matrixdb Institut de Biologie et de Chimie des Prot\u00c3\u00a9ines, 7, passage du Vercors 69 367 Lyon cedex 07 FRANCE matrixdb@ibcp.fr http://matrixdb.ibcp.fr Institut de Biologie et de Chimie des Prot\u00c3\u00a9ines, 7, passage du Vercors 69 367 Lyon cedex 07 FRANCE http://matrixdb.ibcp.fr weiss-2014-1 in vitro In vitro anti bait coip anti bait coimmunoprecipitation anti bait coip anti tag western anti tag western blot anti tag western Weiss T., Brusel M., Rousselle P., Kessler E. ekessler@post.tau.ac.il The international journal of biochemistry & cell biology 2014 imex curation weiss-2014-3 in vitro In vitro solid phase assay solid phase assay antibody detection identification by antibody antibody detection Weiss T., Brusel M., Rousselle P., Kessler E. ekessler@post.tau.ac.il The international journal of biochemistry & cell biology 2014 imex curation weiss-2014-2 in vitro In vitro anti bait coip anti bait coimmunoprecipitation anti bait coip polyclonal western polyclonal antibody western blot polyclonal western Weiss T., Brusel M., Rousselle P., Kessler E. ekessler@post.tau.ac.il The international journal of biochemistry & cell biology 2014 imex curation sdc1_mouse Syndecan-1 Sdc1 Synd-1 Synd1 protein protein mouse Mus musculus Mouse MRRAALWLWLCALALRLQPALPQIVAVNVPPEDQDGSGDDSDNFSGSGTGALPDTLSRQTPSTWKDVWLLTATPTAPEPTSSNTETAFTSVLPAGEKPEEGEPVLHVEAEPGFTARDKEKEVTTRPRETVQLPITQRASTVRVTTAQAAVTSHPHGGMQPGLHETSAPTAPGQPDHQPPRVEGGGTSVIKEVVEDGTANQLPAGEGSGEQDFTFETSGENTAVAAVEPGLRNQPPVDEGATGASQSLLDRKEVLGGVIAGGLVGLIFAVCLVAFMLYRMKKKDEGSYSLEEPKQANGGAYQKPTKQEEFYA pcoc1_human Procollagen C-endopeptidase enhancer 1 PCOLCE PCPE1 Procollagen COOH-terminal proteinase enhancer 1 Type 1 procollagen C-proteinase enhancer protein Type I procollagen COOH-terminal proteinase enhancer protein protein human Homo sapiens Human MLPAATASLLGPLLTACALLPFAQGQTPNYTRPVFLCGGDVKGESGYVASEGFPNLYPPNKECIWTITVPEGQTVSLSFRVFDLELHPACRYDALEVFAGSGTSGQRLGRFCGTFRPAPLVAPGNQVTLRMTTDEGTGGRGFLLWYSGRATSGTEHQFCGGRLEKAQGTLTTPNWPESDYPPGISCSWHIIAPPDQVIALTFEKFDLEPDTYCRYDSVSVFNGAVSDDSRRLGKFCGDAVPGSISSEGNELLVQFVSDLSVTADGFSASYKTLPRGTAKEGQGPGPKRGTEPKVKLPPKSQPPEKTEESPSAPDAPTCPKQCRRTGTLQSNFCASSLVVTATVKSMVREPGEGLAVTVSLIGAYKTGGLDLPSPPTGASLKFYVPCKQCPPMKKGVSYLLMGQVEENRGPVLPPESFVVLHRPNQDQILTNLSKRKCPSQPVRAAASQD sdc2_mouse Syndecan-2 Fibroglycan Heparan sulfate proteoglycan core protein Sdc2 Hspg1 Synd2 protein protein mouse Mus musculus Mouse MQRAWILLTLGLMACVSAETRTELTSDKDMYLDNSSIEEASGVYPIDDDDYSSASGSGADEDIESPVLTTSQLIPRIPLTSAASPKVETMTLKTQSITPAQTESPEETDKEEVDISEAEEKLGPAIKSTDVYTEKHSDNLFKRTEVLAAVIAGGVIGFLFAIFLILLLVYRMRKKDEGSYDLGERKPSSAAYQKAPTKEFYA sdc4_mouse Syndecan-4 Sdc4 Ryudocan core protein protein protein mouse Mus musculus Mouse MAPACLLAPLLLLLLGGFPLVPGESIRETEVIDPQDLLEGRYFSGALPDDEDAGGSDDFELSGSGDLDDTEEPRPFPEVIEPLVPLDNHIPENAQPGIRVPSEPKELEENEVIPKRAPSDVGDDMSNKVSMSSTAQGSNIFERTEVLAALIVGGVVGILFAVFLILLLVYRMKKKDEGSYDLGKKPIYKKAPTNEFYA sdc1_human Syndecan-1 SDC1 SDC protein protein human Homo sapiens Human MRRAALWLWLCALALSLQPALPQIVATNLPPEDQDGSGDDSDNFSGSGAGALQDITLSQQTPSTWKDTQLLTAIPTSPEPTGLEATAASTSTLPAGEGPKEGEAVVLPEVEPGLTAREQEATPRPRETTQLPTTHLASTTTATTAQEPATSHPHRDMQPGHHETSTPAGPSQADLHTPHTEDGGPSATERAAEDGASSQLPAAEGSGEQDFTFETSGENTAVVAVEPDRRNQSPVDQGATGASQGLLDRKEVLGGVIAGGLVGLIFAVCLVGFMLYRMKKKDEGSYSLEEPKQANGGAYQKPTKQEEFYA lama3_human Laminin subunit alpha-3 Epiligrin 170 kDa subunit Nicein subunit alpha LAMA3 LAMNA Laminin-5 subunit alpha Laminin-6 subunit alpha Laminin-7 subunit alpha Kalinin subunit alpha Epiligrin subunit alpha protein protein human Homo sapiens Human MAAAARPRGRALGPVLPPTPLLLLVLRVLPACGATARDPGAAAGLSLHPTYFNLAEAARIWATATCGERGPGEGRPQPELYCKLVGGPTAPGSGHTIQGQFCDYCNSEDPRKAHPVTNAIDGSERWWQSPPLSSGTQYNRVNLTLDLGQLFHVAYILIKFANSPRPDLWVLERSVDFGSTYSPWQYFAHSKVDCLKEFGREANMAVTRDDDVLCVTEYSRIVPLENGEVVVSLINGRPGAKNFTFSHTLREFTKATNIRLRFLRTNTLLGHLISKAQRDPTVTRRYYYSIKDISIGGQCVCNGHAEVCNINNPEKLFRCECQHHTCGETCDRCCTGYNQRRWRPAAWEQSHECEACNCHGHASNCYYDPDVERQQASLNTQGIYAGGGVCINCQHNTAGVNCEQCAKGYYRPYGVPVDAPDGCIPCSCDPEHADGCEQGSGRCHCKPNFHGDNCEKCAIGYYNFPFCLRIPIFPVSTPSSEDPVAGDIKGCDCNLEGVLPEICDAHGRCLCRPGVEGPRCDTCRSGFYSFPICQACWCSALGSYQMPCSSVTGQCECRPGVTGQRCDRCLSGAYDFPHCQGSSSACDPAGTINSNLGYCQCKLHVEGPTCSRCKLLYWNLDKENPSGCSECKCHKAGTVSGTGECRQGDGDCHCKSHVGGDSCDTCEDGYFALEKSNYFGCQGCQCDIGGALSSMCSGPSGVCQCREHVVGKVCQRPENNYYFPDLHHMKYEIEDGSTPNGRDLRFGFDPLAFPEFSWRGYAQMTSVQNDVRITLNVGKSSGSLFRVILRYVNPGTEAVSGHITIYPSWGAAQSKEIIFLPSKEPAFVTVPGNGFADPFSITPGIWVACIKAEGVLLDYLVLLPRDYYEASVLQLPVTEPCAYAGPPQENCLLYQHLPVTRFPCTLACEARHFLLDGEPRPVAVRQPTPAHPVMVDLSGREVELHLRLRIPQVGHYVVVVEYSTEAAQLFVVDVNVKSSGSVLAGQVNIYSCNYSVLCRSAVIDHMSRIAMYELLADADIQLKGHMARFLLHQVCIIPIEEFSAEYVRPQVHCIASYGRFVNQSATCVSLAHETPPTALILDVLSGRPFPHLPQQSSPSVDVLPGVTLKAPQNQVTLRGRVPHLGRYVFVIHFYQAAHPTFPAQVSVDGGWPRAGSFHASFCPHVLGCRDQVIAEGQIEFDISEPEVAATVKVPEGKSLVLVRVLVVPAENYDYQILHKKSMDKSLEFITNCGKNSFYLDPQTASRFCKNSARSLVAFYHKGALPCECHPTGATGPHCSPEGGQCPCQPNVIGRQCTRCATGHYGFPRCKPCSCGRRLCEEMTGQCRCPPRTVRPQCEVCETHSFSFHPMAGCEGCNCSRRGTIEAAMPECDRDSGQCRCKPRITGRQCDRCASGFYRFPECVPCNCNRDGTEPGVCDPGTGACLCKENVEGTECNVCREGSFHLDPANLKGCTSCFCFGVNNQCHSSHKRRTKFVDMLGWHLETADRVDIPVSFNPGSNSMVADLQELPATIHSASWVAPTSYLGDKVSSYGGYLTYQAKSFGLPGDMVLLEKKPDVQLTGQHMSIIYEETNTPRPDRLHHGRVHVVEGNFRHASSRAPVSREELMTVLSRLADVRIQGLYFTETQRLTLSEVGLEEASDTGSGRIALAVEICACPPAYAGDSCQGCSPGYYRDHKGLYTGRCVPCNCNGHSNQCQDGSGICVNCQHNTAGEHCERCQEGYYGNAVHGSCRACPCPHTNSFATGCVVNGGDVRCSCKAGYTGTQCERCAPGYFGNPQKFGGSCQPCSCNSNGQLGSCHPLTGDCINQEPKDSSPAEECDDCDSCVMTLLNDLATMGEQLRLVKSQLQGLSASAGLLEQMRHMETQAKDLRNQLLNYRSAISNHGSKIEGLERELTDLNQEFETLQEKAQVNSRKAQTLNNNVNRATQSAKELDVKIKNVIRNVHILLKQISGTDGEGNNVPSGDFSREWAEAQRMMRELRNRNFGKHLREAEADKRESQLLLNRIRTWQKTHQGENNGLANSIRDSLNEYEAKLSDLRARLQEAAAQAKQANGLNQENERALGAIQRQVKEINSLQSDFTKYLTTADSSLLQTNIALQLMEKSQKEYEKLAASLNEARQELSDKVRELSRSAGKTSLVEEAEKHARSLQELAKQLEEIKRNASGDELVRCAVDAATAYENILNAIKAAEDAANRAASASESALQTVIKEDLPRKAKTLSSNSDKLLNEAKMTQKKLKQEVSPALNNLQQTLNIVTVQKEVIDTNLTTLRDGLHGIQRGDIDAMISSAKSMVRKANDITDEVLDGLNPIQTDVERIKDTYGRTQNEDFKKALTDADNSVNKLTNKLPDLWRKIESINQQLLPLGNISDNMDRIRELIQQARDAASKVAVPMRFNGKSGVEVRLPNDLEDLKGYTSLSLFLQRPNSRENGGTENMFVMYLGNKDASRDYIGMAVVDGQLTCVYNLGDREAELQVDQILTKSETKEAVMDRVKFQRIYQFARLNYTKGATSSKPETPGVYDMDGRNSNTLLNLDPENVVFYVGGYPPDFKLPSRLSFPPYKGCIELDDLNENVLSLYNFKKTFNLNTTEVEPCRRRKEESDKNYFEGTGYARVPTQPHAPIPTFGQTIQTTVDRGLLFFAENGDRFISLNIEDGKLMVRYKLNSELPKERGVGDAINNGRDHSIQIKIGKLQKRMWINVDVQNTIIDGEVFDFSTYYLGGIPIAIRERFNISTPAFRGCMKNLKKTSGVVRLNDTVGVTKKCSEDWKLVRSASFSRGGQLSFTDLGLPPTDHLQASFGFQTFQPSGILLDHQTWTRNLQVTLEDGYIELSTSDSGSPIFKSPQTYMDGLLHYVSVISDNSGLRLLIDDQLLRNSKRLKHISSSRQSLRLGGSNFEGCISNVFVQRLSLSPEVLDLTSNSLKRDVSLGGCSLNKPPFLMLLKGSTRFNKTKTFRINQLLQDTPVASPRSVKVWQDACSPLPKTQANHGALQFGDIPTSHLLFKLPQELLKPRSQFAVDMQTTSSRGLVFHTGTKNSFMALYLSKGRLVFALGTDGKKLRIKSKEKCNDGKWHTVVFGHDGEKGRLVVDGLRAREGSLPGNSTISIRAPVYLGSPPSGKPKSLPTNSFVGCLKNFQLDSKPLYTPSSSFGVSSCLGGPLEKGIYFSEEGGHVVLAHSVLLGPEFKLVFSIRPRSLTGILIHIGSQPGKHLCVYLEAGKVTASMDSGAGGTSTSVTPKQSLCDGQWHSVAVTIKQHILHLELDTDSSYTAGQIPFPPASTQEPLHLGGAPANLTTLRIPVWKSFFGCLRNIHVNHIPVPVTEALEVQGPVSLNGCPDQ heparin Heparin small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) finc_bovin Fibronectin FN1 protein protein bovin Bos taurus (Bovine) Bovine MLGGPGPGLLLLLAVLSLGTAVPSAGASKSRRQAQQIVQPQSPLTVSQSKPGCYDNGKHYQINQQWERTYLGSALVCTCYGGSRGFNCESKPEPEETCFDKYTGNTYRVGDTYERPKDSMIWDCTCIGAGRGRISCTIANRCHEGGQSYKIGDTWRRPHETGGYMLECVCLGNGKGEWTCKPIAEKCFDQAAGTSYVVGETWEKPYQGWMMVDCTCLGEGSGRITCTSRNRCNDQDTRTSYRIGDTWSKKDNRGNLLQCICTGNGRGEWKCERHTSLQTTSAGSGSFTDVRTAIYQPQPHPQPPPYGHCVTDSGVVYSVGMQWLKTQGNKQMLCTCLGNGVSCQETAVTQTYGGNSNGEPCVLPFTYNGKTFYSCTTEGRQDGHLWCSTTSNYEQDQKYSFCTDHTVLVQTRGGNSNGALCHFPFLYNNHNYTDCTSEGRRDNMKWCGTTQNYDADQKFGFCPMAAHEEICTTNEGVMYRIGDQWDKQHDMGHMMRCTCVGNGRGEWTCVAYSQLRDQCIVDGITYNVNDTFHKRHEEGHMLNCTCFGQGRGRWKCDPVDQCQDSETRTFYQIGDSWEKYLQGVRYQCYCYGRGIGEWACQPLQTYPDTSGPVQVIITETPSQPNSHPIQWSAPESSHISKYILRWKPKNSPDRWKEATIPGHLNSYTIKGLRPGVVYEGQLISVQHYGQREVTRFDFTTTSTSPAVTSNTVTGETTPLSPVVATSESVTEITASSFVVSWVSASDTVSGFRVEYELSEEGDEPQYLDLPSTATSVNIPDLLPGRKYTVNVYEISEEGEQNLILSTSQTTAPDAPPDPTVDQVDDTSIVVRWSRPRAPITGYRIVYSPSVEGSSTELNLPETANSVTLSDLQPGVQYNITIYAVEENQESTPVFIQQETTGVPRSDKVPPPRDLQFVEVTDVKITIMWTPPESPVTGYRVDVIPVNLPGEHGQRLPVSRNTFAEVTGLSPGVTYHFKVFAVNQGRESKPLTAQQATKLDAPTNLQFINETDTTVIVTWTPPRARIVGYRLTVGLTRGGQPKQYNVGPAASQYPLRNLQPGSEYAVSLVAVKGNQQSPRVTGVFTTLQPLGSIPHYNTEVTETTIVITWTPAPRIGFKLGVRPSQGGEAPREVTSESGSIVVSGLTPGVEYVYTISVLRDGQERDAPIVKKVVTPLSPPTNLHLEANPDTGVLTVSWERSTTPDITGYRITTTPTNGQQGYSLEEVVHADQSSCTFENLSPGLEYNVSVYTVKDDKESVPISDTIIPEVPQLTDLSFVDITDSSIGLRWTPLNSSTIIGYRITVVAAGEGIPIFEDFVDSSVGYYTVTGLEPGIDYDISVITLINGGESAPTTLTQQTAVPPPTDLRFTNVGPDTMRVTWAPPSSIELTNLLVRYSPVKNEEDVAELSISPSDNAVVLTNLLPGTEYLVSVSSVYEQHESIPLRGRQKTALDSPSGIDFSDITANSFTVHWIAPRATITGYRIRHHPENMGGRPREDRVPPSRNSITLTNLNPGTEYVVSIVALNSKEESLPLVGQQSTVSDVPRDLEVIAATPTSLLISWDAPAVTVRYYRITYGETGGSSPVQEFTVPGSKSTATISGLKPGVDYTITVYAVTGRGDSPASSKPVSINYRTEIDKPSQMQVTDVQDNSISVRWLPSSSPVTGYRVTTAPKNGPGPSKTKTVGPDQTEMTIEGLQPTVEYVVSVYAQNQNGESQPLVQTAVTNIDRPKGLAFTDVDVDSIKIAWESPQGQVSRYRVTYSSPEDGIHELFPAPDGEEETAELQGLRPGSEYTVSVVALHDDMESQPLIGTQSTTIPAPTNLKFTQVTPTSLTAQWTAPNVQLTGYRVRVTPKEKTGPMKEINLAPDSSSVVVSGLMVATKYEVSVYALKDTLTSRPAQGVVTTLENVSPPRRARVTDATETTITISWRTKTETITGFQVDAIPANGQTPIQRTIRPDVRSYTITGLQPGTDYKIHLYTLNDNARSSPVVIDASTAIDAPSNLRFLATTPNSLLVSWQPPRARITGYIIKYEKPGSPPREVVPRPRPGVTEATITGLEPGTEYTIQVIALKNNQKSEPLIGRKKTDELPQLVTLPHPNLHGPEILDVPSTVQKTPFITNPGYDTGNGIQLPGTSGQQPSLGQQMIFEEHGFRRTTPPTTATPVRHRPRPYPPNVNEEIQIGHVPRGDVDHHLYPHVVGLNPNASTGQEALSQTTISWTPFQESSEYIISCHPVGIDEEPLQFRVPGTSASATLTGLTRGATYNIIVEAVKDQQRQKVREEVVTVGNSVDQGLSQPTDDSCFDPYTVSHYAIGEEWERLSDSGFKLSCQCLGFGSGHFRCDSSKWCHDNGVNYKIGEKWDRQGENGQMMSCTCLGNGKGEFKCDPHEATCYDDGKTYHVGEQWQKEYLGAICSCTCFGGQRGWRCDNCRRPGAEPGNEGSTAHSYNQYSQRYHQRTNTNVNCPIECFMPLDVQADREDSRE pcolce-sdc1-1 1907051 N/A 1907054 unspecified role unspecified role bait bait PTM Heparan sulfate chains heparan sulfate d-glucuronosyl-d-galactosyl-d-galactosyl-d-xylosyl-l-serine heparan sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine heparan sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine heparin heparitin sulfate poly[alpha-1,4-(2-sulfate D-glucopyranuronosyl)-beta-1,4-(2-sulfamino-2-deoxy-6-sulfate D-glucosyl)]-beta-1,4-D-glucopyranuronosyl-beta-1,3-D-galactosyl-beta-1,3-D-galactosyl-beta-1,4-D-xylosyl-beta-1,3-L-serine undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false PTM Chondroitin sulfate chondroitin sulfate d-glucuronosyl-d-galactosyl-d-galactosyl-d-xylosyl-l-serine chondroitin sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine chondroitin 4-sulfate (chondroitin sulfate A) chondroitin 6-sulfate (chondroitin sulfate C) chondroitin sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine poly[beta-1,4-D-glucopyranuronosyl-beta-1,3-(2-acetamido-2-deoxy-4-sulfate-D-galactosyl)]-beta-1,4-D-glucopyranuronosyl-beta-1,3-D-galactosyl-beta-1,3-D-galactosyl-beta-1,4-D-xylosyl-beta-1,3-L-serine; poly[beta-1,4-D-glucopyranuronosyl-beta-1,3-(2-acetami undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false mouse-3t3 Mus musculus embryo cells 3t3 Mouse embryo fibroblast cells N/A 1907055 unspecified role unspecified role prey prey tag 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 false human-293 Homo sapiens transformed primary embryonal kidney cells Human 293 Transformed human primary embryonal kidney cells. The Cell type named 293 is synonymous with HEK-293. physical association physical association false false false FiG 1A PCPE-Flag binding to syndecan-1 was completely blocked upon removal of the GAG chains by heparitinase I indicating that the GAG chains are required for binding. pcolce-sdc2-1 1907051 N/A 1907056 unspecified role unspecified role bait bait PTM Heparan sulfate chains heparan sulfate d-glucuronosyl-d-galactosyl-d-galactosyl-d-xylosyl-l-serine heparan sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine heparan sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine heparin heparitin sulfate poly[alpha-1,4-(2-sulfate D-glucopyranuronosyl)-beta-1,4-(2-sulfamino-2-deoxy-6-sulfate D-glucosyl)]-beta-1,4-D-glucopyranuronosyl-beta-1,3-D-galactosyl-beta-1,3-D-galactosyl-beta-1,4-D-xylosyl-beta-1,3-L-serine undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false mouse-3t3 Mus musculus embryo cells 3t3 Mouse embryo fibroblast cells N/A 1907055 unspecified role unspecified role prey prey tag 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 false Binding site NTR domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false human-293 Homo sapiens transformed primary embryonal kidney cells Human 293 Transformed human primary embryonal kidney cells. The Cell type named 293 is synonymous with HEK-293. physical association physical association false false false FiG. 2B pcolce-sdc4-1 1907051 N/A 1907057 unspecified role unspecified role bait bait PTM Heparan sulfate chains heparan sulfate d-glucuronosyl-d-galactosyl-d-galactosyl-d-xylosyl-l-serine heparan sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine heparan sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine heparin heparitin sulfate poly[alpha-1,4-(2-sulfate D-glucopyranuronosyl)-beta-1,4-(2-sulfamino-2-deoxy-6-sulfate D-glucosyl)]-beta-1,4-D-glucopyranuronosyl-beta-1,3-D-galactosyl-beta-1,3-D-galactosyl-beta-1,4-D-xylosyl-beta-1,3-L-serine undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false mouse-3t3 Mus musculus embryo cells 3t3 Mouse embryo fibroblast cells PCPE-Flag binding to syndecan-4 was greatly reduced upon removal of the GAG chains by heparitinse I and chondroitinase ABC indicating that the GAG chains are required for binding. N/A 1907055 unspecified role unspecified role prey prey tagf 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 false human-293 Homo sapiens transformed primary embryonal kidney cells Human 293 Transformed human primary embryonal kidney cells. The Cell type named 293 is synonymous with HEK-293. physical association physical association false false false FIG. 1B PCPE-Flag binding to syndecan-4 was greatly reduced upon removal of the GAG chains by heparitinase I and chondroitinase ABC indicating that the GAG chains are required for binding. pcolce-sdc1-2 1907051 N/A 1907055 unspecified role unspecified role bait bait tag Flag tag 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 false human-293 Homo sapiens transformed primary embryonal kidney cells Human 293 Transformed human primary embryonal kidney cells. The Cell type named 293 is synonymous with HEK-293. N/A 1907054 unspecified role unspecified role prey prey PTM Heparan sulfate chains heparan sulfate d-glucuronosyl-d-galactosyl-d-galactosyl-d-xylosyl-l-serine heparan sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine heparan sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine heparin heparitin sulfate poly[alpha-1,4-(2-sulfate D-glucopyranuronosyl)-beta-1,4-(2-sulfamino-2-deoxy-6-sulfate D-glucosyl)]-beta-1,4-D-glucopyranuronosyl-beta-1,3-D-galactosyl-beta-1,3-D-galactosyl-beta-1,4-D-xylosyl-beta-1,3-L-serine undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false PTM Chondroitin sulfate chains chondroitin sulfate d-glucuronosyl-d-galactosyl-d-galactosyl-d-xylosyl-l-serine chondroitin sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine chondroitin 4-sulfate (chondroitin sulfate A) chondroitin 6-sulfate (chondroitin sulfate C) chondroitin sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine poly[beta-1,4-D-glucopyranuronosyl-beta-1,3-(2-acetamido-2-deoxy-4-sulfate-D-galactosyl)]-beta-1,4-D-glucopyranuronosyl-beta-1,3-D-galactosyl-beta-1,3-D-galactosyl-beta-1,4-D-xylosyl-beta-1,3-L-serine; poly[beta-1,4-D-glucopyranuronosyl-beta-1,3-(2-acetami undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false human-keratocyte Human corneal keratocyte keratocyte corneal keratocyte physical association physical association false false false Figure 1C Glycosidase treatment (heparitinase I + chondroitinase ABC) was required for syndecan-1 detection pcolce-sdc4-2 1907051 N/A 1907055 unspecified role unspecified role bait bait tag Flag tag 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 false human-293 Homo sapiens transformed primary embryonal kidney cells Human 293 Transformed human primary embryonal kidney cells. The Cell type named 293 is synonymous with HEK-293. N/A 1907057 unspecified role unspecified role prey prey PTM Heparan sulfate chains heparan sulfate d-glucuronosyl-d-galactosyl-d-galactosyl-d-xylosyl-l-serine heparan sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine heparan sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine heparin heparitin sulfate poly[alpha-1,4-(2-sulfate D-glucopyranuronosyl)-beta-1,4-(2-sulfamino-2-deoxy-6-sulfate D-glucosyl)]-beta-1,4-D-glucopyranuronosyl-beta-1,3-D-galactosyl-beta-1,3-D-galactosyl-beta-1,4-D-xylosyl-beta-1,3-L-serine undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false mouse-3t3 Mus musculus embryo cells 3t3 Mouse embryo fibroblast cells physical association physical association false false false Glycosidase treatment (heparitinase I + chondroitinase ABC) was required to release the core protein of syndecan-4 for detection Figure 1D pcolce-sdc2-2 1907051 N/A 1907056 unspecified role unspecified role prey prey PTM Heparan sulfate chains heparan sulfate d-glucuronosyl-d-galactosyl-d-galactosyl-d-xylosyl-l-serine heparan sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine heparan sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine heparin heparitin sulfate poly[alpha-1,4-(2-sulfate D-glucopyranuronosyl)-beta-1,4-(2-sulfamino-2-deoxy-6-sulfate D-glucosyl)]-beta-1,4-D-glucopyranuronosyl-beta-1,3-D-galactosyl-beta-1,3-D-galactosyl-beta-1,4-D-xylosyl-beta-1,3-L-serine undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false mouse-3t3 Mus musculus embryo cells 3t3 Mouse embryo fibroblast cells N/A 1907055 unspecified role unspecified role bait bait tag Flag tag 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 false human-293 Homo sapiens transformed primary embryonal kidney cells Human 293 Transformed human primary embryonal kidney cells. The Cell type named 293 is synonymous with HEK-293. physical association physical association false false false Figure 2A lama3-sdc1-1 1907051 N/A 1907058 unspecified role unspecified role prey prey tag Flag tag flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false human-keratocyte Human corneal keratocyte keratocyte corneal keratocyte N/A 1907059 unspecified role unspecified role bait bait Binding site LG45 domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false human-293 ebna Homo sapiens 293 ebna 293 ebna physical association physical association false false false Figure 1E lane 3 pcolce-pcolce-1 1907051 N/A 1907055 unspecified role unspecified role prey prey tag Flag tag 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 false human-293 Homo sapiens transformed primary embryonal kidney cells Human 293 Transformed human primary embryonal kidney cells. The Cell type named 293 is synonymous with HEK-293. N/A 1907055 competitor competitor competitor prey prey Binding site NTR domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false tag Flag tag 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 false human-293 Homo sapiens transformed primary embryonal kidney cells Human 293 Transformed human primary embryonal kidney cells. The Cell type named 293 is synonymous with HEK-293. N/A 1907054 unspecified role unspecified role bait bait PTM Heparan sulfate chains heparan sulfate d-glucuronosyl-d-galactosyl-d-galactosyl-d-xylosyl-l-serine heparan sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine heparan sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine heparin heparitin sulfate poly[alpha-1,4-(2-sulfate D-glucopyranuronosyl)-beta-1,4-(2-sulfamino-2-deoxy-6-sulfate D-glucosyl)]-beta-1,4-D-glucopyranuronosyl-beta-1,3-D-galactosyl-beta-1,3-D-galactosyl-beta-1,4-D-xylosyl-beta-1,3-L-serine undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false PTM Chondroitin sulfate chains chondroitin sulfate d-glucuronosyl-d-galactosyl-d-galactosyl-d-xylosyl-l-serine chondroitin sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine chondroitin 4-sulfate (chondroitin sulfate A) chondroitin 6-sulfate (chondroitin sulfate C) chondroitin sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine poly[beta-1,4-D-glucopyranuronosyl-beta-1,3-(2-acetamido-2-deoxy-4-sulfate-D-galactosyl)]-beta-1,4-D-glucopyranuronosyl-beta-1,3-D-galactosyl-beta-1,3-D-galactosyl-beta-1,4-D-xylosyl-beta-1,3-L-serine; poly[beta-1,4-D-glucopyranuronosyl-beta-1,3-(2-acetami undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false mouse-3t3 Mus musculus embryo cells 3t3 Mouse embryo fibroblast cells association association false false false Figure 3A The NTR domain strongly inhibited binding of PCPE-1 to syndecan-1 heparin-pcolce-1 1907051 N/A 1907060 competitor competitor competitor prey prey pig-gastric mucosa Sus scrofa gastric mucosa gastric_mucosa gastric mucosa N/A 1907055 unspecified role unspecified role prey prey tag Flag tag 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 false human-293 Homo sapiens transformed primary embryonal kidney cells Human 293 Transformed human primary embryonal kidney cells. The Cell type named 293 is synonymous with HEK-293. N/A 1907054 unspecified role unspecified role bait bait PTM Heparan sulfate chains heparan sulfate d-glucuronosyl-d-galactosyl-d-galactosyl-d-xylosyl-l-serine heparan sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine heparan sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine heparin heparitin sulfate poly[alpha-1,4-(2-sulfate D-glucopyranuronosyl)-beta-1,4-(2-sulfamino-2-deoxy-6-sulfate D-glucosyl)]-beta-1,4-D-glucopyranuronosyl-beta-1,3-D-galactosyl-beta-1,3-D-galactosyl-beta-1,4-D-xylosyl-beta-1,3-L-serine undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false PTM Chondroitin sulfate chains chondroitin sulfate d-glucuronosyl-d-galactosyl-d-galactosyl-d-xylosyl-l-serine chondroitin sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine chondroitin 4-sulfate (chondroitin sulfate A) chondroitin 6-sulfate (chondroitin sulfate C) chondroitin sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine poly[beta-1,4-D-glucopyranuronosyl-beta-1,3-(2-acetamido-2-deoxy-4-sulfate-D-galactosyl)]-beta-1,4-D-glucopyranuronosyl-beta-1,3-D-galactosyl-beta-1,3-D-galactosyl-beta-1,4-D-xylosyl-beta-1,3-L-serine; poly[beta-1,4-D-glucopyranuronosyl-beta-1,3-(2-acetami undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false mouse-3t3 Mus musculus embryo cells 3t3 Mouse embryo fibroblast cells association association false false false Figure 3B Heparin fully inhibits the interaction of PCPE-Flag with syndecan-1 heparin-pcolce-2 1907051 N/A 1907056 unspecified role unspecified role bait bait PTM Heparan sulfate chains heparan sulfate d-glucuronosyl-d-galactosyl-d-galactosyl-d-xylosyl-l-serine heparan sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine heparan sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine heparin heparitin sulfate poly[alpha-1,4-(2-sulfate D-glucopyranuronosyl)-beta-1,4-(2-sulfamino-2-deoxy-6-sulfate D-glucosyl)]-beta-1,4-D-glucopyranuronosyl-beta-1,3-D-galactosyl-beta-1,3-D-galactosyl-beta-1,4-D-xylosyl-beta-1,3-L-serine undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false mouse-3t3 Mus musculus embryo cells 3t3 Mouse embryo fibroblast cells N/A 1907060 competitor competitor competitor prey prey pig-gastric mucosa Sus scrofa gastric mucosa gastric_mucosa gastric mucosa N/A 1907055 unspecified role unspecified role prey prey tag Flag tag 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 false human-293 Homo sapiens transformed primary embryonal kidney cells Human 293 Transformed human primary embryonal kidney cells. The Cell type named 293 is synonymous with HEK-293. association association false false false Heparin inhibits PCPE-Flag binding to syndecan-2. Figure 3C pcolce-sdc1-4 1907051 N/A 1907058 unspecified role unspecified role prey prey human-keratocyte Human corneal keratocyte keratocyte corneal keratocyte N/A 1907055 unspecified role unspecified role bait bait human-293 Homo sapiens transformed primary embryonal kidney cells Human 293 Transformed human primary embryonal kidney cells. The Cell type named 293 is synonymous with HEK-293. physical association physical association false false false Figure 1E lane 2 pcolce-sdc2-3 1907052 N/A 1907056 unspecified role unspecified role prey prey mouse-3t3 Mus musculus embryo cells 3t3 Mouse embryo fibroblast cells N/A 1907055 unspecified role unspecified role bait bait Flag Flag tag 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 false human-293 Homo sapiens transformed primary embryonal kidney cells Human 293 Transformed human primary embryonal kidney cells. The Cell type named 293 is synonymous with HEK-293. physical association physical association false false false Figure 2C fn1-pcolce-1 1907052 N/A 1907061 unspecified role unspecified role bait bait bovin-serum Bovine serum serum Serum N/A 1907055 unspecified role unspecified role prey prey tag Flag tag 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 false Binding site NTR domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false human-293 Homo sapiens transformed primary embryonal kidney cells Human 293 Transformed human primary embryonal kidney cells. The Cell type named 293 is synonymous with HEK-293. direct interaction direct interaction false false false Figure4A, 4B fn1-pcolce-2 1907053 N/A 1907061 unspecified role unspecified role prey prey bovin-serum Bovine serum serum Serum N/A 1907055 unspecified role unspecified role bait bait tag Flag tag 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 false Binding site NTR domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false human-293 Homo sapiens transformed primary embryonal kidney cells Human 293 Transformed human primary embryonal kidney cells. The Cell type named 293 is synonymous with HEK-293. direct interaction direct interaction false false false Figure 4C