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/ Structural specializations of α(4)β(7), an integrin that mediates rolling adhesion. Structural specializations of α(4)β(7), an integrin that mediates rolling adhesion. The Journal of cell biology 2012 imex curation Yu Y., Zhu J., Mi LZ., Walz T., Sun H., Chen J., Springer TA. IBD - Inflammatory bowel disease Crohn's disease - Interactions of proteins identified as having a link to Crohn's disease springer@idi.harvard.edu 22-Feb-2016: Contacted by IntAct-Help. Only protein-protein interactions in vitro In vitro electron microscopy electron microscopy Electron crystallography Electron cryomicroscopy Electron crystallography Electron cryomicroscopy predetermined predetermined participant predetermined Yu Y., Zhu J., Mi LZ., Walz T., Sun H., Chen J., Springer TA. IBD - Inflammatory bowel disease Crohn's disease - Interactions of proteins identified as having a link to Crohn's disease Hi Sandra, did you mean to create separate EM experiments? or create new interactions within the same EM experiment? I did the latter. Ectodomain and headpiece sequence boundaries are not described in the paper, the schematic figure of the integrin domains do not correspond with the ones described in Uniprot. I made some fuzzy sequence locations for the Beta7 headpiece (50..50-605..605), and for the ectodomain I used 20-512. It is not clear to me if for the mutated R558A alpha 4 integrin I need to also make a feature for the sequence (34-620)used in the crystallography. As soon as the above is clarified I should get this done pretty fast. EM data with humanized Act-1 antibody, vedolizumab, was not curated because its sequence is not available nor an identifier. springer@idi.harvard.edu Accepted 2016-JAN-22 AT 09:40 GMT AT 09:40 GMT by ORCHARD The Journal of cell biology 2012 imex curation Structural specializations of α(4)β(7), an integrin that mediates rolling adhesion. Structural specializations of α(4)β(7), an integrin that mediates rolling adhesion. The Journal of cell biology 2012 imex curation Yu Y., Zhu J., Mi LZ., Walz T., Sun H., Chen J., Springer TA. IBD - Inflammatory bowel disease Crohn's disease - Interactions of proteins identified as having a link to Crohn's disease springer@idi.harvard.edu 22-Feb-2016: Contacted by IntAct-Help. Only protein-protein interactions in vitro In vitro x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Yu Y., Zhu J., Mi LZ., Walz T., Sun H., Chen J., Springer TA. IBD - Inflammatory bowel disease Crohn's disease - Interactions of proteins identified as having a link to Crohn's disease springer@idi.harvard.edu Accepted 2016-JAN-22 AT 09:40 GMT AT 09:40 GMT by ORCHARD The Journal of cell biology 2012 imex curation itb7_human Integrin beta-7 Gut homing receptor beta subunit ITGB7 protein protein human Homo sapiens Human MVALPMVLVLLLVLSRGESELDAKIPSTGDATEWRNPHLSMLGSCQPAPSCQKCILSHPSCAWCKQLNFTASGEAEARRCARREELLARGCPLEELEEPRGQQEVLQDQPLSQGARGEGATQLAPQRVRVTLRPGEPQQLQVRFLRAEGYPVDLYYLMDLSYSMKDDLERVRQLGHALLVRLQEVTHSVRIGFGSFVDKTVLPFVSTVPSKLRHPCPTRLERCQSPFSFHHVLSLTGDAQAFEREVGRQSVSGNLDSPEGGFDAILQAALCQEQIGWRNVSRLLVFTSDDTFHTAGDGKLGGIFMPSDGHCHLDSNGLYSRSTEFDYPSVGQVAQALSAANIQPIFAVTSAALPVYQELSKLIPKSAVGELSEDSSNVVQLIMDAYNSLSSTVTLEHSSLPPGVHISYESQCEGPEKREGKAEDRGQCNHVRINQTVTFWVSLQATHCLPEPHLLRLRALGFSEELIVELHTLCDCNCSDTQPQAPHCSDGQGHLQCGVCSCAPGRLGRLCECSVAELSSPDLESGCRAPNGTGPLCSGKGHCQCGRCSCSGQSSGHLCECDDASCERHEGILCGGFGRCQCGVCHCHANRTGRACECSGDMDSCISPEGGLCSGHGRCKCNRCQCLDGYYGALCDQCPGCKTPCERHRDCAECGAFRTGPLATNCSTACAHTNVTLALAPILDDGWCKERTLDNQLFFFLVEDDARGTVVLRVRPQEKGADHTQAIVLGCVGGIVAVGLGLVLAYRLSVEIYDRREYSRFEKEQQQLNWKQDSNPLYKSAITTTINPRFQEADSPTL CBE275E0E9992385 ita4_human Integrin alpha-4 Integrin alpha-IV VLA-4 subunit alpha CD49 antigen-like family member D ITGA4 CD49D protein protein human Homo sapiens Human MAWEARREPGPRRAAVRETVMLLLCLGVPTGRPYNVDTESALLYQGPHNTLFGYSVVLHSHGANRWLLVGAPTANWLANASVINPGAIYRCRIGKNPGQTCEQLQLGSPNGEPCGKTCLEERDNQWLGVTLSRQPGENGSIVTCGHRWKNIFYIKNENKLPTGGCYGVPPDLRTELSKRIAPCYQDYVKKFGENFASCQAGISSFYTKDLIVMGAPGSSYWTGSLFVYNITTNKYKAFLDKQNQVKFGSYLGYSVGAGHFRSQHTTEVVGGAPQHEQIGKAYIFSIDEKELNILHEMKGKKLGSYFGASVCAVDLNADGFSDLLVGAPMQSTIREEGRVFVYINSGSGAVMNAMETNLVGSDKYAARFGESIVNLGDIDNDGFEDVAIGAPQEDDLQGAIYIYNGRADGISSTFSQRIEGLQISKSLSMFGQSISGQIDADNNGYVDVAVGAFRSDSAVLLRTRPVVIVDASLSHPESVNRTKFDCVENGWPSVCIDLTLCFSYKGKEVPGYIVLFYNMSLDVNRKAESPPRFYFSSNGTSDVITGSIQVSSREANCRTHQAFMRKDVRDILTPIQIEAAYHLGPHVISKRSTEEFPPLQPILQQKKEKDIMKKTINFARFCAHENCSADLQVSAKIGFLKPHENKTYLAVGSMKTLMLNVSLFNAGDDAYETTLHVKLPVGLYFIKILELEEKQINCEVTDNSGVVQLDCSIGYIYVDHLSRIDISFLLDVSSLSRAEEDLSITVHATCENEEEMDNLKHSRVTVAIPLKYEVKLTVHGFVNPTSFVYGSNDENEPETCMVEKMNLTFHVINTGNSMAPNVSVEIMVPNSFSPQTDKLFNILDVQTTTGECHFENYQRVCALEQQKSAMQTLKGIVRFLSKTDKRLLYCIKADPHCLNFLCNFGKMESGKEASVHIQLEGRPSILEMDETSALKFEIRATGFPEPNPRVIELNKDENVAHVLLEGLHHQRPKRYFTIVIISSSLLLGLIVLLLISYVMWKAGFFKRQYKSILQEENRRDSWSYINSKSNDD DIP protein P13612 original sequence version: 131 DIP protein P13612-1 original sequence version: 171 DIP protein P13612 original sequence version: 138 73EC1204DE78CD35 calcium(2+) small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) madca_human Mucosal addressin cell adhesion molecule 1 MADCAM1 protein protein human Homo sapiens Human MDFGLALLLAGLLGLLLGQSLQVKPLQVEPPEPVVAVALGASRQLTCRLACADRGASVQWRGLDTSLGAVQSDTGRSVLTVRNASLSAAGTRVCVGSCGGRTFQHTVQLLVYAFPDQLTVSPAALVPGDPEVACTAHKVTPVDPNALSFSLLVGGQELEGAQALGPEVQEEEEEPQGDEDVLFRVTERWRLPPLGTPVPPALYCQATMRLPGLELSHRQAIPVLHSPTSPEPPDTTSPESPDTTSPESPDTTSQEPPDTTSPEPPDKTSPEPAPQQGSTHTPRSPGSTRTRRPEISQAGPTQGEVIPTGSSKPAGDQLPAALWTSSAVLGLLLLALPTYHLWKRCRHLAEDDTHPPASLRLLPQVSAWAGLRGTGQVGISPS 9DCA60C30BA61E62 n-(2,6-dichlorobenzoyl)-4-[1,6-dimethyl-2-oxo-4-(trifluoromethyl)-1,2-dihydropyridin-3-yl]-l-phenylalanine N-(2,6-dichlorobenzoyl)-4-[1,6-dimethyl-2-oxo-4-(trifluoromethyl)-1,2-dihydropyridin-3-yl]-L-phenylalanine 0DU RO0505376 small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) manganese(2+) Manganese (2+) small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) magnesium(2+) Magnesium(2+) small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) itga4-itgb7-5 2 3 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain region his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined crigr-cho chinese hamster ovary cell line cho chinese hamster ovary cell line Also called LR73 cells. 4 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain P13612:p.Arg558Ala mutation mutation certain certain sequence position certain certain certain sequence position certain R A Wed May 02 15:42:57 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'arg558ala' Tue Jun 30 18:23:10 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Arg558Ala' crigr-cho chinese hamster ovary cell line cho chinese hamster ovary cell line Also called LR73 cells. 15 12 direct interaction direct interaction Table 1 3.15 A R_work 22%, R_free25.1% Two antibody fragments were also present in the crystal but could not be mapped to a protein product. itga4-3 1 4 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain crigr-cho chinese hamster ovary cell line cho chinese hamster ovary cell line Also called LR73 cells. 3 unspecified role unspecified role neutral component neutral component region his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain crigr-cho chinese hamster ovary cell line cho chinese hamster ovary cell line Also called LR73 cells. 9 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) 5 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) 19 22 direct interaction direct interaction Fig. 7A, S4A itga4-itgb7-1 2 3 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain region his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined crigr-cho chinese hamster ovary cell line cho chinese hamster ovary cell line Also called LR73 cells. 4 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain P13612:p.Arg558Ala mutation mutation certain certain sequence position certain certain certain sequence position certain R A Wed May 02 17:42:28 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'arg558ala' Tue Jun 30 15:43:03 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Arg558Ala' crigr-cho chinese hamster ovary cell line cho chinese hamster ovary cell line Also called LR73 cells. 7 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) 27 30 direct interaction direct interaction Table 1 3.1 A R_work 20%, R_free23.1% Two antibody fragments were also present in the crystal but could not be mapped to a protein product. itga4-4 1 9 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) 5 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) 6 unspecified role unspecified role neutral component neutral component crigr-cho chinese hamster ovary cell line cho chinese hamster ovary cell line Also called LR73 cells. 4 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain crigr-cho chinese hamster ovary cell line cho chinese hamster ovary cell line Also called LR73 cells. 3 unspecified role unspecified role neutral component neutral component region his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined region sufficient to bind sufficient binding region sufficient to bind range range range range crigr-cho chinese hamster ovary cell line cho chinese hamster ovary cell line Also called LR73 cells. 41 38 direct interaction direct interaction Fig. 7F, Fig. S4F itga4-itgb7-3 1 5 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) 9 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) 4 unspecified role unspecified role neutral component neutral component P13612:p.Arg558Ala mutation mutation certain certain sequence position certain certain certain sequence position certain R A Wed May 02 15:00:46 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'arg558ala' Tue Jun 30 19:58:48 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Arg558Ala' crigr-cho chinese hamster ovary cell line cho chinese hamster ovary cell line Also called LR73 cells. 3 unspecified role unspecified role neutral component neutral component region his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain crigr-cho chinese hamster ovary cell line cho chinese hamster ovary cell line Also called LR73 cells. 49 46 direct interaction direct interaction Fig. 7B, Fig S4B, Fig. S4L Fig.7B and Fig. S4B interactions with Natalizumab (CHEMBL1201607). Fig. S4L interaction with Act-1 Fab, this interactor does not have a sequence identifier. itga4-itgb7-4 1 9 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) 5 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) 4 unspecified role unspecified role neutral component neutral component P13612:p.Arg558Ala mutation mutation certain certain sequence position certain certain certain sequence position certain R A Wed May 02 17:48:47 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'arg558ala' Tue Jun 30 18:32:17 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Arg558Ala' crigr-cho chinese hamster ovary cell line cho chinese hamster ovary cell line Also called LR73 cells. 3 unspecified role unspecified role neutral component neutral component region headpiece sufficient to bind sufficient binding region sufficient to bind range range range range region his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined crigr-cho chinese hamster ovary cell line cho chinese hamster ovary cell line Also called LR73 cells. direct interaction direct interaction Fig. 7C, Fig. 7D, Fig. S4C, Fig.S4D Fig. 7C Interaction with Natalizumab (CHEMBL1201607) Fig. 7D interaction with Act-1 Fab, however, there is no available sequence identifier for Act-1 interactor. itga4-itgb7-6 1 5 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) 9 unspecified role unspecified role neutral component neutral component crigr-cho chinese hamster ovary cell line cho chinese hamster ovary cell line Also called LR73 cells. 7 unspecified role unspecified role neutral component neutral component crigr-cho chinese hamster ovary cell line cho chinese hamster ovary cell line Also called LR73 cells. 4 unspecified role unspecified role neutral component neutral component P13612:p.Arg558Ala mutation mutation certain certain sequence position certain certain certain sequence position certain R A Wed May 02 19:22:30 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'arg558ala' Tue Jun 30 20:09:47 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Arg558Ala' crigr-cho chinese hamster ovary cell line cho chinese hamster ovary cell line Also called LR73 cells. 3 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind range range range range region his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined crigr-cho chinese hamster ovary cell line cho chinese hamster ovary cell line Also called LR73 cells. direct interaction direct interaction Fig. 7E, Fig. S4E This interaction was done with Act-1 Fab. calcium(2+)-itga4-4 1 8 unspecified role unspecified role unspecified role unspecified role chemical synthesis Chemical synthesis (Chemical synthesis) 6 unspecified role unspecified role neutral component neutral component 4 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain crigr-cho chinese hamster ovary cell line cho chinese hamster ovary cell line Also called LR73 cells. 3 unspecified role unspecified role neutral component neutral component region his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined region sufficient to bind sufficient binding region sufficient to bind range range range range crigr-cho chinese hamster ovary cell line cho chinese hamster ovary cell line Also called LR73 cells. 71 74 direct interaction direct interaction Fig. 7G, Fig S4G calcium(2+)-itga4-3 1 5 unspecified role unspecified role unspecified role unspecified role 9 unspecified role unspecified role unspecified role unspecified role 7 unspecified role unspecified role unspecified role unspecified role 4 unspecified role unspecified role neutral component neutral component P13612:p.Arg558Ala mutation mutation certain certain sequence position certain certain certain sequence position certain R A Wed May 02 17:21:05 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'arg558ala' Tue Jun 30 17:23:17 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Arg558Ala' 3 unspecified role unspecified role neutral component neutral component region headpiece sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain region his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined direct interaction direct interaction Fig. S4I