpt1-3 1531593 n/a 1531599 unspecified role unspecified role neutral component neutral component n/a 1531597 unspecified role unspecified role neutral component neutral component required_phosphores phosres phosphorylated residue PhosRes Phospho Phosphorylation Phosphorylation (O of Serine, Threonine, Tyrosine and Aspartate, N epsilon of Lysine) undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false colocalization colocalization false false false 3A, Table 1 ncl-pou5f1-1 1531594 n/a 1531601 unspecified role unspecified role neutral component neutral component n/a 1531602 unspecified role unspecified role neutral component neutral component proximity proximity close-contact colocalization neighbourhood interaction false false false 3 D/E ncl-pou5f1-2 1531594 n/a 1531603 unspecified role unspecified role neutral component neutral component n/a 1531602 unspecified role unspecified role neutral component neutral component proximity proximity close-contact colocalization neighbourhood interaction false false false Supp 2B Positive control tpt1-actb 1531595 n/a 1531604 unspecified role unspecified role prey prey mouse-embryonic_stem cell Mus musculus embryonic stem cell es cells embryonic stem cells n/a 1531605 unspecified role unspecified role prey prey mouse-embryonic_stem cell Mus musculus embryonic stem cell es cells embryonic stem cells n/a 1531606 unspecified role unspecified role prey prey mouse-embryonic_stem cell Mus musculus embryonic stem cell es cells embryonic stem cells n/a 1531607 unspecified role unspecified role prey prey mouse-embryonic_stem cell Mus musculus embryonic stem cell es cells embryonic stem cells n/a 1531608 unspecified role unspecified role prey prey mouse-embryonic_stem cell Mus musculus embryonic stem cell es cells embryonic stem cells n/a 1531609 unspecified role unspecified role prey prey mouse-embryonic_stem cell Mus musculus embryonic stem cell es cells embryonic stem cells n/a 1531597 unspecified role unspecified role prey prey mouse-embryonic_stem cell Mus musculus embryonic stem cell es cells embryonic stem cells n/a 1531598 unspecified role unspecified role bait bait n_terminus s tag s tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false n_terminus 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 false ecoli Escherichia coli (strain K12) association association false false false Figure 1 Several other proteins are stated to have been found on the gel, but have been ambiguously identified, notably:- Myosin heavy polypeptide 9. Actin - cytoplasmic type 8, gamma-actin, Ribosomal protein L10, Tropomyosin. tpt1-ncl 1531596 n/a 1531598 unspecified role unspecified role bait bait n/a 1531597 unspecified role unspecified role prey prey possible_phosphores phosres phosphorylated residue PhosRes Phospho Phosphorylation Phosphorylation (O of Serine, Threonine, Tyrosine and Aspartate, N epsilon of Lysine) undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false physical association physical association false false false Co-immunoprecipitation of Ncl-P was detected in the presence of 1m NaCl, but not in the presence of 0.1M citrate. 2 D