mbinfo MBInfo http://www.mechanobio.info/ http://www.mechanobio.info/ martynova-2008-4 The LIM-domain protein Zyxin binds the homeodomain factor Xanf1/Hesx1 and modulates its activity in the anterior neural plate of Xenopus laevis embryo. yeast Saccharomyces cerevisiae Baker's yeast 2 hybrid two hybrid 2H 2h Gal4 transcription regeneration two-hybrid yeast two hybrid 2-hybrid classical two hybrid classical two hybrid 2H two-hybrid 2-hybrid Gal4 transcription regeneration 2h yeast two hybrid Y2H Y-2H 2 hybrid nucleotide sequence nucleotide sequence identification sequence cloning sequence cloning nucleotide sequence Martynova N.Y., Eroshkin F.M., Ermolina L.V., Ermakova G.V., Korotaeva A.L., Smurova K.M., Gyoeva F.K., Zaraisky A.G. In the colocalization experiment (Fig. 6), since both the proteins are not visualized in the same image, this data cannot be curated. The coprecipitated proteins were primarily detected by immunoblotting with anti-tag antibodies. But in the instance were microinjected myc-xanf1 were used to precipitate endogenous zyxin (fig. 3 lanes 8,9,10,11), the coprecipitated zyxin was detected with anti-zyxin antibodies. The source of Xanf1, zyxin, XIRG, LANP and Sam68 provided by the authors. Zar@humgen.siobc.ras.ru cDNA expression library from X. laevis embryos of the late gastrula–early neurula stage Dev. Dyn. (1058-8388) 2008 Only protein-protein interactions imex curation martynova-2008-1 The LIM-domain protein Zyxin binds the homeodomain factor Xanf1/Hesx1 and modulates its activity in the anterior neural plate of Xenopus laevis embryo. xenla-embryo Xenopus laevis embryo embryo Embryo Defined as the development stage prior to the initiation of tissue differentiation. anti tag coip anti tag coimmunoprecipitation anti tag coip anti tag western anti tag western blot anti tag western Martynova N.Y., Eroshkin F.M., Ermolina L.V., Ermakova G.V., Korotaeva A.L., Smurova K.M., Gyoeva F.K., Zaraisky A.G. In the colocalization experiment (Fig. 6), since both the proteins are not visualized in the same image, this data cannot be curated. The coprecipitated proteins were primarily detected by immunoblotting with anti-tag antibodies. But in the instance were microinjected myc-xanf1 were used to precipitate endogenous zyxin (fig. 3 lanes 8,9,10,11), the coprecipitated zyxin was detected with anti-zyxin antibodies. The source of Xanf1, zyxin, XIRG, LANP and Sam68 provided by the authors. Zar@humgen.siobc.ras.ru Dev. Dyn. (1058-8388) 2008 Only protein-protein interactions imex curation martynova-2008-2 The LIM-domain protein Zyxin binds the homeodomain factor Xanf1/Hesx1 and modulates its activity in the anterior neural plate of Xenopus laevis embryo. yeast Saccharomyces cerevisiae Baker's yeast 2 hybrid two hybrid 2H 2h Gal4 transcription regeneration two-hybrid yeast two hybrid 2-hybrid classical two hybrid classical two hybrid 2H two-hybrid 2-hybrid Gal4 transcription regeneration 2h yeast two hybrid Y2H Y-2H 2 hybrid predetermined predetermined participant predetermined Martynova N.Y., Eroshkin F.M., Ermolina L.V., Ermakova G.V., Korotaeva A.L., Smurova K.M., Gyoeva F.K., Zaraisky A.G. In the colocalization experiment (Fig. 6), since both the proteins are not visualized in the same image, this data cannot be curated. The coprecipitated proteins were primarily detected by immunoblotting with anti-tag antibodies. But in the instance were microinjected myc-xanf1 were used to precipitate endogenous zyxin (fig. 3 lanes 8,9,10,11), the coprecipitated zyxin was detected with anti-zyxin antibodies. The source of Xanf1, zyxin, XIRG, LANP and Sam68 provided by the authors. Zar@humgen.siobc.ras.ru Dev. Dyn. (1058-8388) 2008 Only protein-protein interactions imex curation martynova-2008-3 The LIM-domain protein Zyxin binds the homeodomain factor Xanf1/Hesx1 and modulates its activity in the anterior neural plate of Xenopus laevis embryo. in vitro In vitro pull down pull down anti tag western anti tag western blot anti tag western Martynova N.Y., Eroshkin F.M., Ermolina L.V., Ermakova G.V., Korotaeva A.L., Smurova K.M., Gyoeva F.K., Zaraisky A.G. In the colocalization experiment (Fig. 6), since both the proteins are not visualized in the same image, this data cannot be curated. The coprecipitated proteins were primarily detected by immunoblotting with anti-tag antibodies. But in the instance were microinjected myc-xanf1 were used to precipitate endogenous zyxin (fig. 3 lanes 8,9,10,11), the coprecipitated zyxin was detected with anti-zyxin antibodies. The source of Xanf1, zyxin, XIRG, LANP and Sam68 provided by the authors. Zar@humgen.siobc.ras.ru Dev. Dyn. (1058-8388) 2008 Only protein-protein interactions imex curation zyx_xenla Zyxin zyx protein protein xenla Xenopus laevis (African clawed frog) African clawed frog MDPAAPATRMTSSFTINISTPSFYNPPKKFAPVVPPKPKINPFKAPEEPQSLVPQENSAGPGLHQAFVGKVGEMPPGVDHDDFVLPPPPPSEESISPPSSSFPPPPPSFGDEGLGSPSGGSFPPPPPPEFSEPFPPPIEEFFPSPPPLEECVSDTQDLPVPVPPPPPPPLPSPPAAPPPKPSAPCEAPKPAPVFPKSSPPPAFPKPEPPSVAPKAASSIFIPKPSAPMAVAPKPLAPPPVAAKPSGPVSFAPPSPAPHTFSPDPSAPAHTFSPKTVTFSPKSAPHTFMPKPSAPVTYPQKTTEPPAEASQSSPKVTPAAKHEAPPPTVPSGGRAPGFSFAQQRERPRVLEKPRANLQGSEPEHEPTVEVQVERTRSLGPQTESGRSPGAQSTGGKDMKPLPEGLRSQKPMSDGIHRTGGQHSGHKVTGQQDQTLGSQGLNMKEVEELEMLTQQLMREMDKPPTAEAHSMELCGFCGRGLSRTETVVRAGEHLYHVACFTCSRCDQQLQGQQYYESAGKPLCDECYQDTLECCAVCDKKITERLLKAIGKSYHPSCFTCAVCKCSLQGEPFIVDDNKLPHCVNDYHRRYAPRCCVCGDPIAPEPGRDETVRVVALEKNFHMMCYKCEDCGCPLSIEADDAGCFPLDGHVLCKKCHTVRARAALG hesxb_xenla Homeobox expressed in ES cells 1-B hesx1-b anf-1 anf1 Homeobox protein ANF-1 protein protein xenla Xenopus laevis (African clawed frog) African clawed frog MSPALQKGSSLMENRSPPSSFSIEHILGLDKKTDVASSPIIKHHRPWIECSSKGVVNGTCWQIPVIACDLPIQVHAVHRSEEEETKIRLEKCFGDEDRLTYKRELSWYRGRRPRTAFTRSQIEILENVFRVNSYPGIDVREELASKLALDEDRIQIWFQNRRAKLKRSHRESQFLIVKDSLSSKIQE q9dgg0_xenla xirg protein protein xenla Xenopus laevis (African clawed frog) African clawed frog MFSSTLQNTKKLQQVCRQLHSAALKVAVSPQYEESVTNTFASFITDIRPEHLSDIVRHRSKRMILDNIGVGLVGTTTHVFNIILQYCQDLHSSGYGNTAVSSVYGRKDLMLSPTLAAYVNGVAVHSMDFDDTWHPATHPSGAVVPSILALSQLLSKEKRISGEDLLTAYNVGIEVQGRLMCFSKEAKNIPKKFHPPSVVGTMGSAAAAAKLLSLNKEQCTHALAIAASLAGAPMANAATLSKPLHIGNATRLGLEAALLASRGMEANALILDYVPGCAGFSAFYGDYHPKSLSPAGEDYEFLLEKQDIAFKSFPAHLGMHWIADASVSVRNRLINHYGSFNPSAIQSIILRVPVSKYINRPYPESEHEARHSFQFNACTALLDGEVNISSFNDDNMHRPDLHSLLKKVVLEHPEDNVANFDKMYGEVVIVLKDGDVKIGRTDTFYGHWRNPLSRESLLKKFRSNALHVLEEGQVEDVIEMVENMESVSDVSQLPLSLQ an32a_xenla Acidic leucine-rich nuclear phosphoprotein 32 family member A anp32a protein protein xenla Xenopus laevis (African clawed frog) African clawed frog MDMKKRIHLELRNRTPADVKELVLDNCRSKEGKIEGLTDEFEGLEFLSTINVCLSSIANLPKLNKLKKLELSDNNISGGLEVLAEKCPNLTHLNLSGNRIKDLSTIEPLKKLEHLKSLDLFNCEVTNLNDYRENLFKLLPQLTYLDGYDRDDKEAPDSDAEGYVEGLDDDEDDEDEDDYDEDVPPGEEGEDDDDEEEGEEEEVSGEEEEDEDASREGEEDEGDEEAEHGEKRKRDQDDEGEDDD q7syh0_xenla protein protein xenla Xenopus laevis (African clawed frog) African clawed frog YEDSYAEPSYEGYEGYYSQSQGETEYYDYGHGEGPESYENYGQDNWNGSRPPPLKVPSSRALKGGAYREHPYGRF hesx1_b-zyx-4 1272805 n/a 1272809 unspecified role unspecified role prey prey n/a 1272810 unspecified role unspecified role bait bait physical association physical association false false false hesx1_b-irg1 1272805 n/a 1272810 unspecified role unspecified role bait bait n/a 1272811 unspecified role unspecified role prey prey physical association physical association false false false The XIRG protein is not annotated in swissprot and thus has been referenced with a TrEMBL identifier. anp32a-hesx1b 1272805 n/a 1272812 unspecified role unspecified role prey prey n/a 1272810 unspecified role unspecified role bait bait physical association physical association false false false hesx1_b-q7syh0 1272805 n/a 1272813 unspecified role unspecified role prey prey n/a 1272810 unspecified role unspecified role bait bait physical association physical association false false false The Sam68 protein is not annotated in swissprot and is referenced only by a TrEMBL entry. This TrEMBL entry for Sam68 corresponds to a partial protein sequence and not the full length protein. hesx1_b-zyx 1272806 n/a 1272809 unspecified role unspecified role prey prey n-terminus 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 false c-terminal region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false The author provides contradictory sequence lengths for zyxin in the text and in the sequence representation. But since the uniprot also has a sequence length of 663 amino acids for Xenopus laevis zyxin, the binding site here would be [373-663] and not [373-664] as provided by the author in the text. n/a 1272810 unspecified role unspecified role bait bait n-terminus myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false physical association physical association false false false Fig. 3 (Lanes 1,2,8,9,10 and 11). hesx1_b-zyx-2 1272806 n/a 1272809 unspecified role unspecified role bait bait c-terminal region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false The author provides contradictory sequence lengths for zyxin in the text and in the sequence representation. But since the uniprot also has a sequence length of 663 amino acids for Xenopus laevis zyxin, the binding site here would be [373-663] and not [373-664] as provided by the author in the text. n-terminus 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 false n/a 1272810 unspecified role unspecified role prey prey n-terminus myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false eh1 domain required to bind necessary binding region required to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain false 1272838 1272834 physical association physical association false false false Fig. 3 (Lanes 3,4) and 5C. zyx -hesx1-b 1272807 n/a 1272810 unspecified role unspecified role prey prey n-terminal region required to bind necessary binding region required to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain false The N-terminal region [1-77] contains the Engrailed Homology 1 domain (sequence not provided by authors) which is responsible for the interaction with zyxin. n/a 1272809 unspecified role unspecified role bait bait lim2 domain required to bind necessary binding region required to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain false 1272843 1272841 physical association physical association false false false Fig. 4A and 5A. hesx1_b-zyx-1 1272808 n/a 1272810 unspecified role unspecified role prey prey n-terminus myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false xenla-oocyte Xenopus laevis oocyte Oocyte n/a 1272809 unspecified role unspecified role bait bait lim2 domain required to bind necessary binding region required to bind certain certain sequence position certain certain certain sequence position certain false n-terminus gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst 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) physical association physical association false false false Fig. 4B and 5B.