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/ Suppressors of the Chloroplast Protein Import Mutant tic40 Reveal a Genetic Link between Protein Import and Thylakoid Biogenesis. Suppressors of the Chloroplast Protein Import Mutant tic40 Reveal a Genetic Link between Protein Import and Thylakoid Biogenesis. The Plant cell 2017 imex curation Bédard J., Trösch R., Wu F., Ling Q., Flores-Pérez Ú., Töpel M., Nawaz F., Jarvis P. not available-free- until July next year;please ask me for PDF of the publication + suppllement. STIC2:-They state to have used "For protein alignments" NP_001189586 - which corresponds to isoform 2 - but in fig 6A they use a construct of 182 aas length which is isoform1 - so no isoform info added. request via Pablo. see pmids: 26265777 and 28684427 "In each case, I supply the Arabidopsis gene identifier on first appearance. " There are two main protein-protein interactions, which are as follows: STIC2 (At2g24020) vs. STIC1(ALB4) (At1g24490) This interaction was supported by: in vitro pull-downs (Fig. 6A); BiFC (Fig. 7); and co-IP (Fig. 6D). STIC2 vs. ALB3 (At2g28800) This interaction was supported by: in vitro pull-downs (Fig. 6C); BiFC (Fig. 7); and co-IP (Fig. 6D). A third, weaker interaction was also observed: STIC1(ALB4) vs. ALB3 This interaction was supported by co-IP only (Fig. 6D). (This interaction is also shown in second paper below; pubmed/26265777). paul.jarvis@plants.ox.ac.uk 09-May-2019: Contacted by IntAct-Help. Only protein-protein interactions imex curation arath-seedling Arabidopsis thaliana seedling density sedimentation cosedimentation through density gradient density sedimentation western blot western blot Immuno blot Immuno blot Bédard J., Trösch R., Wu F., Ling Q., Flores-Pérez Ú., Töpel M., Nawaz F., Jarvis P. not available-free- until July next year;please ask me for PDF of the publication + suppllement. STIC2:-They state to have used "For protein alignments" NP_001189586 - which corresponds to isoform 2 - but in fig 6A they use a construct of 182 aas length which is isoform1 - so no isoform info added. paul.jarvis@plants.ox.ac.uk Accepted 2018-JUN-20 AT 12:35 BST AT 12:35 BST by PPORRAS The Plant cell 2017 Only protein-protein interactions imex curation imex curation altered Suppressors of the Chloroplast Protein Import Mutant tic40 Reveal a Genetic Link between Protein Import and Thylakoid Biogenesis. Suppressors of the Chloroplast Protein Import Mutant tic40 Reveal a Genetic Link between Protein Import and Thylakoid Biogenesis. The Plant cell 2017 imex curation Bédard J., Trösch R., Wu F., Ling Q., Flores-Pérez Ú., Töpel M., Nawaz F., Jarvis P. not available-free- until July next year;please ask me for PDF of the publication + suppllement. STIC2:-They state to have used "For protein alignments" NP_001189586 - which corresponds to isoform 2 - but in fig 6A they use a construct of 182 aas length which is isoform1 - so no isoform info added. request via Pablo. see pmids: 26265777 and 28684427 "In each case, I supply the Arabidopsis gene identifier on first appearance. " There are two main protein-protein interactions, which are as follows: STIC2 (At2g24020) vs. STIC1(ALB4) (At1g24490) This interaction was supported by: in vitro pull-downs (Fig. 6A); BiFC (Fig. 7); and co-IP (Fig. 6D). STIC2 vs. ALB3 (At2g28800) This interaction was supported by: in vitro pull-downs (Fig. 6C); BiFC (Fig. 7); and co-IP (Fig. 6D). A third, weaker interaction was also observed: STIC1(ALB4) vs. ALB3 This interaction was supported by co-IP only (Fig. 6D). (This interaction is also shown in second paper below; pubmed/26265777). paul.jarvis@plants.ox.ac.uk 09-May-2019: Contacted by IntAct-Help. Only protein-protein interactions imex curation arath-seedling Arabidopsis thaliana seedling crosslink cross-linking study crosslink western blot western blot Immuno blot Immuno blot Bédard J., Trösch R., Wu F., Ling Q., Flores-Pérez Ú., Töpel M., Nawaz F., Jarvis P. not available-free- until July next year;please ask me for PDF of the publication + suppllement. STIC2:-They state to have used "For protein alignments" NP_001189586 - which corresponds to isoform 2 - but in fig 6A they use a construct of 182 aas length which is isoform1 - so no isoform info added. Cross-linker dithiobis succinimidyl propionate (DSP) was used followed by anti-flag IP. paul.jarvis@plants.ox.ac.uk Accepted 2018-JUN-20 AT 12:35 BST AT 12:35 BST by PPORRAS The Plant cell 2017 Only protein-protein interactions imex curation imex curation altered Suppressors of the Chloroplast Protein Import Mutant tic40 Reveal a Genetic Link between Protein Import and Thylakoid Biogenesis. Suppressors of the Chloroplast Protein Import Mutant tic40 Reveal a Genetic Link between Protein Import and Thylakoid Biogenesis. The Plant cell 2017 imex curation Bédard J., Trösch R., Wu F., Ling Q., Flores-Pérez Ú., Töpel M., Nawaz F., Jarvis P. not available-free- until July next year;please ask me for PDF of the publication + suppllement. STIC2:-They state to have used "For protein alignments" NP_001189586 - which corresponds to isoform 2 - but in fig 6A they use a construct of 182 aas length which is isoform1 - so no isoform info added. request via Pablo. see pmids: 26265777 and 28684427 "In each case, I supply the Arabidopsis gene identifier on first appearance. " There are two main protein-protein interactions, which are as follows: STIC2 (At2g24020) vs. STIC1(ALB4) (At1g24490) This interaction was supported by: in vitro pull-downs (Fig. 6A); BiFC (Fig. 7); and co-IP (Fig. 6D). STIC2 vs. ALB3 (At2g28800) This interaction was supported by: in vitro pull-downs (Fig. 6C); BiFC (Fig. 7); and co-IP (Fig. 6D). A third, weaker interaction was also observed: STIC1(ALB4) vs. ALB3 This interaction was supported by co-IP only (Fig. 6D). (This interaction is also shown in second paper below; pubmed/26265777). paul.jarvis@plants.ox.ac.uk 09-May-2019: Contacted by IntAct-Help. Only protein-protein interactions imex curation in vitro In vitro pull down pull down weight by comassie molecular weight estimation by coomasie staining weight by comassie Bédard J., Trösch R., Wu F., Ling Q., Flores-Pérez Ú., Töpel M., Nawaz F., Jarvis P. not available-free- until July next year;please ask me for PDF of the publication + suppllement. STIC2:-They state to have used "For protein alignments" NP_001189586 - which corresponds to isoform 2 - but in fig 6A they use a construct of 182 aas length which is isoform1 - so no isoform info added. paul.jarvis@plants.ox.ac.uk Accepted 2018-JUN-20 AT 12:35 BST AT 12:35 BST by PPORRAS The Plant cell 2017 Only protein-protein interactions imex curation imex curation altered Suppressors of the Chloroplast Protein Import Mutant tic40 Reveal a Genetic Link between Protein Import and Thylakoid Biogenesis. Suppressors of the Chloroplast Protein Import Mutant tic40 Reveal a Genetic Link between Protein Import and Thylakoid Biogenesis. The Plant cell 2017 imex curation Bédard J., Trösch R., Wu F., Ling Q., Flores-Pérez Ú., Töpel M., Nawaz F., Jarvis P. not available-free- until July next year;please ask me for PDF of the publication + suppllement. STIC2:-They state to have used "For protein alignments" NP_001189586 - which corresponds to isoform 2 - but in fig 6A they use a construct of 182 aas length which is isoform1 - so no isoform info added. request via Pablo. see pmids: 26265777 and 28684427 "In each case, I supply the Arabidopsis gene identifier on first appearance. " There are two main protein-protein interactions, which are as follows: STIC2 (At2g24020) vs. STIC1(ALB4) (At1g24490) This interaction was supported by: in vitro pull-downs (Fig. 6A); BiFC (Fig. 7); and co-IP (Fig. 6D). STIC2 vs. ALB3 (At2g28800) This interaction was supported by: in vitro pull-downs (Fig. 6C); BiFC (Fig. 7); and co-IP (Fig. 6D). A third, weaker interaction was also observed: STIC1(ALB4) vs. ALB3 This interaction was supported by co-IP only (Fig. 6D). (This interaction is also shown in second paper below; pubmed/26265777). paul.jarvis@plants.ox.ac.uk 09-May-2019: Contacted by IntAct-Help. Only protein-protein interactions imex curation arath-protoplast Arabidopsis thaliana protoplast Protoplast defined as a membrane-bound cell from which the outer wall has been partially or completely removed. bifc bimolecular fluorescence complementation bifc tag fluorescence tag visualisation by fluorescence tag fluorescence Bédard J., Trösch R., Wu F., Ling Q., Flores-Pérez Ú., Töpel M., Nawaz F., Jarvis P. Vectors pSAT4(A)-nEYFP-N1 and pSAT4(A)-cEYFP-N1: EYGP fragments were deduced to be fused to the C terminus of any protein. (Tzfira et al., 2005) pmid:15821977 not available-free- until July next year;please ask me for PDF of the publication + suppllement. STIC2:-They state to have used "For protein alignments" NP_001189586 - which corresponds to isoform 2 - but in fig 6A they use a construct of 182 aas length which is isoform1 - so no isoform info added. paul.jarvis@plants.ox.ac.uk Accepted 2018-JUN-20 AT 12:35 BST AT 12:35 BST by PPORRAS The Plant cell 2017 Only protein-protein interactions imex curation imex curation altered alb4_arath ALBINO3-like protein 1, chloroplastic ALB4 ALB ALB3L1 ART1 Arabidopsis thaliana envelope membrane integrase Protein ALBINA 4 Protein ARTEMIS STIC1 Suppressor of tic40 protein 1 F21J9.16 F21J9_170 At1g24490 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MSSTISLKPTHLILSSFSTGKVLQFRRSRFSHTPSSSSSRYRTLVAQLGFRPDSFDFIKDHAENLLYTIADAAVSSSETFESVAGTTTKTTQSNDWFSGIANYMETILKVLKDGLSTVHVPYSYGFAIILLTVLVKAATFPLTKKQVESAMAMKSLTPQIKAIQERYAGDQEKIQLETARLYKLAGINPLAGCLPTLATIPVWIGLYRALSNVADEGLLTEGFFWIPSLAGPTTVAARQNGSGISWLFPFIEGHPPLGWPDTLAYLVLPLLLVFSQYLSIQIMQSSQSNDPAMKSSQAVTKLLPLMIGYFALSVPSGLSLYWLTNNILSTAQQVWLQKYGGAKNPVEKFTNLVTKEDKTQQIEKSFSEPLVQKSVSELKIPREKGGEKVTPECPKPGERFRLLKEQEAKRRREKEERQKAEAALSNQNTDKAHEQDEKSDTAIVAEDDKKTELSAVDETSDGTVAVNGKPSIQKDETTNGTFGIGHDTEQQHSHETEKR 4AC2A1EE3524FB70 alb3_arath Inner membrane protein ALBINO3, chloroplastic ALB3 F8N16.9 At2g28800 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MARVLVSSPSSFFGSPLIKPSSSLRHSGVGGGGTAQFLPYRSNNNKLFTTSTTVRFSLNEIPPFHGLDSSVDIGAIFTRAESLLYTIADAAVVGADSVVTTDSSAVQKSGGWFGFISDAMELVLKILKDGLSAVHVPYAYGFAIILLTIIVKAATYPLTKQQVESTLAMQNLQPKIKAIQQRYAGNQERIQLETSRLYKQAGVNPLAGCLPTLATIPVWIGLYQALSNVANEGLFTEGFFWIPSLGGPTSIAARQSGSGISWLFPFVDGHPPLGWYDTVAYLVLPVLLIASQYVSMEIMKPPQTDDPAQKNTLLVFKFLPLMIGYFALSVPSGLSIYWLTNNVLSTAQQVYLRKLGGAKPNMDENASKIISAGRAKRSIAQPDDAGERFRQLKEQEKRSKKNKAVAKDTVELVEESQSESEEGSDDEEEEAREGALASSTTSKPLPEVGQRRSKRSKRKRTV 2BBF7AF5BA2E6DDE psad1_arath Photosystem I reaction center subunit II-1, chloroplastic psaD1 Photosystem I 20 kDa subunit 1 T5J8.7 At4g02770 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MATQAAGIFNSAITTAATSGVKKLHFFSTTHRPKSLSFTKTAIRAEKTDSSAAAAAAPATKEAPVGFTPPQLDPNTPSPIFAGSTGGLLRKAQVEEFYVITWNSPKEQIFEMPTGGAAIMREGPNLLKLARKEQCLALGTRLRSKYKITYQFYRVFPNGEVQYLHPKDGVYPEKANPGREGVGLNMRSIGKNVSPIEVKFTGKQSYDL 92F1667DDE0CB713 ti110_arath Protein TIC110, chloroplastic TIC110 Translocon at the inner envelope membrane of chloroplasts 110 F4H5.1 F10K1.33 At1g06950 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MNPSLVTAINAPISPSPRSPLLSHFLPTLPHRFSKSECLSRRRYRVSFPRSSAASSDQLSVSTQAKNPGIHGNKKELTGLQPIVEKMTPPVRLATSAVVLAASLATGYGLGLRLAGSRNIAFGGAAVAGAAGGAVVYALNSAVPEVAAISLHNYVAEFEDPASVTKDDVEKIADRYGVNKGDEAFQAEICDIYCRYVTSVLPTEGQSLKGDEVAKIVKFKNALGIDEPDAAAMHMEIGRRIFRQRLETGEREGDAEQRRAFMRLVYVSALVFGDASSFLLPWKRVLKVTDAQVEIAIRENAKQLYAERLKLVGRDINVENLVDLRKSQLSFKLSDELAEDLFREHTRKVVVENISSALSILKSRTRAAKSLASVVEELEKVLEFNNLLVSLKSHSEADQFARGVGPISLIGDESDFERRMDDLKLLYRAYVTDALSGGRLEENKLVAMSQLRNILGLGKREAEAISVDVTSKSYRKRLANAVSSGDLEAQDSKAKYLQKLCEELHFDAQKAGAIHEEIYRQKLQQCVTDGELSDDNVAALLRLRVMLCIPQQTVDTAHAEICGTIFEKVVRDAISSGVDGYDAETRKSVRKAAHGLRLSRETAMSIASKAVRRVFTNYIRRARAAENRTDSAKELKKMIAFNTLVVTEMVADIKGESSDKAPEEDPVQEKEEDDEDEEWGSLESLRKTRPDKELAEKMGKPGQTEITLKDDLPDRDRIDLYKTYLLYCVTGEVTRIPFGAQITTKRDDSEYLLLNQLGGILGLSSKEIVNIHVGLAEQAFRQQAEVILADGQLTKARVEQLDELQKQVGLPQPQAEKVIKNITTTKMANAIETAVNQGRLNIKQIRELKEANVSLDSMIAVSLREKLFKKTVSDIFSSGTGEFDETEVYQTIPSDLSIDVEKAKRVVHDLAQSRLSNSLVQAVALLRQRNSKGVVLSLNDLLACDKAVPAEPMSWEVSEELSDLYAIYSKSDPKPAPEKVLRLQYLLGIDDSTATALREMEDGALSSAAEEGNFVF 814CCDE07EB5D0EA ebfc2_arath Nucleoid-associated protein At2g24020, chloroplastic STIC2 Suppressor of tic40 protein 2 T29E15.22 At2g24020 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MASMAATTNFTKSMLFPFSHVSGNASLNSQRRTWPKQYKSKNGYRSLRVNGLFGGGNKDNNSEDGQSKAGIFGNMQNMYETVKKAQMVVQVEAVRVQKELAAAEFDGYCAGELVKVTLSGNQQPIRTDITEAAMELGSEKLSQLVTEAYKDAHAKSVVAMKERMSDLAQSLGMPPGLSEGMK 6AB58B1BB171211D 090u90-1 1 5 unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed c_terminus 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 6 unspecified role unspecified role neutral component neutral component physiological level physiological level endogenous level endogenous endogenous endogenous level 8 unspecified role unspecified role neutral component neutral component physiological level physiological level endogenous level endogenous endogenous endogenous level colocalization colocalization 3B LHCP (lightharvesting chlorophyll binding protein) was also detected, but the exact protein(s) could not be identified. alb3-alb3l1-1 1 6 unspecified role unspecified role neutral component neutral component physiological level physiological level endogenous level endogenous endogenous endogenous level 8 unspecified role unspecified role neutral component neutral component physiological level physiological level endogenous level endogenous endogenous endogenous level colocalization colocalization 3C LHCP (lightharvesting chlorophyll binding protein) was also detected, but the exact protein(s) could not be identified. STIC2 -Flag colocalised with the small subunit of Rubisco (SSU) in the choroloplast stroma, but the exact protein (SSU) could not be identified. (SSU; 25245-1 3 5 unspecified role unspecified role bait bait over-expressed over expressed level over-expressed cell lysate cell lysate region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain Q9FYL3:p.Gly397Ser mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain G S Wed May 02 20:08:05 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'gly397ser' Tue Jun 30 20:06:35 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Gly397Ser' 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 ecoli Escherichia coli (strain K12) 9 unspecified role unspecified role prey prey over-expressed over expressed level over-expressed cell lysate cell lysate 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 region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain ecoli Escherichia coli (strain K12) physical association physical association 6A STIC2 interacts specifically with the C terminus of STIC1/ALB4 and indicate that the Gly-397 residue is important for this interaction alb3l1-ebfc2_arath-1 3 6 unspecified role unspecified role bait bait over-expressed over expressed level over-expressed cell lysate cell lysate region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain 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 ecoli Escherichia coli (strain K12) 9 unspecified role unspecified role prey prey over-expressed over expressed level over-expressed cell lysate cell lysate 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 region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain ecoli Escherichia coli (strain K12) physical association physical association 6C STIC2 interacts not only with STIC1/ALB4 but also with ALB3 alb3-alb3l1-2 2 5 unspecified role unspecified role bait bait over-expressed over expressed level over-expressed c_terminus 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 6 unspecified role unspecified role prey prey physiological level physiological level endogenous level endogenous endogenous endogenous level 9 unspecified role unspecified role prey prey physiological level physiological level endogenous level endogenous endogenous endogenous level physical association physical association 3D-LHS alb3-alb3l1-3 2 5 unspecified role unspecified role prey prey over-expressed over expressed level over-expressed 6 unspecified role unspecified role prey prey physiological level physiological level endogenous level endogenous endogenous endogenous level 9 unspecified role unspecified role bait bait physiological level physiological level endogenous level endogenous endogenous endogenous level c_terminus 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 physical association physical association 3D-RHS rudru-1 4 7 unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed living cell living cell c_terminus nyfp nYFP c-term range C-terminal range c-term range c-term range C-terminal range c-term range 7 unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed living cell living cell c_terminus cyfp cYFP c-term range C-terminal range c-term range c-term range C-terminal range c-term range physical association physical association 7 positive control. The sequence of protein PSI-D was shown to correspond to UniProt enty Q9S7H1 (At4g02770) by Blast of primers given in Trösch et al.-2015. psad1-psad1-1 4 9 unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed living cell living cell c_terminus nyfp nYFP c-term range C-terminal range c-term range c-term range C-terminal range c-term range 5 unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed living cell living cell c_terminus cyfp cYFP c-term range C-terminal range c-term range c-term range C-terminal range c-term range Q9FYL3:p.Gly397Ser mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction certain certain sequence position certain certain certain sequence position certain G S Wed May 02 14:40:01 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'gly397ser' Tue Jun 30 19:25:26 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Gly397Ser' physical association physical association 7-1 alb3l1-ebfc2_arath-2 4 9 unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed living cell living cell c_terminus nyfp nYFP c-term range C-terminal range c-term range c-term range C-terminal range c-term range 6 unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed living cell living cell c_terminus cyfp cYFP c-term range C-terminal range c-term range c-term range C-terminal range c-term range physical association physical association 7-2 alb3-ebfc2_arath-1 4 6 unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed living cell living cell c_terminus nyfp nYFP c-term range C-terminal range c-term range c-term range C-terminal range c-term range 9 unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed living cell living cell c_terminus cyfp cYFP c-term range C-terminal range c-term range c-term range C-terminal range c-term range physical association physical association 7-2i